4UOI

Unexpected structure for the N-terminal domain of Hepatitis C virus envelope glycoprotein E1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Unexpected Structure for the N-Terminal Domain of Hepatitis C Virus Envelope Glycoprotein E1

El Omari, K.Iourin, O.Kadlec, J.Fearn, R.Hall, D.R.Harlos, K.Grimes, J.M.Stuart, D.I.

(2014) Acta Crystallogr.,Sect.D 70: 2197

  • DOI: 10.1107/S139900471401339X

  • PubMed Abstract: 
  • Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by ...

    Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by the paucity of the signal at the usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here, the data collection and structure solution of the N-terminal domain of the ectodomain of HCV E1 from crystals that diffracted very weakly is reported. By combining the data from 32 crystals, it was possible to solve the sulfur substructure and calculate initial maps at 7 Å resolution, and after density modication and phase extension using a higher resolution native data set to 3.5 Å resolution model building was achievable.


    Related Citations: 
    • Unexpected Structure for the N-Terminal Domain of Hepatitis C Virus Envelope Glycoprotein E1.
      El Omari, K.,Iourin, O.,Kadlec, J.,Sutton, G.,Harlos, K.,Grimes, J.M.,Stuart, D.I.
      (2014) Nat.Commun. 5: 4874


    Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GENOME POLYPROTEIN
A, B, C, D, E, F
88Hepacivirus CMutation(s): 1 
Find proteins for H9XGD6 (Hepacivirus C)
Go to UniProtKB:  H9XGD6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.006α = 90.00
b = 105.006β = 90.00
c = 204.740γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
BUSTERrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references, Other
  • Version 1.2: 2015-03-04
    Type: Database references
  • Version 1.3: 2019-04-03
    Type: Data collection, Derived calculations, Other, Source and taxonomy