SAXSdb — 2x4y

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

PEREGRIN

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	HISTONE H3.2 × 1 （Q71DI3） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	HISTONE H3.2 × 1 （Q71DI3） SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	HISTONE H3.2 × 1 （Q71DI3） SULFATE ION × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	HISTONE H3.2 × 1 （Q71DI3） SULFATE ION × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	HISTONE H3.2 × 1 （Q71DI3） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	HISTONE H3.2 × 1 （Q71DI3） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	HISTONE H3.2 × 1 （Q71DI3） water × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	HISTONE H3.2 × 1 （Q71DI3） SULFATE ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRPF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–132； UniProt 1076–1205 Author chain C； PDBConstruct 3–132； UniProt 1076–1205 Author chain E； PDBConstruct 3–132； UniProt 1076–1205 Author chain G； PDBConstruct 3–132； UniProt 1076–1205 Author chain I； PDBConstruct 3–132； UniProt 1076–1205 Author chain K； PDBConstruct 3–132； UniProt 1076–1205 Author chain M； PDBConstruct 3–132； UniProt 1076–1205 Author chain O； PDBConstruct 3–132； UniProt 1076–1205

HISTONE H3.2

OrganismNot specified

UniProt Q71DI3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PEREGRIN × 1 （P55201） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PEREGRIN × 1 （P55201） SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	PEREGRIN × 1 （P55201） SULFATE ION × 2 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	PEREGRIN × 1 （P55201） SULFATE ION × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	PEREGRIN × 1 （P55201） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	PEREGRIN × 1 （P55201） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	PEREGRIN × 1 （P55201） water × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	PEREGRIN × 1 （P55201） SULFATE ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–21； UniProt 23–43 Author chain D； PDBConstruct 1–21； UniProt 23–43 Author chain F； PDBConstruct 1–21； UniProt 23–43 Author chain H； PDBConstruct 1–21； UniProt 23–43 Author chain J； PDBConstruct 1–21； UniProt 23–43 Author chain L； PDBConstruct 1–21； UniProt 23–43 Author chain N； PDBConstruct 1–21； UniProt 23–43 Author chain P； PDBConstruct 1–21； UniProt 23–43

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	2x4y
Deposition date deposition_date	2010-02-02
Structure title title	Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
Keywords keywords	TRANSCRIPTION, METAL-BINDING, ZINC-FINGER, CHROMATIN REGULATOR, TRANSCRIPTION REGULATION, NUCLEOSOME; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2x4y__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2x4y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2x4y__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.10 Å
Rg (electron density)	14.71 Å
Total Rg	15.98 Å
Atom count	1101
Residues	135
Excluded volume	19849 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2x4y__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2x4y__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2x4y__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2x4y__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2x4y__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2x4y__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2x4y__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2x4y__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PEREGRIN
Molecular weight formula_weight	15249.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	10140

GGSEDEDSPLDALDLVWAKCRGYPSYPALIIDPKMPREGMFHHGVPIPVPPLEVLKLGEQMTQEAREHLYLVLFFDNKRTWQWLPRTKLVPLGVNQDLDKEKMLEGRKSNIRKSVQIAYHRALQHRSKVQGE

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 polymer

Description description	HISTONE H3.2
Molecular weight formula_weight	2330.8 kDa
Source method src_method	syn
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P

TKAARKSAPATGGVKKPHRYR

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1078

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2x4yA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2x4yC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2x4yE01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2x4yG01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2x4yI01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2x4yK01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2x4yM01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2x4yO01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

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Unit-cell length a length_a	35.757 Å
Unit-cell length b length_b	97.906 Å
Unit-cell length c length_c	102.524 Å
Unit-cell angle α angle_alpha	86.80 °
Unit-cell angle β angle_beta	80.96 °
Unit-cell angle γ angle_gamma	87.24 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	24.771 Å
R factor r_factor	0.1922
R_work r_work	0.1904
R_free r_free	0.2267

Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.

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

PEREGRIN

State in the Current Structure

Other States of the Same Protein in the Database

HISTONE H3.2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2x4y__assembly_1__model_1

2x4y__assembly_1__model_1 | I(q)

2x4y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.

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

PEREGRIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HISTONE H3.2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2x4y__assembly_1__model_1

2x4y__assembly_1__model_1 | I(q)

2x4y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)