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6qld

Structure of inner kinetochore CCAN-Cenp-A complex

Method: ELECTRON MICROSCOPY Dmax: 220.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Inner kinetochore subunit MIF2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P35201

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain C； UniProt 284–305 Not recorded DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2VPV Dimerization Domain of Mif2p Deposited 2008-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 365–530（166 aa） Fragment：DIMERIZATION DOMAIN, RESIDUES 365-530
Chain B 365–530（166 aa） Fragment：DIMERIZATION DOMAIN, RESIDUES 365-530
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR FUSION FROM 3-4% (W/V) PEG 3000, 100 MM IMIDAZOLE (PH 8.0), AND 70-100 MM LI2SO4 OR NA2SO4
Resolution 2.70 Å R-free 0.242

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPC_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 1–22； UniProt 284–305

Inner kinetochore subunit MCM16

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12262

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain H； UniProt 4–136 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6OUA Cryo-EM structure of the yeast Ctf3 complex Deposited 2019-05-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–181（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
6WUC The yeast Ctf3 complex with Cnn1-Wip1 Deposited 2020-05-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–181（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
6YPC Crystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae at 2.9 angstroms Deposited 2020-04-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 137–181（45 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1 M NaH2PO4 and 0.38M K2HPO4 with protein at 5.5 mg/ml
Resolution 2.90 Å R-free 0.283
7L7Q Ctf3c with Ulp2-KIM Deposited 2020-12-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–181（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain H 1–181（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain H 1–181（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain H 1–181（181 aa）
Chain HH 1–181（181 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPH_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain H； PDBConstruct 1–133； UniProt 4–136

Inner kinetochore subunit CTF3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12748

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain I； UniProt 321–728 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain H 1–733（733 aa）
Chain Y 1–733（733 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6OUA Cryo-EM structure of the yeast Ctf3 complex Deposited 2019-05-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–733（733 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain I 335–656（322 aa）
Chain I 690–733（44 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6WUC The yeast Ctf3 complex with Cnn1-Wip1 Deposited 2020-05-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 1–733（733 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
6YPC Crystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae at 2.9 angstroms Deposited 2020-04-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 1–245（245 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1 M NaH2PO4 and 0.38M K2HPO4 with protein at 5.5 mg/ml
Resolution 2.90 Å R-free 0.283
7L7Q Ctf3c with Ulp2-KIM Deposited 2020-12-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–733（733 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain I 1–733（733 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain I 1–733（733 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain I 1–733（733 aa）
Chain II 1–733（733 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPI_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain I； PDBConstruct 1–408； UniProt 321–728

Inner kinetochore subunit MCM22

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P47167

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain K； UniProt 7–128 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6OUA Cryo-EM structure of the yeast Ctf3 complex Deposited 2019-05-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–239（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–133（133 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6WUC The yeast Ctf3 complex with Cnn1-Wip1 Deposited 2020-05-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain K 1–239（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
6YPC Crystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae at 2.9 angstroms Deposited 2020-04-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain K 131–239（109 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1 M NaH2PO4 and 0.38M K2HPO4 with protein at 5.5 mg/ml
Resolution 2.90 Å R-free 0.283
7L7Q Ctf3c with Ulp2-KIM Deposited 2020-12-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–239（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain K 1–239（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain K 1–239（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain K 1–239（239 aa）
Chain KK 1–239（239 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPK_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain K； PDBConstruct 1–122； UniProt 7–128

Inner kinetochore subunit IML3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P38265

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain L； UniProt 2–242 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4IT3 Crystal Structure of Iml3 from S. cerevisiae Deposited 2013-01-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–245（245 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；3.75 M sodium formate, 4% 2,5-diaminopentane, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.256
4JE3 An Iml3-Chl4 heterodimer links the core centromere to factors required for accurate chromosome segregation Deposited 2013-02-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–242（242 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；0.35 M lithium citrate, pH 9, 25% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.28 Å R-free 0.211
4KR1 Crystal structure of the kinetechore protein Iml3 from budding yeast Deposited 2013-05-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–245（245 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；3M Sodium formate, 100mM Cesium chloride, 3% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Resolution 2.50 Å R-free 0.262
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain L 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6QLF Structure of inner kinetochore CCAN complex with mask1 Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain L 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain L 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain L 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain L 1–245（245 aa）
Chain LL 1–245（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPL_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain L； PDBConstruct 1–241； UniProt 2–242

Inner kinetochore subunit CHL4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P38907

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain N； UniProt 5–451 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4JE3 An Iml3-Chl4 heterodimer links the core centromere to factors required for accurate chromosome segregation Deposited 2013-02-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 361–458（98 aa） Fragment：UNP residues 361-458
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；0.35 M lithium citrate, pH 9, 25% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.28 Å R-free 0.211
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain E 1–458（458 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain N 1–458（458 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6QLF Structure of inner kinetochore CCAN complex with mask1 Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain N 1–458（458 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain N 1–458（458 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain N 1–458（458 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain N 1–458（458 aa）
Chain NN 1–458（458 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPN_YEAST
Isoform —
PDB entities 8
Chains and sequence ranges Author chain N； PDBConstruct 1–447； UniProt 5–451

Inner kinetochore subunit MCM21

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q06675

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain O； UniProt 153–364 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain C 1–368（368 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain O 1–368（368 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6QLF Structure of inner kinetochore CCAN complex with mask1 Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain O 1–368（368 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain O 1–368（368 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OVX Cryo-EM structure of yeast CENP-OPQU+ bound to the CENP-A N-terminus Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain O 1–368（368 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain O 1–368（368 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain O 1–368（368 aa）
Chain OO 1–368（368 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPO_YEAST
Isoform —
PDB entities 9
Chains and sequence ranges Author chain O； PDBConstruct 1–212； UniProt 153–364

Inner kinetochore subunit CTF19

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q02732

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain P； UniProt 97–366 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain D 1–369（369 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain P 1–369（369 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6QLF Structure of inner kinetochore CCAN complex with mask1 Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain P 1–369（369 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain P 1–369（369 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OVX Cryo-EM structure of yeast CENP-OPQU+ bound to the CENP-A N-terminus Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 1–369（369 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain P 1–369（369 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain P 1–369（369 aa）
Chain PP 1–369（369 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPP_YEAST
Isoform —
PDB entities 10
Chains and sequence ranges Author chain P； PDBConstruct 1–270； UniProt 97–366

Inner kinetochore subunit OKP1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P53298

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain Q； UniProt 161–391 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 1–406（406 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain Q 161–406（246 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6QLF Structure of inner kinetochore CCAN complex with mask1 Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain Q 1–406（406 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain Q 1–406（406 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OVX Cryo-EM structure of yeast CENP-OPQU+ bound to the CENP-A N-terminus Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain Q 1–406（406 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain Q 1–406（406 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain Q 1–406（406 aa）
Chain QQ 1–406（406 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8T0P Structure of Cse4 bound to Ame1 and Okp1 Deposited 2023-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 125–275（151 aa） Fragment：residues 125-275
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；19% PEG 8000, 0.55 M Lithium sulfate
Resolution 1.73 Å R-free 0.236

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPQ_YEAST
Isoform —
PDB entities 11
Chains and sequence ranges Author chain Q； PDBConstruct 1–231； UniProt 161–391

Inner kinetochore subunit AME1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P38313

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain U； UniProt 131–320 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain I 1–324（324 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain U 166–324（159 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6QLF Structure of inner kinetochore CCAN complex with mask1 Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 1–320（320 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain U 1–324（324 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OVX Cryo-EM structure of yeast CENP-OPQU+ bound to the CENP-A N-terminus Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain U 1–324（324 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain U 1–324（324 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain U 1–324（324 aa）
Chain UU 1–324（324 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8T0P Structure of Cse4 bound to Ame1 and Okp1 Deposited 2023-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 125–231（107 aa） Fragment：residues 125-231
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；19% PEG 8000, 0.55 M Lithium sulfate
Resolution 1.73 Å R-free 0.236

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPU_YEAST
Isoform —
PDB entities 12
Chains and sequence ranges Author chain U； PDBConstruct 1–190； UniProt 131–320

Inner kinetochore subunit NKP1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q12493

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain Y； UniProt 2–238 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–238（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain Y 1–238（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6QLF Structure of inner kinetochore CCAN complex with mask1 Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain Y 1–238（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain Y 1–238（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OVX Cryo-EM structure of yeast CENP-OPQU+ bound to the CENP-A N-terminus Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain Y 1–238（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain Y 1–238（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain Y 1–238（238 aa）
Chain YY 1–238（238 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NKP1_YEAST
Isoform —
PDB entities 13
Chains and sequence ranges Author chain Y； PDBConstruct 1–237； UniProt 2–238

Inner kinetochore subunit NKP2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q06162

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain Z； UniProt 3–153 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6NUW Yeast Ctf19 complex Deposited 2019-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain J 1–153（153 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
6QLE Structure of inner kinetochore CCAN complex Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain Z 1–153（153 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
6QLF Structure of inner kinetochore CCAN complex with mask1 Deposited 2019-01-31 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain Z 1–153（153 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8OVW Cryo-EM structure of CBF1-CCAN bound topologically to centromeric DNA Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain Z 1–153（153 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OVX Cryo-EM structure of yeast CENP-OPQU+ bound to the CENP-A N-terminus Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain Z 1–153（153 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain Z 1–153（153 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain Z 1–153（153 aa）
Chain ZZ 1–153（153 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NKP2_YEAST
Isoform —
PDB entities 14
Chains and sequence ranges Author chain Z； PDBConstruct 1–151； UniProt 3–153

Histone H3-like centromeric protein CSE4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P36012

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain a； UniProt 137–226 Chain e； UniProt 112–226 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2L5A Structural basis for recognition of centromere specific histone H3 variant by nonhistone Scm3 Deposited 2010-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 151–228（78 aa） Fragment：Cse4(151-228), Scm3(93-172), H4(42-103)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.4；308 K；Ionic strength (raw mmCIF value) 0.00；Pressure ambient
NMR sample composition 0.8-1.0 mM [U-100% 15N] scCSH-1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8-0.85 mM [U-100% 15N] scCSH-2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8-0.85 mM [U-13C methyl; U-15N; U-2H] scCSH-3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8-0.85 mM [U-13C ; U-15N; 35%-2H] scCSH-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8-0.85 mM [U-13C ; U-15N] scCSH-5, 100% D2O | 100% D2O
NMR sample composition 0.8-0.85 mM scCSH-6, 100% D2O | 100% D2O
Resolution not provided
6UPH Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution Deposited 2019-10-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–229（229 aa）
Chain E 1–229（229 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain a 1–229（229 aa）
Chain e 1–229（229 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain a 1–229（229 aa）
Chain e 1–229（229 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8T0P Structure of Cse4 bound to Ame1 and Okp1 Deposited 2023-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 32–49（18 aa） Fragment：residues 32-49
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；19% PEG 8000, 0.55 M Lithium sulfate
Resolution 1.73 Å R-free 0.236

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CENPA_YEAST
Isoform —
PDB entities 15, 18
Chains and sequence ranges Author chain a； PDBConstruct 1–90； UniProt 137–226 Author chain e； PDBConstruct 1–115； UniProt 112–226

Histone H4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P02309

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain b； UniProt 25–103 Chain f； UniProt 25–103 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1E6I Bromodomain from GCN5 complexed with acetylated H4 peptide Deposited 2000-08-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 16–30（15 aa） Fragment：ACETYLATED TAIL, RESIDUES 16-30
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；2.2M AMMONIUM SULPHATE, 20% V/V GLYCEROL, 4MM DITHIOTHREITOL, 100 MM HEPES PH 7.5, 125MM NACL 5:1 PEPTIDE:PROTEIN
Resolution 1.87 Å R-free 0.209
1ID3 CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS Deposited 2001-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, Potassium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.10 Å R-free 0.292
1Q1A Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide Deposited 2003-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 12–21（10 aa） Fragment：Residues 12-21
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；PEG 4K, , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.50 Å R-free 0.210
1SZC Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases Deposited 2004-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 12–21（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 CL CHLORIDE ION × 1 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；Ammonium Sulfate, Bis-tris, pH 6.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.75 Å R-free 0.239
1SZC Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases Deposited 2004-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 12–21（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 CL CHLORIDE ION × 2 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；Ammonium Sulfate, Bis-tris, pH 6.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.75 Å R-free 0.239
1SZD Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases Deposited 2004-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 12–21（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；Ammonium Sulfate, Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.50 Å R-free 0.230
1SZD Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases Deposited 2004-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 12–21（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 ZN ZINC ION × 2 APR ADENOSINE-5-DIPHOSPHORIBOSE × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；Ammonium Sulfate, Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.50 Å R-free 0.230
2E3K Crystal structure of the human Brd2 second bromodomain in complexed with the acetylated histone H4 peptide Deposited 2006-11-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Q 1–15（15 aa） Fragment：N-terminal H4 di-acetylated tail
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG4000, Ammonium Acetate,, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.268
2E3K Crystal structure of the human Brd2 second bromodomain in complexed with the acetylated histone H4 peptide Deposited 2006-11-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 1–15（15 aa） Fragment：N-terminal H4 di-acetylated tail
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；PEG4000, Ammonium Acetate,, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.268
2H2H The Structural basis of sirtuin substrate specificity Deposited 2006-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 75–85（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293.15 K；20 % PEG, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 9.5
Resolution 2.20 Å R-free 0.239
2L5A Structural basis for recognition of centromere specific histone H3 variant by nonhistone Scm3 Deposited 2010-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–103（62 aa） Fragment：Cse4(151-228), Scm3(93-172), H4(42-103)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.4；308 K；Ionic strength (raw mmCIF value) 0.00；Pressure ambient
NMR sample composition 0.8-1.0 mM [U-100% 15N] scCSH-1, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8-0.85 mM [U-100% 15N] scCSH-2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8-0.85 mM [U-13C methyl; U-15N; U-2H] scCSH-3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8-0.85 mM [U-13C ; U-15N; 35%-2H] scCSH-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8-0.85 mM [U-13C ; U-15N] scCSH-5, 100% D2O | 100% D2O
NMR sample composition 0.8-0.85 mM scCSH-6, 100% D2O | 100% D2O
Resolution not provided
2QQF Hst2 bound to ADP-HPD and Acetylated histone H4 Deposited 2007-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 13–23（11 aa） Fragment：SEQUENCE DATABASE RESIDUES 13-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；2.0 M Ammonium Sulfate, 100 mM Na citrate and 200 mM K/Na tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.253
2QQF Hst2 bound to ADP-HPD and Acetylated histone H4 Deposited 2007-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 13–23（11 aa） Fragment：SEQUENCE DATABASE RESIDUES 13-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；2.0 M Ammonium Sulfate, 100 mM Na citrate and 200 mM K/Na tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.253
2QQG Hst2 bound to ADP-HPD, acetyllated histone H4 and nicotinamide Deposited 2007-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 13–23（11 aa） Fragment：sequence database residues 13-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 1 NCA NICOTINAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；2.0 M Ammonium Sulfate, 100 mM Na citrate, pH 5.6, 200 mM K/Na tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60
Resolution 2.05 Å R-free 0.245
2QQG Hst2 bound to ADP-HPD, acetyllated histone H4 and nicotinamide Deposited 2007-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 13–23（11 aa） Fragment：sequence database residues 13-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 2 NCA NICOTINAMIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；2.0 M Ammonium Sulfate, 100 mM Na citrate, pH 5.6, 200 mM K/Na tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60
Resolution 2.05 Å R-free 0.245
3TO6 Crystal structure of yeast Esa1 HAT domain complexed with H4K16CoA bisubstrate inhibitor Deposited 2011-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 12–23（12 aa） Fragment：UNP residues 12-23
Not recorded CMC CARBOXYMETHYL COENZYME *A × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M sodium cacodylate, 1.6 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.10 Å R-free 0.232
4JJN Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome Deposited 2013-03-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.05 M sodium cacodylate, 32% 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.09 Å R-free 0.255
4KUD Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle Deposited 2013-05-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：S2A Mutation：S2A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；289 K；16% PEG 400, 0.1M KCl, 0.01M CaCl2, 0.05M sodium citrate(pH4.8), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.20 Å R-free 0.237
4PSX Crystal structure of histone acetyltransferase complex Deposited 2014-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–49（48 aa） Fragment：UNP residues 2-49
Mutation：I21V COA COENZYME A × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M potassium sodium tartrate, 20%(w/v) polyethylene glycol 3,350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.51 Å R-free 0.223
4PSX Crystal structure of histone acetyltransferase complex Deposited 2014-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 2–49（48 aa） Fragment：UNP residues 2-49
Mutation：I21V COA COENZYME A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M potassium sodium tartrate, 20%(w/v) polyethylene glycol 3,350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.51 Å R-free 0.223
4TWI The structure of Sir2Af1 bound to a succinylated histone peptide Deposited 2014-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 9–21（13 aa） Fragment：UNP residues 9-21
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris pH 8.5, 200 mM MgCl2, and 20% (w/v) PEG 8,000
Resolution 1.79 Å R-free 0.221
4TWJ The structure of Sir2Af2 bound to a myristoylated histone peptide Deposited 2014-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 9–21（13 aa） Fragment：UNP residues 9-21
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 ACT ACETATE ION × 5 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；0.1 M Na-acetate pH 4.8, 14-18% (v/v) 2-propanol, and 14-15% (w/v) PEG 6,000
Resolution 1.65 Å R-free 0.205
5ZBA Crystal structure of Rtt109-Asf1-H3-H4-CoA complex Deposited 2018-02-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–103（103 aa）
Not recorded COA COENZYME A × 1 IOD IODIDE ION × 37 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100mM sodium citrate, pH 5.0, 22% PEG 1500, 400mM sodium iodide
Resolution 3.50 Å R-free 0.294
5ZBB Crystal structure of Rtt109-Asf1-H3-H4 complex Deposited 2018-02-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–103（103 aa）
Not recorded IOD IODIDE ION × 23 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100mM sodium citrate, pH 5.0, 22% PEG 1500, 400mM sodium iodide
Resolution 3.60 Å R-free 0.264
6GEJ Chromatin remodeller-nucleosome complex at 3.6 A resolution. Deposited 2018-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–103（103 aa）
Chain D 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6GEN Chromatin remodeller-nucleosome complex at 4.5 A resolution. Deposited 2018-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–103（103 aa）
Chain D 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6RXJ Crystal structure of CobB wt in complex with H4K16-Acetyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 13–22（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 22% PEG3350
Resolution 1.60 Å R-free 0.188
6RXJ Crystal structure of CobB wt in complex with H4K16-Acetyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 13–22（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 22% PEG3350
Resolution 1.60 Å R-free 0.188
6RXK Crystal structure of CobB wt in complex with H4K16-Butyryl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 13–23（11 aa） Fragment：H4K16Bu
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；22% PEG 3350 0.1M Bis-Tris 0.03 mM HCL
Resolution 1.35 Å R-free 0.188
6RXL Crystal structure of CobB wt in complex with H4K16-Crotonyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 13–23（11 aa） Fragment：H4K16Ac
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1 M Bis-Tris 22% PEG 3350 0.03 M HCl
Resolution 2.30 Å R-free 0.250
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 13–23（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350
Resolution 1.92 Å R-free 0.242
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 13–23（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350
Resolution 1.92 Å R-free 0.242
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 13–23（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350
Resolution 1.92 Å R-free 0.242
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 13–23（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350
Resolution 1.92 Å R-free 0.242
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 13–23（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350
Resolution 1.92 Å R-free 0.242
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 13–23（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350
Resolution 1.92 Å R-free 0.242
6RXO Crystal structure of CobB Ac2 (A76G, I131C, V162A) in complex with H4K16-Buturyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 13–23（11 aa） Fragment：H4K16Ac
Mutation：K16ALY Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350
Resolution 1.95 Å R-free 0.215
6RXO Crystal structure of CobB Ac2 (A76G, I131C, V162A) in complex with H4K16-Buturyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 13–23（11 aa） Fragment：H4K16Ac
Mutation：K16ALY Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350
Resolution 1.95 Å R-free 0.215
6RXP Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16-Crotonyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 13–23（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350
Resolution 1.80 Å R-free 0.234
6RXP Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16-Crotonyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 13–23（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350
Resolution 1.80 Å R-free 0.234
6RXQ Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after soaking Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 13–23（11 aa）
Not recorded KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 mM Bis-Tris, 0.03M HCl, 23% PEG3350, soaked 36h with 1 mM NAD+
Resolution 1.70 Å R-free 0.228
6RXQ Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after soaking Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 13–23（11 aa）
Not recorded KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 mM Bis-Tris, 0.03M HCl, 23% PEG3350, soaked 36h with 1 mM NAD+
Resolution 1.70 Å R-free 0.228
6RXQ Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after soaking Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 13–23（11 aa）
Not recorded KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 mM Bis-Tris, 0.03M HCl, 23% PEG3350, soaked 36h with 1 mM NAD+
Resolution 1.70 Å R-free 0.228
6RXQ Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after soaking Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 13–23（11 aa）
Not recorded KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 mM Bis-Tris, 0.03M HCl, 23% PEG3350, soaked 36h with 1 mM NAD+
Resolution 1.70 Å R-free 0.228
6RXR Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 13–23（11 aa）
Not recorded KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Bis-Tris, 0.02 M HCl, 22% PEG 3350, 1 mM NAD
Resolution 1.70 Å R-free 0.228
6RXR Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 13–23（11 aa）
Not recorded KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Bis-Tris, 0.02 M HCl, 22% PEG 3350, 1 mM NAD
Resolution 1.70 Å R-free 0.228
6RXR Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 13–23（11 aa）
Not recorded KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Bis-Tris, 0.02 M HCl, 22% PEG 3350, 1 mM NAD
Resolution 1.70 Å R-free 0.228
6RXR Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 13–23（11 aa）
Not recorded KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Bis-Tris, 0.02 M HCl, 22% PEG 3350, 1 mM NAD
Resolution 1.70 Å R-free 0.228
7E9C Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome Deposited 2021-03-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7E9F Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome Deposited 2021-03-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7K78 antibody and nucleosome complex Deposited 2020-09-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7K7G nucleosome and Gal4 complex Deposited 2020-09-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XAY Crystal structure of Hat1-Hat2-Asf1-H3-H4 Deposited 2022-03-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 8–103（96 aa）
Not recorded COA COENZYME A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；100 mM Bis-Tris propane, pH 6.5, 20% PEG-3350, and 200 mM sodium nitrate
Resolution 3.30 Å R-free 0.256
7Z0O Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA Deposited 2022-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8GHN Composite model of the yeast Hir Complex with Asf1/H3/H4 Deposited 2023-03-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric
Chain N 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8QKU SWR1-nucleosome complex in configuration 1 Deposited 2023-09-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–103（103 aa）
Chain D 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8QKV SWR1-nucleosome complex in configuration 2 Deposited 2023-09-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–103（103 aa）
Chain D 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
8QYV SWR1-hexasome complex Deposited 2023-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric
Chain C 1–103（103 aa）
Chain D 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8QZ0 SWR1-hexasome-dimer complex Deposited 2023-10-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–103（103 aa）
Chain D 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8XGC Structure of yeast replisome associated with FACT and histone hexamer, Composite map Deposited 2023-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain O 1–103（103 aa）
Chain S 1–103（103 aa）
Not recorded ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9FBW SWR1 lacking Swc5 subunit in complex with hexasome Deposited 2024-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain C 1–103（103 aa）
Chain D 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å

43 other PDB entries and 63 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H4_YEAST
Isoform —
PDB entities 16
Chains and sequence ranges Author chain b； PDBConstruct 1–79； UniProt 25–103 Author chain f； PDBConstruct 1–79； UniProt 25–103

Histone H2B.2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P02294

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain d； UniProt 37–129 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2B.1 × 1 （P02293） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ID3 CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS Deposited 2001-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–130（130 aa）
Chain H 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, Potassium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.10 Å R-free 0.292
4JJN Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome Deposited 2013-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 2–131（130 aa）
Chain H 2–131（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.05 M sodium cacodylate, 32% 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.09 Å R-free 0.255
7E9C Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome Deposited 2021-03-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7E9F Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome Deposited 2021-03-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8F0X Cryo-EM structure of Kap114 bound to H2A-H2B Deposited 2022-11-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–131（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Tris pH 7.5, 300 mM NaCl, 2 mM MgCl2, 1 mM TCEP, and 0.1% NP-40
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
8F1E Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B Deposited 2022-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–131（130 aa）
Not recorded MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
8XGC Structure of yeast replisome associated with FACT and histone hexamer, Composite map Deposited 2023-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain Q 1–131（131 aa）
Not recorded ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2B2_YEAST
Isoform —
PDB entities 17
Chains and sequence ranges Author chain d； PDBConstruct 1–93； UniProt 37–129

Histone H2A.1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P04911

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain g； UniProt 17–121 Chain i； UniProt 17–118 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2B.1 × 1 （P02293） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1ID3 CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS Deposited 2001-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–131（131 aa）
Chain G 1–131（131 aa）
Not recorded MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, Potassium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.10 Å R-free 0.292
3T7K Complex structure of Rtt107p and phosphorylated histone H2A Deposited 2011-07-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 125–132（8 aa） Fragment：phosphorylated C-terminal peptide
Chain D 125–132（8 aa） Fragment：phosphorylated C-terminal peptide
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；283 K；14%(w/v) PEG 1500, 0.2M NaCl, 0.1M MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.03 Å R-free 0.258
3T7K Complex structure of Rtt107p and phosphorylated histone H2A Deposited 2011-07-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 125–132（8 aa） Fragment：phosphorylated C-terminal peptide
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；283 K；14%(w/v) PEG 1500, 0.2M NaCl, 0.1M MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.03 Å R-free 0.258
3T7K Complex structure of Rtt107p and phosphorylated histone H2A Deposited 2011-07-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 125–132（8 aa） Fragment：phosphorylated C-terminal peptide
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；283 K；14%(w/v) PEG 1500, 0.2M NaCl, 0.1M MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.03 Å R-free 0.258
4WNN SPT16-H2A-H2B FACT HISTONE Complex Deposited 2014-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–132（132 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；Crystals of ~ 60 x 60 mm formed within 10 days in 0.1M SPG (succinic acid:sodium dihydrogen phosphate:glycine ) pH 7, 25 % PEG 1500 (A4 of the PACT suite commercial screen (Qiagen).
Resolution 1.80 Å R-free 0.225
4WNN SPT16-H2A-H2B FACT HISTONE Complex Deposited 2014-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–132（132 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；Crystals of ~ 60 x 60 mm formed within 10 days in 0.1M SPG (succinic acid:sodium dihydrogen phosphate:glycine ) pH 7, 25 % PEG 1500 (A4 of the PACT suite commercial screen (Qiagen).
Resolution 1.80 Å R-free 0.225
4WNN SPT16-H2A-H2B FACT HISTONE Complex Deposited 2014-10-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–132（132 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；Crystals of ~ 60 x 60 mm formed within 10 days in 0.1M SPG (succinic acid:sodium dihydrogen phosphate:glycine ) pH 7, 25 % PEG 1500 (A4 of the PACT suite commercial screen (Qiagen).
Resolution 1.80 Å R-free 0.225
4WNN SPT16-H2A-H2B FACT HISTONE Complex Deposited 2014-10-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–132（132 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；Crystals of ~ 60 x 60 mm formed within 10 days in 0.1M SPG (succinic acid:sodium dihydrogen phosphate:glycine ) pH 7, 25 % PEG 1500 (A4 of the PACT suite commercial screen (Qiagen).
Resolution 1.80 Å R-free 0.225
5BT1 histone chaperone Hif1 playing with histone H2A-H2B dimer Deposited 2015-06-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–132（132 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；0.1M Magnesium formate dihydrate, 15% PEG3350
Resolution 2.62 Å R-free 0.262
6GEJ Chromatin remodeller-nucleosome complex at 3.6 A resolution. Deposited 2018-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain E 1–132（132 aa）
Chain F 1–132（132 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6GEN Chromatin remodeller-nucleosome complex at 4.5 A resolution. Deposited 2018-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain E 1–132（132 aa）
Chain F 1–132（132 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7K78 antibody and nucleosome complex Deposited 2020-09-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–132（132 aa）
Chain G 1–132（132 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7K7G nucleosome and Gal4 complex Deposited 2020-09-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–132（132 aa）
Chain G 1–132（132 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7SSA Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome Deposited 2021-11-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–132（131 aa）
Chain G 2–132（131 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain c 1–132（132 aa）
Chain g 1–132（132 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain c 1–132（132 aa）
Chain g 1–132（132 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8QYV SWR1-hexasome complex Deposited 2023-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric
Chain E 1–132（132 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8QZ0 SWR1-hexasome-dimer complex Deposited 2023-10-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain E 1–132（132 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8XGC Structure of yeast replisome associated with FACT and histone hexamer, Composite map Deposited 2023-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain P 1–132（132 aa）
Not recorded ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9C9G S.c INO80 in complex with S.c 0/80 nucleosome Deposited 2024-06-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain C 1–132（132 aa）
Chain G 1–132（132 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 2.91 Å
9C9T S.c INO80 in complex with S.c 0/40 nucleosome, Class 2 Deposited 2024-06-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain C 1–132（132 aa）
Chain G 1–132（132 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.16 Å
9CAU DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome Deposited 2024-06-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–132（132 aa）
Chain G 1–132（132 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 4.18 Å
9CB7 DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, Ino80-Nucleosome Deposited 2024-06-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 1–132（132 aa）
Chain G 1–132（132 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 4.04 Å
9FBW SWR1 lacking Swc5 subunit in complex with hexasome Deposited 2024-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain E 1–132（132 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
9OB1 S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State Deposited 2025-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–132（132 aa）
Chain G 1–132（132 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.20 Å

20 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2A1_YEAST
Isoform —
PDB entities 19, 21
Chains and sequence ranges Author chain g； PDBConstruct 1–105； UniProt 17–121 Author chain i； PDBConstruct 1–102； UniProt 17–118

Histone H2B.1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P02293

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 20 DNA 2 PDB declaration: 22-meric（22） Consistent with all polymer counts Chain h； UniProt 36–129 Not recorded Inner kinetochore subunit MIF2 × 1 （P35201） DNA (125-MER) × 1 Inner kinetochore subunit MCM16 × 1 （Q12262） Inner kinetochore subunit CTF3 × 1 （Q12748） DNA (125-MER) × 1 Inner kinetochore subunit MCM22 × 1 （P47167） Inner kinetochore subunit IML3 × 1 （P38265） Inner kinetochore subunit CHL4 × 1 （P38907） Inner kinetochore subunit MCM21 × 1 （Q06675） Inner kinetochore subunit CTF19 × 1 （Q02732） Inner kinetochore subunit OKP1 × 1 （P53298） Inner kinetochore subunit AME1 × 1 （P38313） Inner kinetochore subunit NKP1 × 1 （Q12493） Inner kinetochore subunit NKP2 × 1 （Q06162） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H4 × 2 （P02309） Histone H2B.2 × 1 （P02294） Histone H3-like centromeric protein CSE4 × 1 （P36012） Histone H2A.1 × 1 （P04911） Histone H2A.1 × 1 （P04911） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.15 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6QLD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2JSS NMR structure of chaperone Chz1 complexed with histone H2A.Z-H2B Deposited 2007-07-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 37–131（95 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；308 K；Ionic strength (raw mmCIF value) 200 mM KCl；Pressure ambient
NMR sample composition 1.0~1.2 mM [U-35%2H]/[U-100% 2H] H2A.Z-H2B/Chz1 | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-100% 13C;U-35%2H]/[U-100% 2H] Chz1/H2A.Z-H2B, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-100%15N;U-100% 2H] Chz1/H2a.Z-H2B, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-100% 13C; U-100% 15N;U-100%2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-10% 13C; U-100% 15N]/[U-100% 2H] Chz1/H2A.Z-H2B, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-100% 15N;U-100%2H]/[U-30%2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-100% 13C;U-30%2H]/[U-100% 2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-13C; U-15N; U-2H]/[U-100% 2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-100% 15N;U-30%2H]/[U-100% 2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-100% 13C;U-35%2H]/[U-100% 2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-100% 15N;U-100%2H]/[U-30%2H] H2A.Z-H2B/Chz1, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-100% 13C;U-35%2H]/[U-100% 2H] Chz1/H2A.Z-H2B, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
NMR sample composition 1.0~1.2 mM [U-100% 15N;U-30%2H]/[U-100% 2H] Chz1/H2A.Z-H2B, 25 mM MES, 200 mM KCl, 1mM EDTA | 90% H2O/10% D2O/100%D2O
Resolution not provided
4KUD Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle Deposited 2013-05-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；289 K；16% PEG 400, 0.1M KCl, 0.01M CaCl2, 0.05M sodium citrate(pH4.8), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.20 Å R-free 0.237
4M6B Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer Deposited 2013-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 37–131（95 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% (w/v) PEG 2000 MME, 100 mM HEPES, pH 7.5, 50 mM Calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.78 Å R-free 0.220
4M6B Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer Deposited 2013-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 37–131（95 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；10% (w/v) PEG 2000 MME, 100 mM HEPES, pH 7.5, 50 mM Calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.78 Å R-free 0.220
4WNN SPT16-H2A-H2B FACT HISTONE Complex Deposited 2014-10-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 31–131（101 aa） Fragment：UNP residues 31-131
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；Crystals of ~ 60 x 60 mm formed within 10 days in 0.1M SPG (succinic acid:sodium dihydrogen phosphate:glycine ) pH 7, 25 % PEG 1500 (A4 of the PACT suite commercial screen (Qiagen).
Resolution 1.80 Å R-free 0.225
4WNN SPT16-H2A-H2B FACT HISTONE Complex Deposited 2014-10-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 31–131（101 aa） Fragment：UNP residues 31-131
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；Crystals of ~ 60 x 60 mm formed within 10 days in 0.1M SPG (succinic acid:sodium dihydrogen phosphate:glycine ) pH 7, 25 % PEG 1500 (A4 of the PACT suite commercial screen (Qiagen).
Resolution 1.80 Å R-free 0.225
4WNN SPT16-H2A-H2B FACT HISTONE Complex Deposited 2014-10-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 31–131（101 aa） Fragment：UNP residues 31-131
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；Crystals of ~ 60 x 60 mm formed within 10 days in 0.1M SPG (succinic acid:sodium dihydrogen phosphate:glycine ) pH 7, 25 % PEG 1500 (A4 of the PACT suite commercial screen (Qiagen).
Resolution 1.80 Å R-free 0.225
4WNN SPT16-H2A-H2B FACT HISTONE Complex Deposited 2014-10-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 31–131（101 aa） Fragment：UNP residues 31-131
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；Crystals of ~ 60 x 60 mm formed within 10 days in 0.1M SPG (succinic acid:sodium dihydrogen phosphate:glycine ) pH 7, 25 % PEG 1500 (A4 of the PACT suite commercial screen (Qiagen).
Resolution 1.80 Å R-free 0.225
5BT1 histone chaperone Hif1 playing with histone H2A-H2B dimer Deposited 2015-06-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–131（131 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；0.1M Magnesium formate dihydrate, 15% PEG3350
Resolution 2.62 Å R-free 0.262
6AE8 Structure insight into histone chaperone Chz1-mediated H2A.Z recognition and replacement Deposited 2018-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 37–131（95 aa） Fragment：UNP residues 37-131, UNP residues 23-119
Not recorded BCN BICINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；Bicine,1,4-Dioxane,PEG 20000
Resolution 1.65 Å R-free 0.216
6AE8 Structure insight into histone chaperone Chz1-mediated H2A.Z recognition and replacement Deposited 2018-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 37–131（95 aa） Fragment：UNP residues 37-131, UNP residues 23-119
Not recorded BCN BICINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；Bicine,1,4-Dioxane,PEG 20000
Resolution 1.65 Å R-free 0.216
6GEJ Chromatin remodeller-nucleosome complex at 3.6 A resolution. Deposited 2018-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain G 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6GEN Chromatin remodeller-nucleosome complex at 4.5 A resolution. Deposited 2018-04-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain G 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7K78 antibody and nucleosome complex Deposited 2020-09-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7K7G nucleosome and Gal4 complex Deposited 2020-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7SSA Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome Deposited 2021-11-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 2–131（130 aa）
Chain H 2–131（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8OW0 Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain d 1–131（131 aa）
Chain h 1–131（131 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain d 1–131（131 aa）
Chain h 1–131（131 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8QKU SWR1-nucleosome complex in configuration 1 Deposited 2023-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain G 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8QKV SWR1-nucleosome complex in configuration 2 Deposited 2023-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain G 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
8QYV SWR1-hexasome complex Deposited 2023-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric
Chain G 1–131（131 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8QZ0 SWR1-hexasome-dimer complex Deposited 2023-10-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain G 1–131（131 aa）
Chain H 1–131（131 aa）
Mutation：S115C ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9C9G S.c INO80 in complex with S.c 0/80 nucleosome Deposited 2024-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain D 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 2.91 Å
9C9T S.c INO80 in complex with S.c 0/40 nucleosome, Class 2 Deposited 2024-06-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain D 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.16 Å
9CAU DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome Deposited 2024-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 4.18 Å
9CB7 DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, Ino80-Nucleosome Deposited 2024-06-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 4.04 Å
9FBW SWR1 lacking Swc5 subunit in complex with hexasome Deposited 2024-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain G 1–131（131 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
9OB1 S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State Deposited 2025-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain D 1–131（131 aa）
Chain H 1–131（131 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.20 Å

23 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2B1_YEAST
Isoform —
PDB entities 20
Chains and sequence ranges Author chain h； PDBConstruct 1–94； UniProt 36–129

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6qld

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6qld
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▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6qld
Deposition date deposition_date2019-01-31
Structure title titleStructure of inner kinetochore CCAN-Cenp-A complex
Keywords keywordsinner kinetochore, DNA, nucleosome, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier62.71 Å
Radius of gyration Rg (electron density) rg_electron62.47 Å
Forward intensity I(0) i03012220000.00
Molecular weight molecular_weight417390.0 kDa
Excluded volume excluded_volume504270 ų
Envelope volume envelope_volume858040 ų
Hydration-shell volume shell_volume115360 ų
Envelope diameter envelope_diameter216.8 Å
Shell Rg shell_rg64.03 Å
Envelope Rg envelope_rg60.05 Å
Shape Rg shape_rg62.46 Å
Total Rg total_rg62.53 Å
Total atoms total_atoms29086
Residues n_residues3405
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax220.4 Å
Rg (real space) rg_real62.72 Å
Rg uncertainty (real space) rg_real_error3.51 Å
I(0) (real space) i0_real3.0120e+09
I(0) uncertainty (real space) i0_real_error7.4190e+07
Rg (reciprocal space) rg_reciprocal62.66 Å
I(0) (reciprocal space) i0_reciprocal3012000000.0000
Solution quality estimate total_estimate0.8625
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary79.3 Å
Skewness Skewness skewness0.316
Kurtosis Kurtosis kurtosis-0.302
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha194500000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.733
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (21)

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8. Citations (1)

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9. Files and Curves (10)