← Back to search
5ymy

The structure of the complex between Rpn13 and K48-diUb

Method: SOLUTION NMR
▼

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

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 3 Proteasomal ubiquitin receptor ADRM1 × 1 （Q16186） 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 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–76； UniProt 1–76 Author chain B； PDBConstruct 1–76； UniProt 1–76

Proteasomal ubiquitin receptor ADRM1

Homo sapiens

UniProt Q16186

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P0CG47） Ubiquitin × 1 （P0CG47） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2kqz 2kr0 2l5v 2mkz 5irs 7kxi

6 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2nbv 4uel 4uem 4wlq 4wlr 5v1y 5v1y 5v1z 5v1z 5ymy 6co4 6oi4

18 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ADRM1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–150； UniProt 1–150

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5ymy
Deposition date deposition_date2017-10-22
Structure title titleThe structure of the complex between Rpn13 and K48-diUb
Keywords keywordscomplex, ubiquitin receptor, compacted, PROTEIN BINDING-SIGNALING PROTEIN complex; PROTEIN BINDING/SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
▼

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.

5ymy__assembly_1__model_1

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

Download this curve (.dat)

5ymy__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5ymy__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）20.40 Å
Rg (electron density)19.20 Å
Total Rg20.16 Å
Atom count4327
Residues266
Excluded volume38299 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5ymy__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 2 5ymy__assembly_1__model_2 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 3 5ymy__assembly_1__model_3 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 4 5ymy__assembly_1__model_4 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 5 5ymy__assembly_1__model_5 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 6 5ymy__assembly_1__model_6 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 7 5ymy__assembly_1__model_7 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 8 5ymy__assembly_1__model_8 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 9 5ymy__assembly_1__model_9 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 10 5ymy__assembly_1__model_10 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 11 5ymy__assembly_1__model_11 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 12 5ymy__assembly_1__model_12 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 13 5ymy__assembly_1__model_13 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 14 5ymy__assembly_1__model_14 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 15 5ymy__assembly_1__model_15 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 16 5ymy__assembly_1__model_16 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 17 5ymy__assembly_1__model_17 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 18 5ymy__assembly_1__model_18 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 19 5ymy__assembly_1__model_19 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
1 20 5ymy__assembly_1__model_20 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

▼

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5ymya_
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_idd5ymyb_
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 (1 domains)

Domain ID domain_id5ymyC00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily70 — Proteasomal ubiquitin receptor Rpn13/ADRM1
▶

7. Citations (1)