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6xwt

drosophila melanogaster CENP-A/H4 bound to N-terminal CAL1 fragment

Method: X-RAY DIFFRACTION Dmax: 81.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H3-like centromeric protein cid

Drosophila melanogaster

UniProt Q9V6Q2

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–225 Chain C； UniProt 1–225 Not recorded Histone H4 × 2 （A0A0B4KFZ9） Chromosome alignment defect 1 × 2 （Q9VEN2） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；291 K；0.01M Cobalt (II) Chloride hexahydrate, 0.1M MES pH 6.5 and 1.8 M Ammonium Sulphate Resolution 3.47 Å R-free 0.286

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 6XWT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6XWS Crystal Structure of Drosophila CAL1 1-160 bound to CENP-A/H4 Deposited 2020-01-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–225（225 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M lithium sulfate, 0.1 M Tris pH 8.5 and 30% PEG 4000
Resolution 4.36 Å R-free 0.323

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

View Construct and Data Evidence
UniProt name CID_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–225； UniProt 1–225 Author chain C； PDBConstruct 1–225； UniProt 1–225

Histone H4

Drosophila melanogaster

UniProt A0A0B4KFZ9

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain B； UniProt 1–103 Chain D； UniProt 1–103 Not recorded Histone H3-like centromeric protein cid × 2 （Q9V6Q2） Chromosome alignment defect 1 × 2 （Q9VEN2） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；291 K；0.01M Cobalt (II) Chloride hexahydrate, 0.1M MES pH 6.5 and 1.8 M Ammonium Sulphate Resolution 3.47 Å R-free 0.286

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 6XWT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6PWE Cryo-EM structure of nucleosome core particle Deposited 2019-07-22 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
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 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
6PWF Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome Deposited 2019-07-22 Different oligomeric state Different experimental method 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 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
6XWS Crystal Structure of Drosophila CAL1 1-160 bound to CENP-A/H4 Deposited 2020-01-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M lithium sulfate, 0.1 M Tris pH 8.5 and 30% PEG 4000
Resolution 4.36 Å R-free 0.323
8PP6 human RYBP-PRC1 bound to H2AK118ub1 nucleosome Deposited 2023-07-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
8PP7 human RYBP-PRC1 bound to mononucleosome Deposited 2023-07-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
9B1E Cryo-EM structure of native SWR1 bound to nucleosome (composite structure) Deposited 2024-03-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain V 1–103（103 aa）
Chain X 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 7.6；80 nM SWR1, 160 nM nucleosomes, 1 mM ADP, 10 mM NaF, 8 mM BeCl2, 0.05% glutaraldehyde, 20 mM HEPES-KOH pH 7.6, 1.5 mM MgCl2, 0.25 mM TCEP, 0.01% IGEPAL CA-630, 1% glycerol
cryo-EM vitrification conditions Cryogen ETHANE；3 second blot time and blot force of 10.
Resolution 4.40 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A0B4KFZ9_DROME
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain D； PDBConstruct 1–103； UniProt 1–103

Chromosome alignment defect 1

Drosophila melanogaster

UniProt Q9VEN2

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain E； UniProt 1–979 Chain F； UniProt 1–979 Not recorded Histone H3-like centromeric protein cid × 2 （Q9V6Q2） Histone H4 × 2 （A0A0B4KFZ9） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；291 K；0.01M Cobalt (II) Chloride hexahydrate, 0.1M MES pH 6.5 and 1.8 M Ammonium Sulphate Resolution 3.47 Å R-free 0.286

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 6XWT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6XWS Crystal Structure of Drosophila CAL1 1-160 bound to CENP-A/H4 Deposited 2020-01-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–47（47 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M lithium sulfate, 0.1 M Tris pH 8.5 and 30% PEG 4000
Resolution 4.36 Å R-free 0.323
6XWV Crystal structure of drosophila melanogaster CENP-C bound to CAL1 Deposited 2020-01-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–979（979 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Calcium acetate, 0.1M Na Cacodylate, pH 6.5, 18% PEG 8000
Resolution 2.27 Å R-free 0.266

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9VEN2_DROME
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–979； UniProt 1–979 Author chain F； PDBConstruct 1–979； UniProt 1–979

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 6xwt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6xwt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6xwt
Deposition date deposition_date2020-01-24
Structure title titledrosophila melanogaster CENP-A/H4 bound to N-terminal CAL1 fragment
Keywords keywordsCentromere, Kinetochore, Cell Division, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.18 Å
Radius of gyration Rg (electron density) rg_electron24.49 Å
Forward intensity I(0) i026843900.00
Molecular weight molecular_weight40025.0 kDa
Excluded volume excluded_volume50337 ų
Envelope volume envelope_volume62640 ų
Hydration-shell volume shell_volume21906 ų
Envelope diameter envelope_diameter85.2 Å
Shell Rg shell_rg30.80 Å
Envelope Rg envelope_rg24.35 Å
Shape Rg shape_rg24.49 Å
Total Rg total_rg25.26 Å
Total atoms total_atoms2803
Residues n_residues352
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 dmax81.8 Å
Rg (real space) rg_real25.20 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real2.6840e+07
I(0) uncertainty (real space) i0_real_error3.8410e+05
Rg (reciprocal space) rg_reciprocal25.20 Å
I(0) (reciprocal space) i0_reciprocal26840000.0000
Solution quality estimate total_estimate0.8950
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.7 Å
Skewness Skewness skewness0.291
Kurtosis Kurtosis kurtosis-0.579
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7197000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.897; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6xwtA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6xwtB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6xwtC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id6xwtD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
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8. Citations (1)

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9. Files and Curves (10)