3u5o

Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide

Method: X-RAY DIFFRACTION

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

E3 ubiquitin-protein ligase TRIM33

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 H3.1 × 1 （P68431） ZINC ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Histone H3.1 × 1 （P68431） ZINC ION × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Histone H3.1 × 1 （P68431） ZINC ION × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Histone H3.1 × 1 （P68431） ZINC ION × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Histone H3.1 × 1 （P68431） ZINC ION × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Histone H3.1 × 1 （P68431） ZINC ION × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Histone H3.1 × 1 （P68431） ZINC ION × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Histone H3.1 × 1 （P68431） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRI33_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–207； UniProt 882–1087 Author chain B； PDBConstruct 2–207； UniProt 882–1087 Author chain C； PDBConstruct 2–207； UniProt 882–1087 Author chain D； PDBConstruct 2–207； UniProt 882–1087 Author chain E； PDBConstruct 2–207； UniProt 882–1087 Author chain F； PDBConstruct 2–207； UniProt 882–1087 Author chain G； PDBConstruct 2–207； UniProt 882–1087 Author chain H； PDBConstruct 2–207； UniProt 882–1087

Histone H3.1

OrganismNot specified

UniProt P68431

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase TRIM33 × 1 （Q9UPN9） ZINC ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase TRIM33 × 1 （Q9UPN9） ZINC ION × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase TRIM33 × 1 （Q9UPN9） ZINC ION × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase TRIM33 × 1 （Q9UPN9） ZINC ION × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase TRIM33 × 1 （Q9UPN9） ZINC ION × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase TRIM33 × 1 （Q9UPN9） ZINC ION × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase TRIM33 × 1 （Q9UPN9） ZINC ION × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	E3 ubiquitin-protein ligase TRIM33 × 1 （Q9UPN9） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H31_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–22； UniProt 2–23 Author chain J； PDBConstruct 1–22； UniProt 2–23 Author chain K； PDBConstruct 1–22； UniProt 2–23 Author chain L； PDBConstruct 1–22； UniProt 2–23 Author chain M； PDBConstruct 1–22； UniProt 2–23 Author chain N； PDBConstruct 1–22； UniProt 2–23 Author chain O； PDBConstruct 1–22； UniProt 2–23 Author chain P； PDBConstruct 1–22； UniProt 2–23

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	3u5o
Deposition date deposition_date	2011-10-11
Structure title title	Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide
Keywords keywords	TRIM33, PHD, Bromodomain, TGF-beta, epigenetics, histone, methylation, K9me3, K14ac, K18ac, TRANSCRIPTION; 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.

3u5o__assembly_1__model_1

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

Download this curve (.dat)

3u5o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3u5o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.03 Å
Rg (electron density)	18.13 Å
Total Rg	19.05 Å
Atom count	1686
Residues	206
Excluded volume	30159 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3u5o__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3u5o__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3u5o__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3u5o__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3u5o__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3u5o__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3u5o__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3u5o__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 (3)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase TRIM33
Molecular weight formula_weight	23830.3 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	13522

SDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEMMKVVQVYADTQEINLKADSEVAQAGKAVALYFEDKLTEIYSDRTFA

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

Entity 2 Entity 2 polymer

Description description	Histone H3.1
Molecular weight formula_weight	2486.9 kDa
Source method src_method	syn
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N,O,P

ARTKQTARKSTGGKAPRKQLAT

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	3u5oA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5oA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5oB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5oB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5oC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5oC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5oD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5oD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5oE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5oE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5oF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5oF02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5oG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5oG02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	3u5oH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3u5oH02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

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Unit-cell length a length_a	63.639 Å
Unit-cell length b length_b	63.650 Å
Unit-cell length c length_c	125.195 Å
Unit-cell angle α angle_alpha	90.05 °
Unit-cell angle β angle_beta	89.98 °
Unit-cell angle γ angle_gamma	89.93 °
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	2.700 Å
Low-resolution limit resolution_low	28.470 Å
R factor r_factor	0.2075
R_work r_work	0.2046
R_free r_free	0.2797

Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide

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

E3 ubiquitin-protein ligase TRIM33

State in the Current Structure

Other States of the Same Protein in the Database

Histone H3.1

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

3u5o__assembly_1__model_1

3u5o__assembly_1__model_1 | I(q)

3u5o__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide

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

E3 ubiquitin-protein ligase TRIM33

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 H3.1

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

3u5o__assembly_1__model_1

3u5o__assembly_1__model_1 | I(q)

3u5o__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)