3JW0

E2~Ubiquitin-HECT

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.252 

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This is version 1.2 of the entry. See complete history. 


Literature

Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex.

Kamadurai, H.B., Souphron, J., Scott, D.C., Duda, D.M., Miller, D.J., Stringer, D., Piper, R.C., Schulman, B.A.

(2009) Mol Cell 36: 1095-1102

  • DOI: 10.1016/j.molcel.2009.11.010
  • Primary Citation of Related Structures:  
    3JVZ, 3JW0

  • PubMed Abstract: 

    • In E1-E2-E3 ubiquitin (Ub) conjugation cascades, the E2 first forms a transient E2 approximately Ub covalent complex and then interacts with an E3 for Ub transfer. For cascades involving E3s in the HECT class, Ub is transferred from an associated E2 to the acceptor cysteine in the HECT domain C lobe ...

    In E1-E2-E3 ubiquitin (Ub) conjugation cascades, the E2 first forms a transient E2 approximately Ub covalent complex and then interacts with an E3 for Ub transfer. For cascades involving E3s in the HECT class, Ub is transferred from an associated E2 to the acceptor cysteine in the HECT domain C lobe. To gain insights into this process, we determined the crystal structure of a complex between the HECT domain of NEDD4L and the E2 UbcH5B bearing a covalently linked Ub at its active site (UbcH5B approximately Ub). Noncovalent interactions between UbcH5B and the HECT N lobe and between Ub and the HECT domain C lobe lead to an overall compact structure, with the Ub C terminus sandwiched between UbcH5B and HECT domain active sites. The structure suggests a model for E2-to-HECT Ub transfer, in which interactions between a donor Ub and an acceptor domain constrain upstream and downstream enzymes for conjugation.

    Organizational Affiliation: 

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2 A, B146Homo sapiensMutation(s): 3 
Gene Names: UBE2D2, UBC4, UBCH5B, PUBC1, UBC5B, UBCH4
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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Go to UniProtKB:  P62837
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PHAROS:  P62837
GTEx:  ENSG00000131508
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase NEDD4-like C, D385Homo sapiensMutation(s): 1 
Gene Names: NEDD4L, KIAA0439, NEDL3
EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
Find proteins for Q96PU5 (Homo sapiens)
Explore Q96PU5 
Go to UniProtKB:  Q96PU5
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PHAROS:  Q96PU5
GTEx:  ENSG00000049759
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin X, Y81Homo sapiensMutation(s): 0 
Gene Names: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
Find proteins for P0CG48 (Homo sapiens)
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PHAROS:  P0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.252 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.167α = 90
b = 200.571β = 90
c = 109.82γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references