8r5h

Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2

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

Cullin-2

Homo sapiens

UniProt Q13617

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 (P62877) Ubiquitin-conjugating enzyme E2 R2 × 1 (Q712K3) Ubiquitin × 1 (P0CG48) Elongin-C × 1 (Q15369) Bromodomain-containing protein 4 × 1 (O60885) Elongin-B × 1 (Q15370) von Hippel-Lindau disease tumor suppressor × 1 (P40337) ZINC ION × 3 5-azanylpentan-2-one × 1 ;(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name CUL2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–745; UniProt 1–745

E3 ubiquitin-protein ligase RBX1, N-terminally processed

Homo sapiens

UniProt P62877

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Cullin-2 × 1 (Q13617) Ubiquitin-conjugating enzyme E2 R2 × 1 (Q712K3) Ubiquitin × 1 (P0CG48) Elongin-C × 1 (Q15369) Bromodomain-containing protein 4 × 1 (O60885) Elongin-B × 1 (Q15370) von Hippel-Lindau disease tumor suppressor × 1 (P40337) ZINC ION × 3 5-azanylpentan-2-one × 1 ;(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RBX1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain R; PDBConstruct 1–104; UniProt 5–108

Ubiquitin-conjugating enzyme E2 R2

Homo sapiens

UniProt Q712K3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Cullin-2 × 1 (Q13617) E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 (P62877) Ubiquitin × 1 (P0CG48) Elongin-C × 1 (Q15369) Bromodomain-containing protein 4 × 1 (O60885) Elongin-B × 1 (Q15370) von Hippel-Lindau disease tumor suppressor × 1 (P40337) ZINC ION × 3 5-azanylpentan-2-one × 1 ;(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name UB2R2_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–192; UniProt 1–192

Ubiquitin

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 8 Cullin-2 × 1 (Q13617) E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 (P62877) Ubiquitin-conjugating enzyme E2 R2 × 1 (Q712K3) Elongin-C × 1 (Q15369) Bromodomain-containing protein 4 × 1 (O60885) Elongin-B × 1 (Q15370) von Hippel-Lindau disease tumor suppressor × 1 (P40337) ZINC ION × 3 5-azanylpentan-2-one × 1 ;(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name UBC_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain U; PDBConstruct 1–75; UniProt 1–75

Elongin-C

Homo sapiens

UniProt Q15369

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Cullin-2 × 1 (Q13617) E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 (P62877) Ubiquitin-conjugating enzyme E2 R2 × 1 (Q712K3) Ubiquitin × 1 (P0CG48) Bromodomain-containing protein 4 × 1 (O60885) Elongin-B × 1 (Q15370) von Hippel-Lindau disease tumor suppressor × 1 (P40337) ZINC ION × 3 5-azanylpentan-2-one × 1 ;(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name ELOC_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain D; PDBConstruct 1–112; UniProt 1–112

Bromodomain-containing protein 4

Homo sapiens

UniProt O60885

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Cullin-2 × 1 (Q13617) E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 (P62877) Ubiquitin-conjugating enzyme E2 R2 × 1 (Q712K3) Ubiquitin × 1 (P0CG48) Elongin-C × 1 (Q15369) Elongin-B × 1 (Q15370) von Hippel-Lindau disease tumor suppressor × 1 (P40337) ZINC ION × 3 5-azanylpentan-2-one × 1 ;(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name BRD4_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F; PDBConstruct 1–115; UniProt 346–460

Elongin-B

Homo sapiens

UniProt Q15370

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Cullin-2 × 1 (Q13617) E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 (P62877) Ubiquitin-conjugating enzyme E2 R2 × 1 (Q712K3) Ubiquitin × 1 (P0CG48) Elongin-C × 1 (Q15369) Bromodomain-containing protein 4 × 1 (O60885) von Hippel-Lindau disease tumor suppressor × 1 (P40337) ZINC ION × 3 5-azanylpentan-2-one × 1 ;(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name ELOB_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain G; PDBConstruct 1–118; UniProt 1–118

von Hippel-Lindau disease tumor suppressor

Homo sapiens

UniProt P40337

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Cullin-2 × 1 (Q13617) E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 (P62877) Ubiquitin-conjugating enzyme E2 R2 × 1 (Q712K3) Ubiquitin × 1 (P0CG48) Elongin-C × 1 (Q15369) Bromodomain-containing protein 4 × 1 (O60885) Elongin-B × 1 (Q15370) ZINC ION × 3 5-azanylpentan-2-one × 1 ;(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide ; × 1 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name VHL_HUMAN
Isoform P40337-3
PDB entities 8
Chains and sequence ranges Author chain H; PDBConstruct 1–160; UniProt 1–160

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_id8r5h
Deposition date deposition_date2023-11-16
Structure title titleUbiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2
Keywords keywordsCUL2, VHL, ELOBC, BRD4, MZ1, PROTAC, Ubiquitin, Ubiquitin Ligase, Monoubiquitylation, LIGASE, NEDD8, RBX1; LIGASE
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.

8r5h__assembly_1__model_1

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

Download this curve (.dat)

8r5h__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.

8r5h__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)49.91 Å
Rg (electron density)50.04 Å
Total Rg50.17 Å
Atom count11277
Residues1453
Excluded volume200950 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8r5h__assembly_1__model_1 octameric (8) 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 (11)

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7. Citations (1)