3FUS

Improved Structure of the Unliganded Simian Immunodeficiency Virus gp120 Core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.346 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2BF1 - determined by Chen, B., Vogan, E.M., Gong, H., Skehel, J.J., Wiley, D.C., Harrison, S.C.  

Literature

Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement.

Chen, X.Lu, M.Poon, B.K.Wang, Q.Ma, J.

(2009) Acta Crystallogr.,Sect.D 65: 339-347

  • DOI: 10.1107/S0907444909003539

  • PubMed Abstract: 
  • The envelope protein gp120/gp41 of simian and human immunodeficiency viruses plays a critical role in viral entry into host cells. However, the extraordinarily high structural flexibility and heavy glycosylation of the protein have presented enormous ...

    The envelope protein gp120/gp41 of simian and human immunodeficiency viruses plays a critical role in viral entry into host cells. However, the extraordinarily high structural flexibility and heavy glycosylation of the protein have presented enormous difficulties in the pursuit of high-resolution structural investigation of some of its conformational states. An unliganded and fully glycosylated gp120 core structure was recently determined to 4.0 A resolution. The rather low data-to-parameter ratio limited refinement efforts in the original structure determination. In this work, refinement of this gp120 core structure was carried out using a normal-mode-based refinement method that has been shown in previous studies to be effective in improving models of a supramolecular complex at 3.42 A resolution and of a membrane protein at 3.2 A resolution. By using only the first four nonzero lowest-frequency normal modes to construct the anisotropic thermal parameters, combined with manual adjustments and standard positional refinement using REFMAC5, the structural model of the gp120 core was significantly improved in many aspects, including substantial decreases in R factors, better fitting of several flexible regions in electron-density maps, the addition of five new sugar rings at four glycan chains and an excellent correlation of the B-factor distribution with known structural flexibility. These results further underscore the effectiveness of this normal-mode-based method in improving models of protein and nonprotein components in low-resolution X-ray structures.


    Related Citations: 
    • Determining the structure of an unliganded and fully glycosylated SIV gp120 envelope glycoprotein.
      Chen, B.,Vogan, E.M.,Gong, H.,Skehel, J.J.,Wiley, D.C.,Harrison, S.C.
      (2005) Structure 13: 197


    Organizational Affiliation

    Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXTERIOR MEMBRANE GLYCOPROTEIN GP120
A
316Simian immunodeficiency virusMutation(s): 0 
Gene Names: env
Find proteins for Q07374 (Simian immunodeficiency virus)
Go to UniProtKB:  Q07374
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
A
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.346 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 108.048α = 90.00
b = 108.048β = 90.00
c = 117.701γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2011-10-05
    Type: Database references
  • Version 1.3: 2017-07-26
    Type: Source and taxonomy