5V3B

Human A20 OTU domain (WT) with acetamidylated C103


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity.

Zammit, N.W.Siggs, O.M.Gray, P.E.Horikawa, K.Langley, D.B.Walters, S.N.Daley, S.R.Loetsch, C.Warren, J.Yap, J.Y.Cultrone, D.Russell, A.Malle, E.K.Villanueva, J.E.Cowley, M.J.Gayevskiy, V.Dinger, M.E.Brink, R.Zahra, D.Chaudhri, G.Karupiah, G.Whittle, B.Roots, C.Bertram, E.Yamada, M.Jeelall, Y.Enders, A.Clifton, B.E.Mabbitt, P.D.Jackson, C.J.Watson, S.R.Jenne, C.N.Lanier, L.L.Wiltshire, T.Spitzer, M.H.Nolan, G.P.Schmitz, F.Aderem, A.Porebski, B.T.Buckle, A.M.Abbott, D.W.Ziegler, J.B.Craig, M.E.Benitez-Aguirre, P.Teo, J.Tangye, S.G.King, C.Wong, M.Cox, M.P.Phung, W.Tang, J.Sandoval, W.Wertz, I.E.Christ, D.Goodnow, C.C.Grey, S.T.

(2019) Nat Immunol 20: 1299-1310

  • DOI: https://doi.org/10.1038/s41590-019-0492-0
  • Primary Citation of Related Structures:  
    5V3B, 5V3P

  • PubMed Abstract: 

    Resisting and tolerating microbes are alternative strategies to survive infection, but little is known about the evolutionary mechanisms controlling this balance. Here genomic analyses of anatomically modern humans, extinct Denisovan hominins and mice revealed a TNFAIP3 allelic series with alterations in the encoded immune response inhibitor A20. Each TNFAIP3 allele encoded substitutions at non-catalytic residues of the ubiquitin protease OTU domain that diminished IκB kinase-dependent phosphorylation and activation of A20. Two TNFAIP3 alleles encoding A20 proteins with partial phosphorylation deficits seemed to be beneficial by increasing immunity without causing spontaneous inflammatory disease: A20 T108A;I207L, originating in Denisovans and introgressed in modern humans throughout Oceania, and A20 I325N, from an N-ethyl-N-nitrosourea (ENU)-mutagenized mouse strain. By contrast, a rare human TNFAIP3 allele encoding an A20 protein with 95% loss of phosphorylation, C243Y, caused spontaneous inflammatory disease in humans and mice. Analysis of the partial-phosphorylation A20 I325N allele in mice revealed diminished tolerance of bacterial lipopolysaccharide and poxvirus inoculation as tradeoffs for enhanced immunity.


  • Organizational Affiliation

    Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor alpha-induced protein 3
A, B, C, D, E
A, B, C, D, E, F
366Homo sapiensMutation(s): 0 
Gene Names: TNFAIP3OTUD7C
EC: 3.4.19.12 (PDB Primary Data), 6.3.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P21580 (Homo sapiens)
Explore P21580 
Go to UniProtKB:  P21580
PHAROS:  P21580
GTEx:  ENSG00000118503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21580
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.719α = 90
b = 80.901β = 102.46
c = 153.429γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description