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7mey

Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase UBR1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P19812

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 Ubiquitin × 1 （P0CG47） Ubiquitin-conjugating enzyme E2 2 × 1 （P06104） Ubiquitin × 1 （P0CG47） Monoubiquitinated N-degron × 1 ZINC ION × 7 2-(ethylamino)ethane-1-thiol × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3nik 3nik 3nik 3nil 3nil 3nil 3nim 3nim 3nim 3nis 3nis 3nis

14 assemblies; showing the first 12

Homodimer
6kgi

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3nih 3nii 3nij 3nik 3nil 3nim 3nin 3nin 7mex 7mey

10 assemblies

View Construct and Data Evidence
UniProt name UBR1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1950； UniProt 1–1950

Ubiquitin

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 E3 ubiquitin-protein ligase UBR1 × 1 （P19812） Ubiquitin-conjugating enzyme E2 2 × 1 （P06104） Monoubiquitinated N-degron × 1 ZINC ION × 7 2-(ethylamino)ethane-1-thiol × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2msg 3ons 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4xof 5dk8

32 assemblies; showing the first 12

Homodimer
4zpz 5emz 5emz 5emz 5gob 5goc 5god 5gog 5goh 5goi 5goj 5khy

25 assemblies; showing the first 12

Homotetramer
5go8 5xdp

2 assemblies

Other homooligomers
3zlz 3zlz 3zlz 5go7 5gok 6oq1 6oq1 6oq2 7cap

9 assemblies

Heteromeric or nucleic-acid complex
2mbb 2mro 2n13 2y5b 2y5b 3o65 3o65 3o65 3o65 3o65 3o65 3oj3

362 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBB_HUMAN
Isoform —
PDB entities 2, 4
Chains and sequence ranges Author chain C； PDBConstruct 1–75； UniProt 1–75 Author chain D； PDBConstruct 1–75； UniProt 1–75

Ubiquitin-conjugating enzyme E2 2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P06104

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 E3 ubiquitin-protein ligase UBR1 × 1 （P19812） Ubiquitin × 1 （P0CG47） Ubiquitin × 1 （P0CG47） Monoubiquitinated N-degron × 1 ZINC ION × 7 2-(ethylamino)ethane-1-thiol × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ayz 1ayz 1ayz

3 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4r62 7mex 7mey 7uv8 7uvc 8ieg

6 assemblies

View Construct and Data Evidence
UniProt name UBC2_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain B； PDBConstruct 1–172； UniProt 1–172

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_id7mey
Deposition date deposition_date2021-04-08
Structure title titleStructure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
Keywords keywordsUbiquitin E3 ligase, ubiquitination, Ubr1, Ubc2, Degron, N-end rule, TRANSFERASE; TRANSFERASE
Experimental Method methodELECTRON MICROSCOPY
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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.

7mey__assembly_1__model_1

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

Download this curve (.dat)

7mey__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

7mey__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）44.44 Å
Rg (electron density)43.95 Å
Total Rg44.18 Å
Atom count16468
Residues2033
Excluded volume294350 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7mey__assembly_1__model_1 pentameric （5） 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 (7)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id7meyA01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily30 —
Domain ID domain_id7meyC01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id7meyD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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7. Citations (1)