2YMT | pdb_00002ymt

gamma 2 adaptin EAR domain crystal structure with phage peptide GEEWGPWV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.242 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2YMT

This is version 1.6 of the entry. See complete history

Literature

The Hepatitis B Virus Pres1 Domain Hijacks Host Trafficking Proteins by Motif Mimicry.

Jurgens, M.C.Voros, J.Rautureau, G.J.P.Shepherd, D.A.Pye, V.E.Muldoon, J.Johnson, C.M.Ashcroft, A.E.Freund, S.M.V.Ferguson, N.

(2013) Nat Chem Biol 9: 540

  • DOI: https://doi.org/10.1038/nchembio.1294
  • Primary Citation Related Structures: 
    2YMT, 3ZHF, 4BCX

  • PubMed Abstract: 

    Hepatitis B virus (HBV) is an infectious, potentially lethal human pathogen. However, there are no effective therapies for chronic HBV infections. Antiviral development is hampered by the lack of high-resolution structures for essential HBV protein-protein interactions. The interaction between preS1, an HBV surface-protein domain, and its human binding partner, γ2-adaptin, subverts the membrane-trafficking apparatus to mediate virion export. This interaction is a putative drug target. We report here atomic-resolution descriptions of the binding thermodynamics and structural biology of the interaction between preS1 and the EAR domain of γ2-adaptin. NMR, protein engineering, X-ray crystallography and MS showed that preS1 contains multiple γ2-EAR-binding motifs that mimic the membrane-trafficking motifs (and binding modes) of host proteins. These motifs localize together to a relatively rigid, functionally important region of preS1, an intrinsically disordered protein. The preS1-γ2-EAR interaction was relatively weak and efficiently outcompeted by a synthetic peptide. Our data provide the structural road map for developing peptidomimetic antivirals targeting the γ2-EAR-preS1 interaction.


  • Organizational Affiliation
    • 1] School of Medicine and Medical Science, University College Dublin, Dublin, Ireland. [2].

Macromolecule Content 

  • Total Structure Weight: 14.8 kDa 
  • Atom Count: 1,172 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 133 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2124Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75843 (Homo sapiens)
Explore O75843 
Go to UniProtKB:  O75843
PHAROS:  O75843
GTEx:  ENSG00000213983 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75843
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PHAGE DISPLAY DERIVED GAMMA 2 ADAPTIN EAR DOMAIN BINDING PEPTIDE9synthetic constructMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PDO

Query on PDO



Download:Ideal Coordinates CCD File
C [auth A]1,3-PROPANDIOL
C3 H8 O2
YPFDHNVEDLHUCE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.242 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.803α = 90
b = 37.772β = 90
c = 105.471γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2013-08-28
    Changes: Database references
  • Version 1.4: 2017-07-12
    Changes: Data collection
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.6: 2024-11-20
    Changes: Structure summary