3ZNI

Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Essentiality of a Non-Ring Element in Priming Donor Ubiquitin for Catalysis by a Monomeric E3.

Dou, H.Buetow, L.Sibbet, G.J.Cameron, K.Huang, D.T.

(2013) Nat.Struct.Mol.Biol. 20: 982

  • DOI: 10.1038/nsmb.2621

  • PubMed Abstract: 
  • RING E3 ligases catalyze the transfer of ubiquitin (Ub) from E2 ubiquitin-conjugating enzyme thioesterified with Ub (E2~Ub) to substrate. For RING E3 dimers, the RING domain of one subunit and tail of the second cooperate to prime Ub, but how this is ...

    RING E3 ligases catalyze the transfer of ubiquitin (Ub) from E2 ubiquitin-conjugating enzyme thioesterified with Ub (E2~Ub) to substrate. For RING E3 dimers, the RING domain of one subunit and tail of the second cooperate to prime Ub, but how this is accomplished by monomeric RING E3s in the absence of a tail-like component is currently unknown. Here, we present a crystal structure of a monomeric RING E3, Tyr363-phosphorylated human CBL-B, bound to a stabilized Ub-linked E2, revealing a similar mechanism in activating E2~Ub. Both pTyr363 and the pTyr363-induced element interact directly with Ub's Ile36 surface, improving the catalytic efficiency of Ub transfer by ~200-fold. Hence, interactions outside the canonical RING domain are crucial for optimizing Ub transfer in both monomeric and dimeric RING E3s. We propose that an additional non-RING Ub-priming element may be a common RING E3 feature.


    Organizational Affiliation

    The Beatson Institute for Cancer Research, Glasgow, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 UBIQUITIN-PROTEIN LIGASE CBL-B
A, E, I, M
394Homo sapiensMutation(s): 1 
Gene Names: CBLB (RNF56)
EC: 2.3.2.27
Find proteins for Q13191 (Homo sapiens)
Go to Gene View: CBLB
Go to UniProtKB:  Q13191
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TYROSINE-PROTEIN KINASE ZAP-70
B, F, J, N
12Homo sapiensMutation(s): 0 
Gene Names: ZAP70 (SRK)
EC: 2.7.10.2
Find proteins for P43403 (Homo sapiens)
Go to Gene View: ZAP70
Go to UniProtKB:  P43403
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-CONJUGATING ENZYME E2 D2
C, G, K, O
146Homo sapiensMutation(s): 2 
Gene Names: UBE2D2 (PUBC1, UBC4, UBC5B, UBCH4, UBCH5B)
EC: 2.3.2.23
Find proteins for P62837 (Homo sapiens)
Go to Gene View: UBE2D2
Go to UniProtKB:  P62837
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
POLYUBIQUITIN-C
D, H, L, P
81Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, E, I, M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, E, I, M
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, E, I, M
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B, E, F, I, J, M, N
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.970α = 90.00
b = 131.800β = 91.92
c = 122.000γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references
  • Version 1.2: 2013-07-24
    Type: Database references, Other, Source and taxonomy
  • Version 1.3: 2013-08-21
    Type: Database references
  • Version 1.4: 2015-09-23
    Type: Data collection
  • Version 1.5: 2017-09-13
    Type: Data collection