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 1.6 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
  • 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE CBL-BA, E, I, M394Homo sapiensMutation(s): 1 
Gene Names: CBLB, RNF56, Nbla00127
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q13191 (Homo sapiens)
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PHAROS:  Q13191
GTEx:  ENSG00000114423
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TYROSINE-PROTEIN KINASE ZAP-70B, F, J, N12Homo sapiensMutation(s): 0 
Gene Names: ZAP70, SRK
EC: 2.7.10.2
Find proteins for P43403 (Homo sapiens)
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PHAROS:  P43403
GTEx:  ENSG00000115085
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 D2C, G, K, O146Homo sapiensMutation(s): 2 
Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
Find proteins for P62837 (Homo sapiens)
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PHAROS:  P62837
GTEx:  ENSG00000131508
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
POLYUBIQUITIN-CD, H, L, P81Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
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PHAROS:  P0CG48
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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], V [auth E], Y [auth I], Z [auth I]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
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		 Ligand Interaction
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		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		A, E, I, ML-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