4NCO

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.7 Å
  • R-Value Free: 0.389 
  • R-Value Work: 0.375 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a soluble cleaved HIV-1 envelope trimer.

Julien, J.P.Cupo, A.Sok, D.Stanfield, R.L.Lyumkis, D.Deller, M.C.Klasse, P.J.Burton, D.R.Sanders, R.W.Moore, J.P.Ward, A.B.Wilson, I.A.

(2013) Science 342: 1477-1483

  • DOI: 10.1126/science.1245625

  • PubMed Abstract: 
  • HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is ...

    HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is stabilized and antigenically near-native (termed the BG505 SOSIP.664 gp140 trimer) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a prefusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the threefold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3, and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BG505 SOSIP gp120
A, E, I
475Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BG505 SOSIP gp41
B, F, J
78N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PGT122 light chain
C, G, K
211N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PGT122 heavy chain
D, H, L
235N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, C, E, G, I, K
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, E, I
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, E, I
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
B, F, J
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.7 Å
  • R-Value Free: 0.389 
  • R-Value Work: 0.375 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 152.200α = 90.00
b = 260.720β = 99.56
c = 283.180γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references