SAXSdb — 4au7

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

HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H2

MUS MUSCULUS

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 1–246	Fragment：SET DOMAIN, RESIDUES 1-246	HISTONE H4 PEPTIDE × 1 （P62806） SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；PROTEIN WAS CRYSTALLIZED FROM 9% PEG 3350, 0.1 M HEPES PH 6.5	Resolution 2.07 Å R-free 0.240
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–246	Fragment：SET DOMAIN, RESIDUES 1-246	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；PROTEIN WAS CRYSTALLIZED FROM 9% PEG 3350, 0.1 M HEPES PH 6.5	Resolution 2.07 Å R-free 0.240

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	SV422_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–247； UniProt 1–246 Author chain B； PDBConstruct 2–247； UniProt 1–246

HISTONE H4 PEPTIDE

OrganismNot specified

UniProt P62806

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 C； UniProt 18–26	Fragment：RESIDUES 18-26 Non-standard monomer：Yes (specific site not provided by mmCIF)	HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H2 × 1 （Q6Q783） SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；PROTEIN WAS CRYSTALLIZED FROM 9% PEG 3350, 0.1 M HEPES PH 6.5	Resolution 2.07 Å R-free 0.240

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 4AU7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F66 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z Deposited 2000-06-20	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 B 1–102（102 aa） Chain F 1–102（102 aa）	Not recorded	MN MANGANESE (II) ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.60 Å R-free 0.249
2WP2 Structure of Brdt bromodomain BD1 bound to a diacetylated histone H4 peptide. Deposited 2009-08-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–21（20 aa） Fragment：RESIDUES 2-21	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；15 MG/ML BRDT-BD1 PROTEIN WAS MIXED WITH H4-ACK5/K8 PEPTIDE IN A 1:20 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD FROM 2.4 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.	Resolution 2.37 Å R-free 0.261
2WP2 Structure of Brdt bromodomain BD1 bound to a diacetylated histone H4 peptide. Deposited 2009-08-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 2–21（20 aa） Fragment：RESIDUES 2-21	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；15 MG/ML BRDT-BD1 PROTEIN WAS MIXED WITH H4-ACK5/K8 PEPTIDE IN A 1:20 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD FROM 2.4 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.	Resolution 2.37 Å R-free 0.261
4DOW Structure of mouse ORC1 BAH domain bound to H4K20me2 Deposited 2012-02-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 15–26（12 aa） Fragment：UNP residues 15-26	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.95 Å R-free 0.257
4DOW Structure of mouse ORC1 BAH domain bound to H4K20me2 Deposited 2012-02-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 15–26（12 aa） Fragment：UNP residues 15-26	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.95 Å R-free 0.257
5B1L The mouse nucleosome structure containing H3t Deposited 2015-12-08	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 B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13	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 0.243
5B1M The mouse nucleosome structure containing H3.1 Deposited 2015-12-08	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 B 1–103（103 aa） Chain F 1–103（103 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 2.34 Å R-free 0.259
5XM0 The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4 Deposited 2017-05-12	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 B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.87 Å R-free 0.255
5XM1 The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4 Deposited 2017-05-12	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 B 1–103（103 aa） Chain F 1–103（103 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 3.45 Å R-free 0.254
7DBH The mouse nucleosome structure containing H3mm18 Deposited 2020-10-20	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 × 8 PDB declaration: decameric	Chain B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7VBM The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv Deposited 2021-08-31	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 × 8 PDB declaration: decameric	Chain B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
8PKI Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 Deposited 2023-06-26	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: 11-meric	Chain B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H4_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–9； UniProt 18–26

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4au7
Deposition date deposition_date	2012-05-14
Structure title title	The structure of the Suv4-20h2 ternary complex with histone H4
Keywords keywords	TRANSFERASE, EPIGENETICS; TRANSFERASE
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	28.09 Å
Radius of gyration Rg (electron density) rg_electron	27.84 Å
Forward intensity I(0) i0	49078000.00
Molecular weight molecular_weight	53305.0 kDa
Excluded volume excluded_volume	66203 Å³
Envelope volume envelope_volume	83120 Å³
Hydration-shell volume shell_volume	26190 Å³
Envelope diameter envelope_diameter	97.0 Å
Shell Rg shell_rg	33.42 Å
Envelope Rg envelope_rg	27.52 Å
Shape Rg shape_rg	27.86 Å
Total Rg total_rg	28.37 Å
Total atoms total_atoms	3731
Residues n_residues	460
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	94.1 Å
Rg (real space) rg_real	28.26 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	4.9080e+07
I(0) uncertainty (real space) i0_real_error	7.7350e+05
Rg (reciprocal space) rg_reciprocal	28.21 Å
I(0) (reciprocal space) i0_reciprocal	49080000.0000
Solution quality estimate total_estimate	0.8590
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.9 Å
Skewness Skewness skewness	0.424
Kurtosis Kurtosis kurtosis	-0.477
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9680000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.843; Smooth: 0.857

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H2
Molecular weight formula_weight	28162.1 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3917

SMGPDRVTARELCENDDLATSLVLDPYLGFRTHKMNVSPVPTLRRQHHLRSALEAFLRQRDLEAAFRALTLGGWMAHYFQSRAPRQEAALKTHIFCYLRAFLPESGFTILPCTRYSMETNGAKIVSTRAWKKNEKLELLVGCIAELREEDEDLLRAGENDFSIMYSTRKRSAQLWLGPAAFINHDCKPNCKFVPSDGNTACVKVLRDIEPGDEVTCFYGEGFFGEKNEHCECYTCERKGEGAFRLQP

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	HISTONE H4 PEPTIDE
Molecular weight formula_weight	1274.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

RHRKVLRDY

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 6 Entity 6 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

CATH v4.4 (4 domains)

Domain ID domain_id	4au7A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1700 — Histone-lysine N-methyltransferase

Domain ID domain_id	4au7A02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	4au7B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1700 — Histone-lysine N-methyltransferase

Domain ID domain_id	4au7B02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

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8. Citations (1)

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Unit-cell length a length_a	37.270 Å
Unit-cell length b length_b	65.170 Å
Unit-cell length c length_c	209.490 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.070 Å
Low-resolution limit resolution_low	55.330 Å
R factor r_factor	0.1950
R_work r_work	0.1925
R_free r_free	0.2404

fit	/app/data/saxs_computation/au/4au7/4au7.fit
pddf	/app/data/pr_computation/au/4au7/4au7.pr.out
profile	/app/data/saxs_computation/au/4au7/4au7.dat

The structure of the Suv4-20h2 ternary complex with histone H4

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

HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H2

State in the Current Structure

Other States of the Same Protein in the Database

HISTONE H4 PEPTIDE

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)