5FYJ

Crystal Structure at 3.4 A Resolution of Fully Glycosylated HIV-1 Clade G X1193.c1 SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122, 35O22 and VRC01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B and G

Stewart-Jones, G.B.E.Soto, C.Lemmin, T.Chuang, G.Y.Druz, A.Kong, R.Thomas, P.V.Wagh, K.Zhou, T.Behrens, A.J.Bylund, T.Choi, C.W.Davison, J.R.Georgiev, I.S.Joyce, M.G.Kwon, Y.D.Pancera, M.Taft, J.Yang, Y.Zhang, B.Shivatare, S.S.Shivatare, V.S.Lee, C.C.D.Wu, C.Y.Bewley, C.A.Burton, D.R.Koff, W.C.Connors, M.Crispin, M.Korber, B.T.Wong, C.H.Mascola, J.R.Kwong, P.D.

(2016) Cell 165: 813

  • DOI: 10.1016/j.cell.2016.04.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The HIV-1-envelope (Env) trimer is covered by a glycan shield of ∼90 N-linked oligosaccharides, which comprises roughly half its mass and is a key component of HIV evasion from humoral immunity. To understand how antibodies can overcome the barriers ...

    The HIV-1-envelope (Env) trimer is covered by a glycan shield of ∼90 N-linked oligosaccharides, which comprises roughly half its mass and is a key component of HIV evasion from humoral immunity. To understand how antibodies can overcome the barriers imposed by the glycan shield, we crystallized fully glycosylated Env trimers from clades A, B, and G, visualizing the shield at 3.4-3.7 Å resolution. These structures reveal the HIV-1-glycan shield to comprise a network of interlocking oligosaccharides, substantially ordered by glycan crowding, that encase the protein component of Env and enable HIV-1 to avoid most antibody-mediated neutralization. The revealed features delineate a taxonomy of N-linked glycan-glycan interactions. Crowded and dispersed glycans are differently ordered, conserved, processed, and recognized by antibody. The structures, along with glycan-array binding and molecular dynamics, reveal a diversity in oligosaccharide affinity and a requirement for accommodating glycans among known broadly neutralizing antibodies that target the glycan-shielded trimer.


    Organizational Affiliation

    International AIDS Vaccine Initiative, New York, NY 10038, USA.,Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.,Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: pdkwong@nih.gov.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA.,Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.,Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.,Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Immunology and Microbial Science, International AIDS Vaccine Initiative Neutralizing Antibody Center, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02142, USA.,HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GP41 ENV ECTODOMAIN
B
161Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
Find proteins for C6ZIG9 (Human immunodeficiency virus 1)
Go to UniProtKB:  C6ZIG9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
35O22
D
243N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
35O22
E
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
GP120 ENV ECTODOMAIN
G
484Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
Find proteins for C6ZIG9 (Human immunodeficiency virus 1)
Go to UniProtKB:  C6ZIG9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PGT122
H
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PGT122
L
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
VRC01
U, V
240N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
B, G
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
G, H, V
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
D, G
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 127.160α = 90.00
b = 127.160β = 90.00
c = 313.650γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-04
    Type: Database references
  • Version 1.2: 2016-05-18
    Type: Database references
  • Version 1.3: 2016-07-27
    Type: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
  • Version 1.4: 2016-08-03
    Type: Structure summary
  • Version 1.5: 2017-07-12
    Type: Advisory, Derived calculations