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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase ARIH1A,
C [auth B]
470Homo sapiensMutation(s): 0 
Gene Names: ARIH1ARIMOP6UBCH7BPHUSSY-27
EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4X5 (Homo sapiens)
Explore Q9Y4X5 
Go to UniProtKB:  Q9Y4X5
PHAROS:  Q9Y4X5
GTEx:  ENSG00000166233 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4X5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 L3B [auth C],
D
156Homo sapiensMutation(s): 1 
Gene Names: UBE2L3UBCE7UBCH7
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P68036 (Homo sapiens)
Explore P68036 
Go to UniProtKB:  P68036
PHAROS:  P68036
GTEx:  ENSG00000185651 
Entity Groups  
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UniProt GroupP68036
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin C variant82Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
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UniProt GroupP0CG48
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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