6V9I | pdb_00006v9i

cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2)

• PDB DOI: https://doi.org/10.2210/pdb6V9I/pdb
• EM Map EMD-21121: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Streptococcus sp. 'group G, Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21, Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-13 Released: 2020-04-29 
• Deposition Author(s): Komives, E.A., Lumpkin, R.J., Baker, R.W., Leschziner, A.E.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Structure and dynamics of the ASB9 CUL-RING E3 Ligase.

Lumpkin, R.J., Baker, R.W., Leschziner, A.E., Komives, E.A.

(2020) Nat Commun 11: 2866-2866

• PubMed: 32513959 
• DOI: https://doi.org/10.1038/s41467-020-16499-9
• Primary Citation Related Structures: 
  6V9H, 6V9I


• PubMed Abstract: 
  

  The Cullin 5 (CUL5) Ring E3 ligase uses adaptors Elongins B and C (ELOB/C) to bind different SOCS-box-containing substrate receptors, determining the substrate specificity of the ligase. The 18-member ankyrin and SOCS box (ASB) family is the largest substrate receptor family. Here we report cryo-EM data for the substrate, creatine kinase (CKB) bound to ASB9-ELOB/C, and for full-length CUL5 bound to the RING protein, RBX2, which binds various E2s. To date, no full structures are available either for a substrate-bound ASB nor for CUL5. Hydrogen-deuterium exchange (HDX-MS) mapped onto a full structural model of the ligase revealed long-range allostery extending from the substrate through CUL5. We propose a revised allosteric mechanism for how CUL-E3 ligases function. ASB9 and CUL5 behave as rigid rods, connected through a hinge provided by ELOB/C transmitting long-range allosteric crosstalk from the substrate through CUL5 to the RBX2 flexible linker.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92092-0378, USA.
Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA.
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA.
Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA.
Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92092-0378, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 113.37 kDa 
• Atom Count: 4,066 
• Modeled Residue Count: 814 
• Deposited Residue Count: 976 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G-binding protein G,Cullin-5	A [auth C]	863	Streptococcus sp. 'group G, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: spg, CUL5, VACM1
UniProt & NIH Common Fund Data Resources
Find proteins for P06654 (Streptococcus sp. group G) Explore P06654  Go to UniProtKB:  P06654
Find proteins for Q93034 (Homo sapiens) Explore Q93034  Go to UniProtKB:  Q93034
PHAROS:  Q93034 GTEx:  ENSG00000166266
UniProt Groups	Q93034P06654

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RING-box protein 2	B [auth R]	113	Mus musculus	Mutation(s): 0  Gene Names: Rnf7, Rbx2, Sag EC: 2.3.2.32 (UniProt), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9WTZ1 (Mus musculus) Explore Q9WTZ1  Go to UniProtKB:  Q9WTZ1
IMPC:  MGI:1337096

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta
RECONSTRUCTION	cryoSPARC	2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Komives, E.A., Lumpkin, R.J., Baker, R.W., Leschziner, A.E.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1817774

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-11-11
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Refinement description, Structure summary