6MFT

Crystal structure of glycosylated 426c HIV-1 gp120 core G459C in complex with glVRC01 A60C heavy chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.315 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core.

Borst, A.J.Weidle, C.E.Gray, M.D.Frenz, B.Snijder, J.Joyce, M.G.Georgiev, I.S.Stewart-Jones, G.B.Kwong, P.D.McGuire, A.T.DiMaio, F.Stamatatos, L.Pancera, M.Veesler, D.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.37688
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4 <sub>BS </sub>) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding VRC01 germline precursors poorly bind to ...

    VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4 BS ) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding VRC01 germline precursors poorly bind to Env. Immunogen design has mostly relied on glycan removal from trimeric Env constructs and has had limited success in eliciting mature VRC01 bnAbs. To better understand elicitation of such bnAbs, we characterized the inferred germline precursor of VRC01 in complex with a modified trimeric 426c Env by cryo-electron microscopy and a 426c gp120 core by X-ray crystallography, biolayer interferometry, immunoprecipitation, and glycoproteomics. Our results show VRC01 germline antibodies interacted with a wild-type 426c core lacking variable loops 1-3 in the presence and absence of a glycan at position Asn276, with the latter form binding with higher affinity than the former. Interactions in the presence of an Asn276 oligosaccharide could be enhanced upon carbohydrate shortening, which should be considered for immunogen design.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, United States.,Department of Global Health, University of Washington, Seattle, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heavy Chain glVRC01
H, A
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Light chain glVRC01
L, B
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Gp120
G, C
347Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for M4Q8P8 (Human immunodeficiency virus 1)
Go to UniProtKB:  M4Q8P8
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

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

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

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

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

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Download CCD File 
G
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
C, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, H
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.315 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 197.082α = 90.00
b = 109.003β = 114.47
c = 103.225γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesAI081625

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references