7BBD

Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination.

Kiss, L.Clift, D.Renner, N.Neuhaus, D.James, L.C.

(2021) Nat Commun 12: 1220-1220

  • DOI: 10.1038/s41467-021-21443-6
  • Primary Citation of Related Structures:  
    7BBD, 7BBF

  • PubMed Abstract: 
  • Attachment of ubiquitin (Ub) to proteins is one of the most abundant and versatile of all posttranslational modifications and affects outcomes in essentially all physiological processes. RING E3 ligases target E2 Ub-conjugating enzymes to the substrate, resulting in its ubiquitination ...

    Attachment of ubiquitin (Ub) to proteins is one of the most abundant and versatile of all posttranslational modifications and affects outcomes in essentially all physiological processes. RING E3 ligases target E2 Ub-conjugating enzymes to the substrate, resulting in its ubiquitination. However, the mechanism by which a ubiquitin chain is formed on the substrate remains elusive. Here we demonstrate how substrate binding can induce a specific RING topology that enables self-ubiquitination. By analyzing a catalytically trapped structure showing the initiation of TRIM21 RING-anchored ubiquitin chain elongation, and in combination with a kinetic study, we illuminate the chemical mechanism of ubiquitin conjugation. Moreover, biochemical and cellular experiments show that the topology found in the structure can be induced by substrate binding. Our results provide insights into ubiquitin chain formation on a structural, biochemical and cellular level with broad implications for targeted protein degradation.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK. lcj@mrc-lmb.cam.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-B,E3 ubiquitin-protein ligase TRIM21A [auth B]164Homo sapiensMutation(s): 0 
Gene Names: UBBTRIM21RNF81RO52SSA1
EC: 2.3.2.27
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PHAROS:  P0CG47
Find proteins for P19474 (Homo sapiens)
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Go to UniProtKB:  P19474
PHAROS:  P19474
GTEx:  ENSG00000132109 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP19474P0CG47
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-CB [auth D]76Homo sapiensMutation(s): 0 
Gene Names: UBC
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PHAROS:  P0CG48
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UniProt GroupP0CG48
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 variant 2C [auth A]150Homo sapiensMutation(s): 0 
Gene Names: UBE2V2MMS2UEV2
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PHAROS:  Q15819
GTEx:  ENSG00000169139 
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UniProt GroupQ15819
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 ND [auth C]153Homo sapiensMutation(s): 2 
Gene Names: UBE2NBLU
EC: 2.3.2.23
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Find proteins for P61088 (Homo sapiens)
Explore P61088 
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PHAROS:  P61088
GTEx:  ENSG00000177889 
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UniProt GroupP61088
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.15α = 90
b = 108.36β = 104.99
c = 75.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomU105181010
Medical Research Council (MRC, United Kingdom)United KingdomU105178934
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references