7y5l

Crystal structure of human CAF-1 core complex in spacegroup C2

Method: X-RAY DIFFRACTION Dmax: 188.8 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chromatin assembly factor 1 subunit A

Homo sapiens

UniProt Q13111

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 442–714 Not recorded Chromatin assembly factor 1 subunit B × 1 (Q13112) Histone-binding protein RBBP4 × 1 (Q09028) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate Resolution 3.42 Å R-free 0.237
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 442–714 Not recorded Chromatin assembly factor 1 subunit B × 1 (Q13112) Histone-binding protein RBBP4 × 1 (Q09028) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate Resolution 3.42 Å R-free 0.237

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.

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAF1A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–273; UniProt 442–714 Author chain D; PDBConstruct 1–273; UniProt 442–714

Chromatin assembly factor 1 subunit B

Homo sapiens

UniProt Q13112

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–419 Not recorded Chromatin assembly factor 1 subunit A × 1 (Q13111) Histone-binding protein RBBP4 × 1 (Q09028) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate Resolution 3.42 Å R-free 0.237
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 1–419 Not recorded Chromatin assembly factor 1 subunit A × 1 (Q13111) Histone-binding protein RBBP4 × 1 (Q09028) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate Resolution 3.42 Å R-free 0.237

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.

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAF1B_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–419; UniProt 1–419 Author chain E; PDBConstruct 1–419; UniProt 1–419

Histone-binding protein RBBP4

Homo sapiens

UniProt Q09028

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–425 Not recorded Chromatin assembly factor 1 subunit A × 1 (Q13111) Chromatin assembly factor 1 subunit B × 1 (Q13112) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate Resolution 3.42 Å R-free 0.237
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 1–425 Not recorded Chromatin assembly factor 1 subunit A × 1 (Q13111) Chromatin assembly factor 1 subunit B × 1 (Q13112) GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate Resolution 3.42 Å R-free 0.237

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.

49 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RBBP4_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–425; UniProt 1–425 Author chain F; PDBConstruct 1–425; UniProt 1–425

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 7y5l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7y5l
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id7y5l
Deposition date deposition_date2022-06-17
Structure title titleCrystal structure of human CAF-1 core complex in spacegroup C2
Keywords keywordsHistone chaperone, Chromatin assembly factor, REPLICATION; REPLICATION
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier58.10
Radius of gyration Rg (electron density) rg_electron58.57
Forward intensity I(0) i0704138000.00
Molecular weight molecular_weight220060.0 kDa
Excluded volume excluded_volume274630 ų
Envelope volume envelope_volume428950 ų
Hydration-shell volume shell_volume65309 ų
Envelope diameter envelope_diameter186.2
Shell Rg shell_rg54.76
Envelope Rg envelope_rg56.31
Shape Rg shape_rg58.50
Total Rg total_rg58.69
Total atoms total_atoms15522
Residues n_residues1964
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax188.8
Rg (real space) rg_real58.16
Rg uncertainty (real space) rg_real_error2.55
I(0) (real space) i0_real7.0410e+08
I(0) uncertainty (real space) i0_real_error1.3920e+07
Rg (reciprocal space) rg_reciprocal58.01
I(0) (reciprocal space) i0_reciprocal703900000.0000
Solution quality estimate total_estimate0.7780
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary83.9
Skewness Skewness skewness0.118
Kurtosis Kurtosis kurtosis-0.770
Angular range angular_range— – 0.1350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26050000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.611; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.849; Smooth: 0.428

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)