5UDH

HHARI/ARIH1-UBCH7~Ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural Studies of HHARI/UbcH7Ub Reveal Unique E2Ub Conformational Restriction by RBR RING1.

Dove, K.K., Olszewski, J.L., Martino, L., Duda, D.M., Wu, X.S., Miller, D.J., Reiter, K.H., Rittinger, K., Schulman, B.A., Klevit, R.E.

(2017) Structure 25: 890-900.e5

  • DOI: https://doi.org/10.1016/j.str.2017.04.013
  • Primary Citation of Related Structures:  
    5UDH

  • PubMed Abstract: 

    • RING-between-RING (RBR) E3s contain RING1 domains that are structurally similar yet mechanistically distinct from canonical RING domains. Both types of E3 bind E2∼ubiquitin (E2∼Ub) via their RINGs but canonical RING E3s promote closed E2∼Ub conformations required for direct Ub transfer from the E2 to substrate, while RBR RING1s promote open E2∼Ub to favor Ub transfer to the E3 active site ...

    RING-between-RING (RBR) E3s contain RING1 domains that are structurally similar yet mechanistically distinct from canonical RING domains. Both types of E3 bind E2∼ubiquitin (E2∼Ub) via their RINGs but canonical RING E3s promote closed E2∼Ub conformations required for direct Ub transfer from the E2 to substrate, while RBR RING1s promote open E2∼Ub to favor Ub transfer to the E3 active site. This different RING/E2∼Ub conformation determines its direct target, which for canonical RING E3s is typically a substrate or substrate-linked Ub, but is the E3 active-site cysteine in the case of RBR-type E3s. Here we show that a short extension of HHARI RING1, namely Zn 2+ -loop II, not present in any RING E3s, acts as a steric wedge to disrupt closed E2∼Ub, providing a structural explanation for the distinctive RING1-dependent conformational restriction mechanism utilized by RBR E3s.

    Organizational Affiliation: 

    Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195, USA. Electronic address: klevit@uw.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase ARIH1A,
C [auth B]		470Homo sapiensMutation(s): 0 
Gene Names: ARIH1, ARI, MOP6, UBCH7BP, HUSSY-27
EC: 2.3.2 (PDB Primary Data), 2.3.2.31 (UniProt)
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PHAROS:  Q9Y4X5
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UniProt GroupQ9Y4X5
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 L3B [auth C],
D		156Homo sapiensMutation(s): 1 
Gene Names: UBE2L3, UBCE7, UBCH7
EC: 2.3.2.23
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Find proteins for P68036 (Homo sapiens)
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PHAROS:  P68036
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin C variantE82Homo sapiensMutation(s): 0 
Gene Names: UBC
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PHAROS:  P0CG48
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UniProt GroupP0CG48
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.571α = 90
b = 76.788β = 107.33
c = 147.724γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
CRANKphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references