8RX0

(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub

PDB DOI: https://doi.org/10.2210/pdb8RX0/pdb
EM Map EMD-19567: EMDB EMDataResource

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-05 Released: 2024-03-06
Deposition Author(s): Crowe, C., Nakasone, M.A.
Funding Organization(s): European Research Council (ERC), Innovative Medicines Initiative, Wellcome Trust, Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub

Crowe, C., Nakasone, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 221.36 kDa
Atom Count: 12,510
Modelled Residue Count: 1,536
Deposited Residue Count: 1,913
Unique protein chains: 9

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	A [auth B]	160	Homo sapiens	Mutation(s): 0 Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337 Go to UniProtKB: P40337
PHAROS: P40337 GTEx: ENSG00000134086
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40337
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	B [auth C]	104	Homo sapiens	Mutation(s): 0 Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370 Go to UniProtKB: Q15370
PHAROS: Q15370 GTEx: ENSG00000103363
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15370
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	C [auth D]	97	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for L7N190 (Myotis lucifugus) Explore L7N190 Go to UniProtKB: L7N190
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L7N190
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-2	D [auth E]	745	Homo sapiens	Mutation(s): 0 Gene Names: CUL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13617 (Homo sapiens) Explore Q13617 Go to UniProtKB: Q13617
PHAROS: Q13617 GTEx: ENSG00000108094
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13617
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RBX1	E [auth R]	307	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD8	F [auth N]	77	Homo sapiens	Mutation(s): 0 Gene Names: NEDD8
UniProt & NIH Common Fund Data Resources
Find proteins for Q15843 (Homo sapiens) Explore Q15843 Go to UniProtKB: Q15843
PHAROS: Q15843 GTEx: ENSG00000129559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15843
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	G [auth U]	76	Homo sapiens	Mutation(s): 0 Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
PHAROS: P0CG48 GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 R1	H [auth G]	236	Homo sapiens	Mutation(s): 0 Gene Names: CDC34, UBCH3, UBE2R1 EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49427 (Homo sapiens) Explore P49427 Go to UniProtKB: P49427
PHAROS: P49427 GTEx: ENSG00000099804
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49427
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform B of Bromodomain-containing protein 4	I [auth A]	111	Homo sapiens	Mutation(s): 0 Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885 Go to UniProtKB: O60885
PHAROS: O60885 GTEx: ENSG00000141867
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60885
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
759 (Subject of Investigation/LOI) Query on 759 Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	(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 C₄₉ H₆₂ Cl N₉ O₈ S₂ HJITZUXCPZGZPX-PYNGZGNASA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth R] SDF format, chain L [auth R] SDF format, chain M [auth R] MOL2 format, chain K [auth R] MOL2 format, chain L [auth R] MOL2 format, chain M [auth R]	K [auth R], L [auth R], M [auth R]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth R] Focus chain L [auth R] Focus chain M [auth R] Interactions & Density Focus chain K [auth R] Focus chain L [auth R] Focus chain M [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-06

Deposition Author(s):

Crowe, C.

Nakasone, M.A.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	ERC-2012-StG-311460
Innovative Medicines Initiative	Switzerland	875510
Wellcome Trust	United Kingdom	223816/Z/21/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	4050845509
European Research Council (ERC)	European Union	851478

Revision History (Full details and data files)

Version 1.0: 2024-03-06
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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Help and Resources

8RX0

(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub

(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 5

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)