6IEQ

Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb PGT124 and 35O22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence.

Sliepen, K.Han, B.W.Bontjer, I.Mooij, P.Garces, F.Behrens, A.J.Rantalainen, K.Kumar, S.Sarkar, A.Brouwer, P.J.M.Hua, Y.Tolazzi, M.Schermer, E.Torres, J.L.Ozorowski, G.van der Woude, P.de la Pena, A.T.van Breemen, M.J.Camacho-Sanchez, J.M.Burger, J.A.Medina-Ramirez, M.Gonzalez, N.Alcami, J.LaBranche, C.Scarlatti, G.van Gils, M.J.Crispin, M.Montefiori, D.C.Ward, A.B.Koopman, G.Moore, J.P.Shattock, R.J.Bogers, W.M.Wilson, I.A.Sanders, R.W.

(2019) Nat Commun 10: 2355-2355

  • DOI: 10.1038/s41467-019-10262-5
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Stabilized HIV-1 envelope glycoproteins (Env) that resemble the native Env are utilized in vaccination strategies aimed at inducing broadly neutralizing antibodies (bNAbs). To limit the exposure of rare isolate-specific antigenic residues/determinant ...

    Stabilized HIV-1 envelope glycoproteins (Env) that resemble the native Env are utilized in vaccination strategies aimed at inducing broadly neutralizing antibodies (bNAbs). To limit the exposure of rare isolate-specific antigenic residues/determinants we generated a SOSIP trimer based on a consensus sequence of all HIV-1 group M isolates (ConM). The ConM trimer displays the epitopes of most known bNAbs and several germline bNAb precursors. The crystal structure of the ConM trimer at 3.9 Å resolution resembles that of the native Env trimer and its antigenic surface displays few rare residues. The ConM trimer elicits strong NAb responses against the autologous virus in rabbits and macaques that are significantly enhanced when it is presented on ferritin nanoparticles. The dominant NAb specificity is directed against an epitope at or close to the trimer apex. Immunogens based on consensus sequences might have utility in engineering vaccines against HIV-1 and other viruses.


    Organizational Affiliation

    Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, 10021, USA. r.w.sanders@amc.uva.nl.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
B
153Human immunodeficiency virus 1Mutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
G
497Human immunodeficiency virus 1Mutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PGT124 Fab Light Chain
L
214Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PGT124 Fab Heavy Chain
H
236Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
35O22 Fab Heavy Chain
D
240Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
35O22 Fab Light Chain
E
216Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
B, G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

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

Download CCD File 
G, H, L
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.59α = 90
b = 127.59β = 90
c = 315.507γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references