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 

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: 10.1016/j.str.2017.04.013

  • 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 conformat ...

    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.,Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA. Electronic address: brenda.schulman@stjude.org.,Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Biochemistry, University of Washington, 1705 Northeast Pacific Street, Seattle, WA 98195, USA. Electronic address: klevit@uw.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase ARIH1
A, B
470Homo sapiensMutation(s): 0 
Gene Names: ARIH1 (ARI, MOP6, UBCH7BP)
EC: 2.3.2.31
Find proteins for Q9Y4X5 (Homo sapiens)
Go to Gene View: ARIH1
Go to UniProtKB:  Q9Y4X5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 L3
C, D
156Homo sapiensMutation(s): 1 
Gene Names: UBE2L3 (UBCE7, UBCH7)
EC: 2.3.2.23
Find proteins for P68036 (Homo sapiens)
Go to Gene View: UBE2L3
Go to UniProtKB:  P68036
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin C variant
E
82Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.571α = 90.00
b = 76.788β = 107.33
c = 147.724γ = 90.00
Software Package:
Software NamePurpose
CRANKphasing
XDSdata reduction
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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