6V9H

Ankyrin repeat and SOCS-box protein 9 (ASB9), ElonginB (ELOB), and ElonginC (ELOC) bound to its substrate Brain-type Creatine Kinase (CKB)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41467-020-16499-9
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92092-0378, USA. ekomives@ucsd.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Creatine kinase B-type
A, B
381Homo sapiensMutation(s): 0 
Gene Names: CKBCKBB
EC: 2.7.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P12277 (Homo sapiens)
Explore P12277 
Go to UniProtKB:  P12277
PHAROS:  P12277
GTEx:  ENSG00000166165 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12277
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ankyrin repeat and SOCS box protein 9314Homo sapiensMutation(s): 0 
Gene Names: ASB9
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DX5 (Homo sapiens)
Explore Q96DX5 
Go to UniProtKB:  Q96DX5
PHAROS:  Q96DX5
GTEx:  ENSG00000102048 
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UniProt GroupQ96DX5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-C97Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
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Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
PHAROS:  Q15369
GTEx:  ENSG00000154582 
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UniProt GroupQ15369
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-B118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
PHAROS:  Q15370
GTEx:  ENSG00000103363 
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UniProt GroupQ15370
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2
MODEL REFINEMENTRosetta

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1817774

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references