Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 140.38 kDa 
• Atom Count: 7722 
• Modelled Residue Count: 967 
• Deposited Residue Count: 1211 
• Unique protein chains: 5

5N4W

Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex

• PDB DOI: 10.2210/pdb5N4W/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-11 Released: 2017-06-07 
• Deposition Author(s): Cardote, T.A.F., Gadd, M.S., Ciulli, A.
• Funding Organization(s): European Research Council, Fundacao para a Ciencia e Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free: 0.346 
• R-Value Work: 0.302 
• R-Value Observed: 0.304 

Literature

Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex.

Cardote, T.A.F., Gadd, M.S., Ciulli, A.

(2017) Structure 25: 901-911.e3

• PubMed: 28591624 
• DOI: 10.1016/j.str.2017.04.009
• Primary Citation of Related Structures:  
  5N4W


• PubMed Abstract: 
  

Cullin RING E3 ubiquitin ligases (CRLs) function in the ubiquitin proteasome system to catalyze the transfer of ubiquitin from E2 conjugating enzymes to specific substrate proteins. CRLs are large dynamic complexes and attractive drug targets for the development of small-molecule inhibitors and chemical inducers of protein degradation. The atomic details of whole CRL assembly and interactions that dictate subunit specificity remain elusive. Here we present the crystal structure of a pentameric CRL2 ^VHL complex, composed of Cul2, Rbx1, Elongin B, Elongin C, and pVHL. The structure traps a closed state of full-length Cul2 and a new pose of Rbx1 in a trajectory from closed to open conformation. We characterize hotspots and binding thermodynamics at the interface between Cul2 and pVHL-EloBC and identify mutations that contribute toward a selectivity switch for Cul2 versus Cul5 recognition. Our findings provide structural and biophysical insights into the whole Cul2 complex that could aid future drug targeting.

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Organizational Affiliation: 

Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-2	A	748	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Von Hippel-Lindau disease tumor suppressor	B [auth V]	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1	C [auth R]	102	Homo sapiens	Mutation(s): 0  Gene Names: RBX1, RNF75, ROC1 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt), 2.3.2.32 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens) Explore P62877  Go to UniProtKB:  P62877
PHAROS:  P62877 GTEx:  ENSG00000100387

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	D [auth B]	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 ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	E [auth C]	97	Homo sapiens	Mutation(s): 0  Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
PHAROS:  Q15369 GTEx:  ENSG00000154582

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth R], G [auth R], H [auth R]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free: 0.346 
• R-Value Work: 0.302 
• R-Value Observed: 0.304 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.038	α = 90
b = 190.962	β = 90
c = 238.885	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-11 
• Released Date: 2017-06-07 
Deposition Author(s): Cardote, T.A.F., Gadd, M.S., Ciulli, A.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	ERC-2012-StG-311460
Fundacao para a Ciencia e Tecnologia	Portugal	SFRH/BD/92417/2013

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-06-21
  Changes: Database references
• Version 1.2: 2018-10-24
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2019-04-24
  Changes: Data collection, Source and taxonomy