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9hmv

Cryo-EM structure of SA2-SCC1 complex at 2.9 angstrom

Method: ELECTRON MICROSCOPY Dmax: 139.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cohesin subunit SA-2

Homo sapiens

UniProt Q8N3U4

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–1231 Not recorded Double-strand-break repair protein rad21 homolog × 1 （O60216） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.90 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 9HMV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4PJU crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1) Deposited 2014-05-12 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 80–1060（981 aa） Fragment：UNP residues 80-1060
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；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).
Resolution 3.05 Å R-free 0.238
4PJW crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1), with bound MES Deposited 2014-05-12 Different construct Different mutation/modification 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 80–1060（981 aa） Fragment：UNP residues 80-1060
Non-standard monomer：Yes (specific site not provided by mmCIF) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).
Resolution 2.85 Å R-free 0.225
4PK7 crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1) with bound MES, native proteins Deposited 2014-05-13 Different construct 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 80–1060（981 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).
Resolution 2.95 Å R-free 0.251
6QNX Structure of the SA2/SCC1/CTCF complex Deposited 2019-02-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 80–1060（981 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K
Resolution 2.70 Å
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1231（1231 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K
Resolution 3.24 Å R-free 0.289
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–1231（1231 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K
Resolution 3.24 Å R-free 0.289
8K4D Structure of the SA2/Scc1/CENP_U complex Deposited 2023-07-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 81–1060（980 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.03 M CaCl2,0.03 M MgCl2, 0.1 M MOPS-HEPES, pH7.5, 10% PEG8000, 20% ethylene glycol
Resolution 3.52 Å R-free 0.269
9EP3 Structure of the SA2/SCC1/WAPL complex Deposited 2024-03-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 80–1060（981 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K
Resolution 3.08 Å R-free 0.268
9HMS Cryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2 Deposited 2024-12-09 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1231（1231 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

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

View Construct and Data Evidence
UniProt name STAG2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1231； UniProt 1–1231

Double-strand-break repair protein rad21 homolog

Homo sapiens

UniProt O60216

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 310–550 Not recorded Cohesin subunit SA-2 × 1 （Q8N3U4） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.90 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 9HMV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4PJU crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1) Deposited 2014-05-12 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 281–420（140 aa） Fragment：UNP residues 281-420
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；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).
Resolution 3.05 Å R-free 0.238
4PJW crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1), with bound MES Deposited 2014-05-12 Different construct Different mutation/modification 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 281–420（140 aa） Fragment：UNP residues 281-420
Non-standard monomer：Yes (specific site not provided by mmCIF) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).
Resolution 2.85 Å R-free 0.225
4PK7 crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1) with bound MES, native proteins Deposited 2014-05-13 Different construct 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 281–420（140 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions).
Resolution 2.95 Å R-free 0.251
6QNX Structure of the SA2/SCC1/CTCF complex Deposited 2019-02-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 281–420（140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K
Resolution 2.70 Å
6RRC Crystal structure of the N-terminal region of human cohesin subunit STAG1 in complex with RAD21 peptide Deposited 2019-05-17 Different construct 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 321–345（25 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；277 K；2.1 M Ammonium Sulfate, 0.1 M MES pH 6.3
Resolution 2.37 Å R-free 0.248
6RRC Crystal structure of the N-terminal region of human cohesin subunit STAG1 in complex with RAD21 peptide Deposited 2019-05-17 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 321–345（25 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；277 K；2.1 M Ammonium Sulfate, 0.1 M MES pH 6.3
Resolution 2.37 Å R-free 0.248
6RRK Crystal structure of the central region of human cohesin subunit STAG1 in complex with RAD21 peptide Deposited 2019-05-20 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 356–395（40 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；16 % PEG 3350, 0.2 M DL-Mallic acid
Resolution 3.17 Å R-free 0.278
6RRK Crystal structure of the central region of human cohesin subunit STAG1 in complex with RAD21 peptide Deposited 2019-05-20 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 356–395（40 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；16 % PEG 3350, 0.2 M DL-Mallic acid
Resolution 3.17 Å R-free 0.278
6WG3 Cryo-EM structure of human Cohesin-NIPBL-DNA complex Deposited 2020-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain C 1–631（631 aa）
Mutation：R172A, D279A, R450A ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å
6WGE Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1 Deposited 2020-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 1–631（631 aa）
Mutation：R172A, D279A, R450A ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7W1M Cryo-EM structure of human cohesin-CTCF-DNA complex Deposited 2021-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–631（631 aa）
Mutation：R172A, D279A, R450A ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.50 Å
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–631（631 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K
Resolution 3.24 Å R-free 0.289
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–631（631 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K
Resolution 3.24 Å R-free 0.289
8K4D Structure of the SA2/Scc1/CENP_U complex Deposited 2023-07-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 281–420（140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.03 M CaCl2,0.03 M MgCl2, 0.1 M MOPS-HEPES, pH7.5, 10% PEG8000, 20% ethylene glycol
Resolution 3.52 Å R-free 0.269
8P0A Human Cohesin ATPase module Deposited 2023-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 558–629（72 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.2
cryo-EM buffer pH 8.2
cryo-EM buffer pH 8.2
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
8PQ5 Human Cohesin ATPase module with an open DNA exit gate Deposited 2023-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 558–629（72 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.2
cryo-EM buffer pH 8.2
cryo-EM buffer pH 8.2
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8RO6 Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Apo closed P-loop conformation Deposited 2024-01-11 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 558–629（72 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Hepes pH 7.0; 10% w/v PEG 6000
Resolution 2.20 Å R-free 0.244
8RO7 Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Open/closed P-loop conformation Deposited 2024-01-11 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 558–629（72 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Hepes pH 7.0; 10% w/v PEG 6000
Resolution 2.09 Å R-free 0.223
8RO8 Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Apo closed P-loop conformation Deposited 2024-01-11 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 558–629（72 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium malonate dibasic monohydrate; 0.1 M Bis-Tris propane pH 6.5; 20% w/v PEG 3350
Resolution 1.90 Å R-free 0.231
8RO9 Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Open/closed P-loop conformation Deposited 2024-01-11 Different construct 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 558–629（72 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide; 0.1 M Bis-Tris propane pH 6.5; 20% w/v PEG 3350
Resolution 1.77 Å R-free 0.218
8RO9 Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Open/closed P-loop conformation Deposited 2024-01-11 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 558–629（72 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide; 0.1 M Bis-Tris propane pH 6.5; 20% w/v PEG 3350
Resolution 1.77 Å R-free 0.218
8ROA Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ADP-bound conformation Deposited 2024-01-11 Different construct 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 558–629（72 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium formate; 20% w/v PEG 3350
Resolution 2.44 Å R-free 0.250
8ROA Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ADP-bound conformation Deposited 2024-01-11 Different construct 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 558–629（72 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium formate; 20% w/v PEG 3350
Resolution 2.44 Å R-free 0.250
8ROB Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ATPgS-Mg-bound conformation Deposited 2024-01-11 Different construct 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 558–629（72 aa）
Not recorded MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MMT pH 7.0; 25% w/v PEG 1500
Resolution 2.50 Å R-free 0.299
8ROC Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - Apo closed P-loop conformation Deposited 2024-01-11 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 558–629（72 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium nitrate pH 6.3; 20% w/v PEG 3350
Resolution 1.85 Å R-free 0.222
8ROD Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - Open/closed P-loop conformation Deposited 2024-01-11 Different construct 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 558–629（72 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium sulfate; 20 % w/v PEG 3350
Resolution 1.50 Å R-free 0.232
8ROE Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-bound conformation Deposited 2024-01-11 Different construct 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 558–629（72 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium malonate; 0.1 M Bis Tris propane pH 6.5; 20 % w/v PEG 3350
Resolution 1.36 Å R-free 0.219
8ROF Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-Mg-bound conformation Deposited 2024-01-11 Different construct 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 558–629（72 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M magnesium chloride; 0.1 M MES pH 6.0; 20 % w/v PEG 6000
Resolution 1.65 Å R-free 0.228
8ROG Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ATPgS-Mg-bound conformation Deposited 2024-01-11 Different construct 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 558–629（72 aa）
Not recorded MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium formate; 0.1 M Bis Tris propane pH 6.5; 20 % w/v PEG 3350
Resolution 1.94 Å R-free 0.253
8ROH Human cohesin SMC3-HD(EQ)/RAD21-N complex - Apo conformation Deposited 2024-01-11 Different construct 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 1–102（102 aa）
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.21M NaSO4 ; 0.1M Bis-tris propane pH 7; 16% w/v PEG3350
Resolution 2.60 Å R-free 0.255
8ROI Human cohesin SMC3-HD(EQ)/RAD21-N complex - ADP-bound conformation Deposited 2024-01-11 Different construct 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 1–102（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Na/K phosphate pH 7.5; 0.1 M HEPES pH 7.5; 15% v/v PEG Smear High; 10% v/v ethylene glycol
Resolution 2.45 Å R-free 0.239
8ROJ Human cohesin SMC3-HD/RAD21-N complex - ADP-Mg-bound conformation Deposited 2024-01-11 Different construct 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 1–102（102 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.075 M magnesium chloride; 0.075 M Sodium citrate tribasic dehydrate; 0.1 M Bis-Tris pH 6.0; 18% v/v PEG Smear Broad
Resolution 3.00 Å R-free 0.264
8ROK Human cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 1 Deposited 2024-01-11 Different construct 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 1–102（102 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.3 M NaCl; 0.05 M L-Arginine; 0.1 M Tris pH7.5; 22.5 % v/v PEG Smear Broad; 0.05 M L-Glutamic acid monosodium salt hydrate
Resolution 2.25 Å R-free 0.253
8ROK Human cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 1 Deposited 2024-01-11 Different construct 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 1–102（102 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.3 M NaCl; 0.05 M L-Arginine; 0.1 M Tris pH7.5; 22.5 % v/v PEG Smear Broad; 0.05 M L-Glutamic acid monosodium salt hydrate
Resolution 2.25 Å R-free 0.253
8ROL Human cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 2 Deposited 2024-01-11 Different construct 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 1–102（102 aa）
Not recorded MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium chloride; 0.1 M Bicine pH 9.0; 20% w/v PEG 550 MME
Resolution 3.11 Å R-free 0.238
9EP3 Structure of the SA2/SCC1/WAPL complex Deposited 2024-03-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 281–420（140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.06M Morpheus Divalents mix, 0.1M Morpheus buffer system 1, 48% (v/v) Morpheus EOD_P8K
Resolution 3.08 Å R-free 0.268
9HMS Cryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2 Deposited 2024-12-09 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 310–550（241 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9HN0 Cryo-EM structure of human separase bound to SCC1 (310-550 aa) Deposited 2024-12-10 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 310–550（241 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9HN4 Cryo-EM structure of human separase bound to phosphorylated SCC1 (310-550 aa) Deposited 2024-12-10 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 310–550（241 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
9HN5 Cryo-EM structure of human separase bound to phosphorylated SCC1 (100-320 aa) Deposited 2024-12-10 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 100–320（221 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9HVY Cryo-EM structure of human separase-SCC1 (1-631) fusion protein Deposited 2025-01-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–631（631 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

35 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAD21_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–241； UniProt 310–550

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 9hmv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9hmv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9hmv
Deposition date deposition_date2024-12-09
Structure title titleCryo-EM structure of SA2-SCC1 complex at 2.9 angstrom
Keywords keywordsSeparase, cell cycle, SCC1, RAD21, protease, chromosome segregation, Auto-cleavage, SA1/2, cohesin; CELL CYCLE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.15 Å
Radius of gyration Rg (electron density) rg_electron40.55 Å
Forward intensity I(0) i0200756000.00
Molecular weight molecular_weight117340.0 kDa
Excluded volume excluded_volume147770 ų
Envelope volume envelope_volume209050 ų
Hydration-shell volume shell_volume43455 ų
Envelope diameter envelope_diameter140.4 Å
Shell Rg shell_rg45.56 Å
Envelope Rg envelope_rg39.82 Å
Shape Rg shape_rg40.54 Å
Total Rg total_rg40.86 Å
Total atoms total_atoms8234
Residues n_residues1013
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 dmax139.5 Å
Rg (real space) rg_real41.20 Å
Rg uncertainty (real space) rg_real_error1.51 Å
I(0) (real space) i0_real2.0080e+08
I(0) uncertainty (real space) i0_real_error4.0190e+06
Rg (reciprocal space) rg_reciprocal41.15 Å
I(0) (reciprocal space) i0_reciprocal200700000.0000
Solution quality estimate total_estimate0.8823
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.1 Å
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.630
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18550000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.897
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)