6B0N

Crystal structure of the cleavage-independent prefusion HIV Env glycoprotein trimer of the clade A BG505 isolate (NFL construct) in complex with Fabs PGT122 and PGV19 at 3.39 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.335 
  • R-Value Observed: 0.336 

wwPDB Validation 3D Report Full Report



Literature

Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer.

Sarkar, A.Bale, S.Behrens, A.J.Kumar, S.Sharma, S.K.de Val, N.Pallesen, J.Irimia, A.Diwanji, D.C.Stanfield, R.L.Ward, A.B.Crispin, M.Wyatt, R.T.Wilson, I.A.

(2018) Nat Commun 9: 1956-1956

  • DOI: 10.1038/s41467-018-04272-y
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Furin cleavage of the HIV envelope glycoprotein is an essential step for cell entry that enables formation of well-folded, native-like glycosylated trimers, releases constraints on the fusion peptide, and limits enzymatic processing of the N-glycan s ...

    Furin cleavage of the HIV envelope glycoprotein is an essential step for cell entry that enables formation of well-folded, native-like glycosylated trimers, releases constraints on the fusion peptide, and limits enzymatic processing of the N-glycan shield. Here, we show that a cleavage-independent, stabilized, soluble Env trimer mimic (BG505 NFL.664) exhibits a "closed-form", native-like, prefusion conformation akin to furin-cleaved Env trimers. The crystal structure of BG505 NFL.664 at 3.39 Å resolution with two potent bNAbs also identifies the full epitopes of PGV19 and PGT122 that target the receptor binding site and N332 supersite, respectively. Quantitative site-specific analysis of the glycan shield reveals that native-like glycan processing is maintained despite furin-independent maturation in the secretory pathway. Thus, cleavage-independent NFL Env trimers exhibit quaternary protein and carbohydrate structures similar to the native viral spike that further validate their potential as vaccine immunogen candidates.


    Organizational Affiliation

    Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. wilson@scripps.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PGV19 Fab heavy chain
D
223Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PGV19 light chain
E
209Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp140
G
638Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PGT122 Fab heavy chain
H
235Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PGT122 light chain
L
213Homo 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 
G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

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

Download CCD File 
G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.335 
  • R-Value Observed: 0.336 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.247α = 90
b = 161.247β = 90
c = 245.651γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release