5T3S

HIV gp140 trimer MD39-10MUTA in complex with Fabs PGT124 and 35022


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies.

Steichen, J.M.Kulp, D.W.Tokatlian, T.Escolano, A.Dosenovic, P.Stanfield, R.L.McCoy, L.E.Ozorowski, G.Hu, X.Kalyuzhniy, O.Briney, B.Schiffner, T.Garces, F.Freund, N.T.Gitlin, A.D.Menis, S.Georgeson, E.Kubitz, M.Adachi, Y.Jones, M.Mutafyan, A.A.Yun, D.S.Mayer, C.T.Ward, A.B.Burton, D.R.Wilson, I.A.Irvine, D.J.Nussenzweig, M.C.Schief, W.R.

(2016) Immunity 45: 483-496

  • DOI: 10.1016/j.immuni.2016.08.016

  • PubMed Abstract: 
  • Broadly neutralizing antibodies (bnAbs) against the N332 supersite of the HIV envelope (Env) trimer are the most common bnAbs induced during infection, making them promising leads for vaccine design. Wild-type Env glycoproteins lack detectable affini ...

    Broadly neutralizing antibodies (bnAbs) against the N332 supersite of the HIV envelope (Env) trimer are the most common bnAbs induced during infection, making them promising leads for vaccine design. Wild-type Env glycoproteins lack detectable affinity for supersite-bnAb germline precursors and are therefore unsuitable immunogens to prime supersite-bnAb responses. We employed mammalian cell surface display to design stabilized Env trimers with affinity for germline-reverted precursors of PGT121-class supersite bnAbs. The trimers maintained native-like antigenicity and structure, activated PGT121 inferred-germline B cells ex vivo when multimerized on liposomes, and primed PGT121-like responses in PGT121 inferred-germline knockin mice. Design intermediates have levels of epitope modification between wild-type and germline-targeting trimers; their mutation gradient suggests sequential immunization to induce bnAbs, in which the germline-targeting prime is followed by progressively less-mutated design intermediates and, lastly, with native trimers. The vaccine design strategies described could be utilized to target other epitopes on HIV or other pathogens.


    Organizational Affiliation

    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
G
481Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
B
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab PGT124 light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fab PGT124 heavy chain
H
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Fab 35022 heavy chain
D
240N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Fab 35022 light chain
E
216N/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 
G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.270 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 127.915α = 90.00
b = 127.915β = 90.00
c = 313.887γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States--

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations