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 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.7 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: https://doi.org/10.1038/nsmb.2621
  • Primary Citation of Related Structures:  
    3ZNI

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE CBL-B
A, E, I, M
394Homo sapiensMutation(s): 1 
EC: 6.3.2.19
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Find proteins for Q13191 (Homo sapiens)
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GTEx:  ENSG00000114423 
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UniProt GroupQ13191
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TYROSINE-PROTEIN KINASE ZAP-70
B, F, J, N
12Homo sapiensMutation(s): 0 
EC: 2.7.10.2
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Find proteins for P43403 (Homo sapiens)
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GTEx:  ENSG00000115085 
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UniProt GroupP43403
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 D2
C, G, K, O
146Homo sapiensMutation(s): 2 
EC: 6.3.2.19
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Find proteins for P62837 (Homo sapiens)
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GTEx:  ENSG00000131508 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
POLYUBIQUITIN-C
D, H, L, P
81Homo sapiensMutation(s): 0 
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Find proteins for P0CG48 (Homo sapiens)
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GTEx:  ENSG00000150991 
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UniProt GroupP0CG48
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth M]
DA [auth M]
Q [auth A]
R [auth A]
U [auth E]
CA [auth M],
DA [auth M],
Q [auth A],
R [auth A],
U [auth E],
V [auth E],
Y [auth I],
Z [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth I],
FA [auth M],
T [auth A],
X [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth I],
EA [auth M],
S [auth A],
W [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, E, I, M
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 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.97α = 90
b = 131.8β = 91.92
c = 122γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Database references, Other, Source and taxonomy
  • Version 1.3: 2013-08-21
    Changes: Database references
  • Version 1.4: 2015-09-23
    Changes: Data collection
  • Version 1.5: 2017-09-13
    Changes: Data collection
  • Version 1.6: 2019-07-31
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.7: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description