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6s53

Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-conjugating enzyme E2 N

Homo sapiens

UniProt P61088

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Polyubiquitin-C × 2 （P0CG48） E3 ubiquitin-protein ligase TRIM21 × 2 （P19474） ZINC ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Polyubiquitin-C × 2 （P0CG48） E3 ubiquitin-protein ligase TRIM21 × 2 （P19474） ZINC ION × 4 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1j7d 2c2v 2c2v 3hct 3hcu 3hcu 3von 3von 3von 3von 3von 3von

74 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBE2N_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 1–152； UniProt 1–152 Author chain E； PDBConstruct 1–152； UniProt 1–152 Author chain I； PDBConstruct 1–152； UniProt 1–152 Author chain K； PDBConstruct 1–152； UniProt 1–152

Polyubiquitin-C

Homo sapiens

UniProt P0CG48

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Ubiquitin-conjugating enzyme E2 N × 2 （P61088） E3 ubiquitin-protein ligase TRIM21 × 2 （P19474） ZINC ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Ubiquitin-conjugating enzyme E2 N × 2 （P61088） E3 ubiquitin-protein ligase TRIM21 × 2 （P19474） ZINC ION × 4 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ogw 2l3z 2ld9 2mi8 2mor 2rsu 2ru6 4boz 4dhj 4dhj 4dhz 4hk2

52 assemblies; showing the first 12

Homodimer
2mbo 2mbq 2n2k 3aul 4zqs

5 assemblies

Homotetramer
3alb 8e7o

2 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
11sy 2lvo 2lvp 2lvq 2lz6 2mcn 2mj5 2mre 2mws 2rr9 3b08 3b08

290 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBC_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–76； UniProt 1–76 Author chain F； PDBConstruct 1–76； UniProt 1–76 Author chain J； PDBConstruct 1–76； UniProt 1–76 Author chain L； PDBConstruct 1–76； UniProt 1–76

E3 ubiquitin-protein ligase TRIM21

Homo sapiens

UniProt P19474

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 6 Ubiquitin-conjugating enzyme E2 N × 2 （P61088） Polyubiquitin-C × 2 （P0CG48） ZINC ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 6 Ubiquitin-conjugating enzyme E2 N × 2 （P61088） Polyubiquitin-C × 2 （P0CG48） ZINC ION × 4 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
5jpx 8y58 8y59 8y5b 9ek5 9ii5 9m3n 9q9o 9q9o 9q9o 9q9o 9q9p

16 assemblies; showing the first 12

Homodimer
5olm

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2iwg 6fga 6fga 6fga 6fga 6s53 6s53 7bbd 8a58 9pll 9plm

11 assemblies

View Construct and Data Evidence
UniProt name RO52_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–85； UniProt 1–85 Author chain B； PDBConstruct 1–85； UniProt 1–85 Author chain G； PDBConstruct 1–85； UniProt 1–85 Author chain H； PDBConstruct 1–85； UniProt 1–85

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_id6s53
Deposition date deposition_date2019-06-30
Structure title titleCrystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate
Keywords keywordsE3 ubiquitin ligase, E2 conjugating enzyme, intracellular immunity, viral defence, TRIM21, Ube2N, ubiquitin, LIGASE; LIGASE
Experimental Method methodX-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.

6s53__assembly_1__model_1

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

Download this curve (.dat)

6s53__assembly_1__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6s53__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）31.43 Å
Rg (electron density)31.51 Å
Total Rg31.45 Å
Atom count4776
Residues607
Excluded volume85674 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6s53__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6s53__assembly_2__model_1 hexameric （6） 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 (6)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6s53c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd6s53d_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd6s53e_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd6s53f_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd6s53i_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd6s53j_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd6s53k_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd6s53l_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related

CATH v4.4 (8 domains)

Domain ID domain_id6s53A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id6s53B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id6s53C00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id6s53E00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id6s53G00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id6s53H00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id6s53I00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id6s53K00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
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7. Citations (1)