5chl

Structural basis of H2A.Z recognition by YL1 histone chaperone component of SRCAP/SWR1 chromatin remodeling complex

Method: X-RAY DIFFRACTION D_max: 91.1 Å Quality: REASONABLE

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

Vacuolar protein sorting-associated protein 72 homolog

Drosophila melanogaster

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–75	Not recorded	Histone H2A.Z × 1 （P0C0S5）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；0.19 mM CYMAL-7, 0.1 M HEPES, pH 7.5, 40% Polyethylene glycol 400	Resolution 1.89 Å R-free 0.231

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	VPS72_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–74； UniProt 2–75

Histone H2A.Z

Homo sapiens

UniProt P0C0S5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 22–113	Not recorded	Vacuolar protein sorting-associated protein 72 homolog × 1 （Q9VKM6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；0.19 mM CYMAL-7, 0.1 M HEPES, pH 7.5, 40% Polyethylene glycol 400	Resolution 1.89 Å R-free 0.231

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5CHL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WA9 The nucleosome containing human H2A.Z.1 Deposited 2013-04-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–128（128 aa） Chain G 1–128（128 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.07 Å R-free 0.271
4CAY Crystal structure of a human Anp32e-H2A.Z-H2B complex Deposited 2013-10-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 19–128（110 aa） Fragment：GLOBULAR DOMAIN, RESIDUES 19-128	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M NA CACODYLATE, PH 7.0, 0.2 M NA FORMATE, 24% TO 30% PEG 3350	Resolution 1.48 Å R-free 0.195
4NFT Crystal structure of human lnkH2B-h2A.Z-Anp32e Deposited 2013-11-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–114（99 aa） Fragment：UNP residues 34-126, 16-114	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.2M Sodium thiocyanate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.61 Å R-free 0.273
4NFT Crystal structure of human lnkH2B-h2A.Z-Anp32e Deposited 2013-11-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 16–114（99 aa） Fragment：UNP residues 34-126, 16-114	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.2M Sodium thiocyanate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.61 Å R-free 0.273
4NFT Crystal structure of human lnkH2B-h2A.Z-Anp32e Deposited 2013-11-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 16–114（99 aa） Fragment：UNP residues 34-126, 16-114	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.2M Sodium thiocyanate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.61 Å R-free 0.273
4NFT Crystal structure of human lnkH2B-h2A.Z-Anp32e Deposited 2013-11-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 16–114（99 aa） Fragment：UNP residues 34-126, 16-114	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.2M Sodium thiocyanate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.61 Å R-free 0.273
5B31 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Deposited 2016-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain G 1–128（128 aa）	Not recorded	MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.20 Å R-free 0.271
5B32 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Deposited 2016-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain G 1–128（128 aa）	Not recorded	CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.35 Å R-free 0.259
5B33 The crystal structure of the H2AZ nucleosome with H3.3. Deposited 2016-02-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–128（128 aa） Chain G 1–128（128 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.92 Å R-free 0.252
5FUG Crystal structure of a human YL1-H2A.Z-H2B complex Deposited 2016-01-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 19–128（110 aa） Fragment：GLOBULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M SUCCINIC ACID/PHOSPHATE/GLYCINE SYSTEM PH 6/7 ; 25% PEG 1500	Resolution 2.70 Å R-free 0.243
5FUG Crystal structure of a human YL1-H2A.Z-H2B complex Deposited 2016-01-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 19–128（110 aa） Fragment：GLOBULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M SUCCINIC ACID/PHOSPHATE/GLYCINE SYSTEM PH 6/7 ; 25% PEG 1500	Resolution 2.70 Å R-free 0.243
5FUG Crystal structure of a human YL1-H2A.Z-H2B complex Deposited 2016-01-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 19–128（110 aa） Fragment：GLOBULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M SUCCINIC ACID/PHOSPHATE/GLYCINE SYSTEM PH 6/7 ; 25% PEG 1500	Resolution 2.70 Å R-free 0.243
5FUG Crystal structure of a human YL1-H2A.Z-H2B complex Deposited 2016-01-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 19–128（110 aa） Fragment：GLOBULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M SUCCINIC ACID/PHOSPHATE/GLYCINE SYSTEM PH 6/7 ; 25% PEG 1500	Resolution 2.70 Å R-free 0.243
5Z30 The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant Deposited 2018-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–128（128 aa） Chain G 1–128（128 aa）	Mutation：R80C Mutation：R80C	CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.45 Å R-free 0.243
6JOU Crystal structure of the human nucleosome containing H2A.Z.1 S42R Deposited 2019-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–128（128 aa） Chain G 1–128（128 aa）	Mutation：S42R Mutation：S42R	MN MANGANESE (II) ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.17 Å R-free 0.250
7YRD histone methyltransferase Deposited 2022-08-09	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 × 9 PDB declaration: undecameric	Chain C 11–123（113 aa） Chain G 11–123（113 aa）	Not recorded	ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7YRG histone methyltransferase Deposited 2022-08-09	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 × 10 PDB declaration: dodecameric	Chain C 11–123（113 aa） Chain G 11–123（113 aa）	Not recorded	ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8JHF Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23	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 × 9 PDB declaration: undecameric	Chain C 14–126（113 aa） Chain G 14–126（113 aa）	Not recorded	ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane	Resolution 3.68 Å
8T9F Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-06-23	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 × 9 PDB declaration: undecameric	Chain C 1–128（128 aa） Chain G 1–128（128 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8THU Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-07-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–128（128 aa） Chain G 1–128（128 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9C62 P400 subcomplex of the native human TIP60 complex Deposited 2024-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain N 1–128（128 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.28 Å
9GCG CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-01	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: 20-meric	Chain O 2–128（127 aa） Chain S 2–128（127 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
9GE4 CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain O 2–128（127 aa） Chain S 2–128（127 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å
9INC High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z domain Deposited 2024-07-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 17–114（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；45% PEG200 0.1 M HEPES pH 7.5	Resolution 2.01 Å R-free 0.257
9INC High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z domain Deposited 2024-07-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 17–114（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；45% PEG200 0.1 M HEPES pH 7.5	Resolution 2.01 Å R-free 0.257
9INC High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z domain Deposited 2024-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 17–114（98 aa） Chain D 17–114（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；45% PEG200 0.1 M HEPES pH 7.5	Resolution 2.01 Å R-free 0.257
9OGR Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v1) Deposited 2025-05-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 2–128（127 aa） Chain G 2–128（127 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9OGS Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v1) Deposited 2025-05-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 2–128（127 aa） Chain G 2–128（127 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
9OGZ Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v2) Deposited 2025-05-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 2–128（127 aa） Chain G 2–128（127 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
9OH0 Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v2) Deposited 2025-05-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 2–128（127 aa） Chain G 2–128（127 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9OH1 Cryo-EM analysis of human H2A.Z on 601L DNA Deposited 2025-05-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 2–128（127 aa） Chain G 2–128（127 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
9OH2 Cryo-EM analysis of human H2A.Z on methylated 601L DNA Deposited 2025-05-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 2–128（127 aa） Chain G 2–128（127 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
9UBD The Structural Basis of the Recognition of the Histone Variant H2A.Z by the SRCAP Catalytic Subunit Deposited 2025-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 17–114（98 aa） Chain D 17–114（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Potassium thiocyanate 15 % w/v PEG 3,350 pH 7.0	Resolution 2.53 Å R-free 0.288

25 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H2AZ_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 95–186； UniProt 22–113

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5chl
Deposition date deposition_date	2015-07-10
Structure title title	Structural basis of H2A.Z recognition by YL1 histone chaperone component of SRCAP/SWR1 chromatin remodeling complex
Keywords keywords	remodeling complex, histone, chaperone; CHAPERONE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.72 Å
Radius of gyration Rg (electron density) rg_electron	21.67 Å
Forward intensity I(0) i0	14216500.00
Molecular weight molecular_weight	27195.0 kDa
Excluded volume excluded_volume	33669 Å³
Envelope volume envelope_volume	44993 Å³
Hydration-shell volume shell_volume	18617 Å³
Envelope diameter envelope_diameter	92.9 Å
Shell Rg shell_rg	26.46 Å
Envelope Rg envelope_rg	23.71 Å
Shape Rg shape_rg	21.64 Å
Total Rg total_rg	22.47 Å
Total atoms total_atoms	1917
Residues n_residues	244
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	91.1 Å
Rg (real space) rg_real	23.04 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	1.4220e+07
I(0) uncertainty (real space) i0_real_error	2.1000e+05
Rg (reciprocal space) rg_reciprocal	22.96 Å
I(0) (reciprocal space) i0_reciprocal	14220000.0000
Solution quality estimate total_estimate	0.7367
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.841
Kurtosis Kurtosis kurtosis	0.756
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2966000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.360; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.505; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Vacuolar protein sorting-associated protein 72 homolog
Molecular weight formula_weight	8585.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2064

AASRSRRNNAGNKIAHLLNEEEEDDFYKTSYGGFQEDEEDKEYEQKDEEEDVVDSDFSIDENDEPVSDQEEAPE

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	Fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone H2A.Z
Molecular weight formula_weight	21161.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSKQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHLVPRGSH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5chlb1
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.0 — automated matches

Domain ID domain_id	d5chlb2
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.0 — automated matches

Domain ID domain_id	d5chlb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	5chlB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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8. Citations (1)

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Unit-cell length a length_a	108.047 Å
Unit-cell length b length_b	108.047 Å
Unit-cell length c length_c	58.243 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.892 Å
Low-resolution limit resolution_low	29.967 Å
R factor r_factor	0.2018
R_work r_work	0.2003
R_free r_free	0.2313

fit	/app/data/saxs_computation/ch/5chl/5chl.fit
pddf	/app/data/pr_computation/ch/5chl/5chl.pr.out
profile	/app/data/saxs_computation/ch/5chl/5chl.dat

Structural basis of H2A.Z recognition by YL1 histone chaperone component of SRCAP/SWR1 chromatin remodeling complex

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

Vacuolar protein sorting-associated protein 72 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2A.Z

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)