6pwf

Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome

Method: ELECTRON MICROSCOPY Dmax: 147.3 Å Quality: GOOD

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

Histone H3

Drosophila melanogaster

UniProt P02299

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–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric(11) Consistent with all polymer counts Chain A; UniProt 1–136 Chain E; UniProt 1–136 Not recorded Histone H4 × 2 (A0A0B4KFZ9) Histone H2A × 2 (P84051) Histone H2B × 2 (P02283) DNA (147-MER) × 1 DNA (147-MER) × 1 chromatin remodeling factor ISWI × 1 (G0S9L5) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.07 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.

23 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H3_DROME
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–136; UniProt 1–136 Author chain E; PDBConstruct 1–136; UniProt 1–136

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–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric(11) Consistent with all polymer counts Chain B; UniProt 1–103 Chain F; UniProt 1–103 Not recorded Histone H3 × 2 (P02299) Histone H2A × 2 (P84051) Histone H2B × 2 (P02283) DNA (147-MER) × 1 DNA (147-MER) × 1 chromatin remodeling factor ISWI × 1 (G0S9L5) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.07 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.

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 F; PDBConstruct 1–103; UniProt 1–103

Histone H2A

Drosophila melanogaster

UniProt P84051

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–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric(11) Consistent with all polymer counts Chain C; UniProt 1–124 Chain G; UniProt 1–124 Not recorded Histone H3 × 2 (P02299) Histone H4 × 2 (A0A0B4KFZ9) Histone H2B × 2 (P02283) DNA (147-MER) × 1 DNA (147-MER) × 1 chromatin remodeling factor ISWI × 1 (G0S9L5) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.07 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.

20 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2A_DROME
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–124; UniProt 1–124 Author chain G; PDBConstruct 1–124; UniProt 1–124

Histone H2B

Drosophila melanogaster

UniProt P02283

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–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric(11) Consistent with all polymer counts Chain D; UniProt 1–123 Chain H; UniProt 1–123 Not recorded Histone H3 × 2 (P02299) Histone H4 × 2 (A0A0B4KFZ9) Histone H2A × 2 (P84051) DNA (147-MER) × 1 DNA (147-MER) × 1 chromatin remodeling factor ISWI × 1 (G0S9L5) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.07 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.

21 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2B_DROME
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–123; UniProt 1–123 Author chain H; PDBConstruct 1–123; UniProt 1–123

chromatin remodeling factor ISWI

Chaetomium thermophilum

UniProt G0S9L5

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–DNA Heteromer Protein × 9 DNA 2 PDB declaration: undecameric(11) Consistent with all polymer counts Chain K; UniProt 77–134 Chain K; UniProt 167–722 Fragment:UNP residues 77-134,167-722 Histone H3 × 2 (P02299) Histone H4 × 2 (A0A0B4KFZ9) Histone H2A × 2 (P84051) Histone H2B × 2 (P02283) DNA (147-MER) × 1 DNA (147-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.07 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name G0S9L5_CHATD
Isoform
PDB entities 7
Chains and sequence ranges Author chain K; PDBConstruct 23–80; UniProt 77–134 Author chain K; PDBConstruct 85–640; UniProt 167–722

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 6pwf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6pwf
Deposition date deposition_date2019-07-22
Structure title titleCryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome
Keywords keywordsnucleosome, DNA-binding protein, ATP-dependent chromatin remodeler, ISWI, STRUCTURAL PROTEIN-DNA complex; STRUCTURAL PROTEIN/DNA
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier44.58
Radius of gyration Rg (electron density) rg_electron43.28
Forward intensity I(0) i01167640000.00
Molecular weight molecular_weight221160.0 kDa
Excluded volume excluded_volume251490 ų
Envelope volume envelope_volume394220 ų
Hydration-shell volume shell_volume75175 ų
Envelope diameter envelope_diameter146.3
Shell Rg shell_rg48.93
Envelope Rg envelope_rg42.60
Shape Rg shape_rg43.24
Total Rg total_rg43.59
Total atoms total_atoms15197
Residues n_residues1500
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 dmax147.3
Rg (real space) rg_real44.45
Rg uncertainty (real space) rg_real_error1.25
I(0) (real space) i0_real1.1680e+09
I(0) uncertainty (real space) i0_real_error2.0720e+07
Rg (reciprocal space) rg_reciprocal44.58
I(0) (reciprocal space) i0_reciprocal1168000000.0000
Solution quality estimate total_estimate0.8184
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.5
Skewness Skewness skewness0.222
Kurtosis Kurtosis kurtosis-0.461
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha129400000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)