← Back to search
5l7a

The crystal structure of the Human SNF5/INI1 domain

Method: X-RAY DIFFRACTION Dmax: 59.9 Å Quality: EXCELLENT
▼

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

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

Homo sapiens

UniProt Q12824

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 184–252 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；277 K；1.4 M tri-sodium citrate and 100 mM HEPES pH 7.5 Resolution 2.10 Å R-free 0.260
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 184–252 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；277 K；1.4 M tri-sodium citrate and 100 mM HEPES pH 7.5 Resolution 2.10 Å R-free 0.260
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 184–252 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；277 K；1.4 M tri-sodium citrate and 100 mM HEPES pH 7.5 Resolution 2.10 Å R-free 0.260
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 184–252 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；277 K；1.4 M tri-sodium citrate and 100 mM HEPES pH 7.5 Resolution 2.10 Å R-free 0.260

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 5L7A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5AJ1 Solution Structure of the Smarc Domain Deposited 2015-02-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–113（112 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 100；Pressure 1.0
NMR sample composition 95% WATER/5% D2O
Resolution not provided
5GJK Crystal Structure of BAF47 and BAF155 Complex Deposited 2016-06-30 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 B 183–249（67 aa） Fragment：UNP RESIDUES 183-249
Not recorded GOL GLYCEROL × 6 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.4；293 K；1 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic, pH 5.4
Resolution 2.05 Å R-free 0.213
5L7B Solution structure of the human SNF5/INI1 domain Deposited 2016-06-02 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 184–258（75 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 120；Pressure 1
NMR sample composition 20 mM potassium phosphate, 100 mM sodium chloride, 5 mM [U-100% 2H] beta-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM potassium phosphate, 100 mM sodium chloride, 5 mM [U-100% 2H] beta-mercaptoethanol, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6AX5 RPT1 region of INI1/SNF5/SMARCB1_HUMAN - SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1. Deposited 2017-09-06 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 174–256（83 aa） Fragment：UNP Residues 174-256
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 160；Pressure 1
NMR sample composition 400 uM [U-99% 13C; U-99% 15N] Rpt1/INI1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6KAG Crystal structure of the SMARCB1/SMARCC2 subcomplex Deposited 2019-06-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 160–376（217 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；150 mM CsCl2, 15% PEG3350.
Resolution 2.60 Å R-free 0.240
6KZ7 The crystal structure of BAF155 SWIRM domain and N-terminal elongated hSNF5 RPT1 domain complex: Chromatin remodeling complex Deposited 2019-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 171–252（82 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；288 K；TACSIMATE, HEPES, PEC3350, MICROBATCH, TEMPERATURE 288K
Resolution 2.28 Å R-free 0.200
6KZ7 The crystal structure of BAF155 SWIRM domain and N-terminal elongated hSNF5 RPT1 domain complex: Chromatin remodeling complex Deposited 2019-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 171–252（82 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；288 K；TACSIMATE, HEPES, PEC3350, MICROBATCH, TEMPERATURE 288K
Resolution 2.28 Å R-free 0.200
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 M 1–385（385 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 mutation/modification 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 M 1–113（113 aa） Fragment：UNP residues 1-113, UNP residues 172-385
Chain M 172–385（214 aa） Fragment：UNP residues 1-113, UNP residues 172-385
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6UCH SMARCB1 nucleosome-interacting C-terminal alpha helix Deposited 2019-09-16 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 351–385（35 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；288 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 300 uM [U-100% 13C; U-100% 15N] SMARCB1CC, 137 mM NaCl, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 230 uM SMARCB1CC, 137 mM NaCl, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 100% D2O | 100% D2O
Resolution not provided
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 V 1–385（385 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 M 1–385（385 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 M 1–385（385 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 M 1–385（385 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 experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain M 1–385（385 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
9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain M 1–385（385 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SNF5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–72； UniProt 184–252 Author chain B； PDBConstruct 4–72； UniProt 184–252 Author chain C； PDBConstruct 4–72； UniProt 184–252 Author chain D； PDBConstruct 4–72； UniProt 184–252

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 5l7a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5l7a
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5l7a
Deposition date deposition_date2016-06-02
Structure title titleThe crystal structure of the Human SNF5/INI1 domain
Keywords keywordsSNF5 INI1 domain crystal, 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_guinier19.96 Å
Radius of gyration Rg (electron density) rg_electron18.78 Å
Forward intensity I(0) i015834800.00
Molecular weight molecular_weight30266.0 kDa
Excluded volume excluded_volume38059 ų
Envelope volume envelope_volume46469 ų
Hydration-shell volume shell_volume20466 ų
Envelope diameter envelope_diameter60.1 Å
Shell Rg shell_rg25.17 Å
Envelope Rg envelope_rg18.89 Å
Shape Rg shape_rg18.78 Å
Total Rg total_rg19.74 Å
Total atoms total_atoms2117
Residues n_residues265
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 dmax59.9 Å
Rg (real space) rg_real19.79 Å
Rg uncertainty (real space) rg_real_error0.27 Å
I(0) (real space) i0_real1.5830e+07
I(0) uncertainty (real space) i0_real_error1.5950e+05
Rg (reciprocal space) rg_reciprocal19.82 Å
I(0) (reciprocal space) i0_reciprocal15840000.0000
Solution quality estimate total_estimate0.9046
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.0 Å
Skewness Skewness skewness0.082
Kurtosis Kurtosis kurtosis-0.497
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4797000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.990
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

9. Files and Curves (10)