5WDU

HIV-1 Env BG505 SOSIP.664 H72C-H564C trimer in complex with bNAbs PGT122 Fab, 35O22 Fab and NIH45-46 scFv


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.00 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.301 
  • R-Value Observed: 0.304 

wwPDB Validation 3D Report Full Report



Literature

Improving the Immunogenicity of Native-like HIV-1 Envelope Trimers by Hyperstabilization.

Torrents de la Pena, A.Julien, J.P.de Taeye, S.W.Garces, F.Guttman, M.Ozorowski, G.Pritchard, L.K.Behrens, A.J.Go, E.P.Burger, J.A.Schermer, E.E.Sliepen, K.Ketas, T.J.Pugach, P.Yasmeen, A.Cottrell, C.A.Torres, J.L.Vavourakis, C.D.van Gils, M.J.LaBranche, C.Montefiori, D.C.Desaire, H.Crispin, M.Klasse, P.J.Lee, K.K.Moore, J.P.Ward, A.B.Wilson, I.A.Sanders, R.W.

(2017) Cell Rep 20: 1805-1817

  • DOI: 10.1016/j.celrep.2017.07.077
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The production of native-like recombinant versions of the HIV-1 envelope glycoprotein (Env) trimer requires overcoming the natural flexibility and instability of the complex. The engineered BG505 SOSIP.664 trimer mimics the structure and antigenicity ...

    The production of native-like recombinant versions of the HIV-1 envelope glycoprotein (Env) trimer requires overcoming the natural flexibility and instability of the complex. The engineered BG505 SOSIP.664 trimer mimics the structure and antigenicity of native Env. Here, we describe how the introduction of new disulfide bonds between the glycoprotein (gp)120 and gp41 subunits of SOSIP trimers of the BG505 and other genotypes improves their stability and antigenicity, reduces their conformational flexibility, and helps maintain them in the unliganded conformation. The resulting next-generation SOSIP.v5 trimers induce strong autologous tier-2 neutralizing antibody (NAb) responses in rabbits. In addition, the BG505 SOSIP.v6 trimers induced weak heterologous NAb responses against a subset of tier-2 viruses that were not elicited by the prototype BG505 SOSIP.664. These stabilization methods can be applied to trimers from multiple genotypes as components of multivalent vaccines aimed at inducing broadly NAbs (bNAbs).


    Organizational Affiliation

    Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA. Electronic address: rws2002@med.cornell.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
F, G, Q
471Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
bnAb NIH45-46 scFv
D, O, W
250Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
A, J, R
147Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
bnAb PGT122 Fab light chain
B, K, S
210Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
bnAb PGT122 Fab heavy chain
C, L, T
232Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
bnAb 35O55 Fab heavy chain
H, M, U
242Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
bnAb 35O22 Fab light chain
I, N, V
213Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, F, G, J, Q, R
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
F, G, Q
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
F, G, Q
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
D,O,WL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.00 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.301 
  • R-Value Observed: 0.304 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 361.81α = 90
b = 215.85β = 114.03
c = 176.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI110657
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesScripps CHAVI-ID UM1 AI100663
International AIDS Vaccine InitiativeUnited StatesIAVI

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2019-12-11
    Changes: Author supporting evidence, Polymer sequence
  • Version 3.0: 2020-01-01
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary