← Back to search
7cyu

Crystal structure of human BAF57 HMG domain

Method: X-RAY DIFFRACTION Dmax: 52.3 Å Quality: GOOD
▼

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

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1

Homo sapiens

UniProt Q969G3

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 31–99 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；290 K；2.0M Ammonium sulfate, 0.1M Sodium acetate Resolution 2.55 Å R-free 0.275

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 7CYU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6LTH Structure of human BAF Base module Deposited 2020-01-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain Q 1–411（411 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6LTJ Structure of nucleosome-bound human BAF complex Deposited 2020-01-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain Q 1–411（411 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7VDV The overall structure of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain Z 1–411（411 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7Y8R The nucleosome-bound human PBAF complex Deposited 2022-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain Q 1–411（411 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain Q 1–411（411 aa）
Not recorded PTD PENTANEDIAL × 16 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain Q 1–411（411 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain Q 1–411（411 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å

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

View Construct and Data Evidence
UniProt name SMCE1_HUMAN
Isoform Q969G3-4
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–71； UniProt 31–99

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 7cyu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7cyu
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id7cyu
Deposition date deposition_date2020-09-04
Structure title titleCrystal structure of human BAF57 HMG domain
Keywords keywordsChromatin remodeling, SWI/SNF, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier15.04 Å
Radius of gyration Rg (electron density) rg_electron13.93 Å
Forward intensity I(0) i01380630.00
Molecular weight molecular_weight7729.0 kDa
Excluded volume excluded_volume9567 ų
Envelope volume envelope_volume11534 ų
Hydration-shell volume shell_volume7915 ų
Envelope diameter envelope_diameter52.4 Å
Shell Rg shell_rg18.00 Å
Envelope Rg envelope_rg14.32 Å
Shape Rg shape_rg13.90 Å
Total Rg total_rg14.97 Å
Total atoms total_atoms541
Residues n_residues62
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
▼

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

Maximum dimension Dmax dmax52.3 Å
Rg (real space) rg_real15.10 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real1.3810e+06
I(0) uncertainty (real space) i0_real_error1.5270e+04
Rg (reciprocal space) rg_reciprocal15.10 Å
I(0) (reciprocal space) i0_reciprocal1381000.0000
Solution quality estimate total_estimate0.8730
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.2 Å
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.403
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha154800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.787; Smooth: 0.986
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7cyuA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily10 — High mobility group box domain
▶

8. Citations (1)

▶

9. Files and Curves (10)