7P70

The PDZ-domain of SNTB1 complexed with the PDZ-binding motif of HPV35-E6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Quantitative fragmentomics allow affinity mapping of interactomes.

Gogl, G.Zambo, B.Kostmann, C.Cousido-Siah, A.Morlet, B.Durbesson, F.Negroni, L.Eberling, P.Jane, P.Nomine, Y.Zeke, A.Ostergaard, S.Monsellier, E.Vincentelli, R.Trave, G.

(2022) Nat Commun 13: 5472-5472

  • DOI: https://doi.org/10.1038/s41467-022-33018-0
  • Primary Citation of Related Structures:  
    7P70, 7P71, 7P72, 7P73, 7P74

  • PubMed Abstract: 

    Human protein networks have been widely explored but most binding affinities remain unknown, hindering quantitative interactome-function studies. Yet interactomes rely on minimal interacting fragments displaying quantifiable affinities. Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. We calculate interactomic distances, identify hot spots for viral interference, generate binding profiles and specificity logos, and explain selected cases by crystallographic studies. Mass spectrometry experiments on cell extracts and literature surveys show that quantitative fragmentomics effectively complements protein interactomics by providing affinities and completeness of coverage, putting a full human interactome affinity survey within reach. Finally, we show that interactome hijacking by the viral PBM of human papillomavirus E6 oncoprotein substantially impacts the host cell proteome beyond immediate E6 binders, illustrating the complex system-wide relationship between interactome and function.


  • Organizational Affiliation

    Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404, Illkirch, France. goglg@igbmc.fr.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein E6A [auth C]13human papillomavirus 35Mutation(s): 0 
UniProt
Find proteins for P27228 (Human papillomavirus 35)
Explore P27228 
Go to UniProtKB:  P27228
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27228
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-1-syntrophin,Annexin A2B [auth A]414Homo sapiensMutation(s): 0 
Gene Names: SNTB1SNT2B1ANXA2ANX2ANX2L4CAL1HLPC2D
UniProt & NIH Common Fund Data Resources
Find proteins for Q13884 (Homo sapiens)
Explore Q13884 
Go to UniProtKB:  Q13884
PHAROS:  Q13884
GTEx:  ENSG00000172164 
Find proteins for P07355 (Homo sapiens)
Explore P07355 
Go to UniProtKB:  P07355
PHAROS:  P07355
GTEx:  ENSG00000182718 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP07355Q13884
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.8α = 90
b = 60.58β = 90
c = 140.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description