6CH7

XFEL crystal structure of a natively-glycosylated BG505 SOSIP.664 HIV-1 Envelope Trimer in complex with the broadly-neutralizing antibodies BG18 and 35O22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural characterization of a highly-potent V3-glycan broadly neutralizing antibody bound to natively-glycosylated HIV-1 envelope.

Barnes, C.O.Gristick, H.B.Freund, N.T.Escolano, A.Lyubimov, A.Y.Hartweger, H.West, A.P.Cohen, A.E.Nussenzweig, M.C.Bjorkman, P.J.

(2018) Nat Commun 9: 1251-1251


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp41
B
153Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
Find proteins for Q2N0S7 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
35O22 Heavy Chain
D
243N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
35O22 Light Chain
E
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp120
G
479Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
BG18 Heavy Chain
Q
241N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
BG18 Light Chain
R
215N/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
MAN
Query on MAN

Download SDF File 
Download CCD File 
B, D, G, Q
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
B, D, G
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
D
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
BMA
Query on BMA

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.232 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 238.944α = 90.00
b = 238.944β = 90.00
c = 354.014γ = 120.00
Software Package:
Software NamePurpose
cctbx.xfeldata reduction
PHASERphasing
BUSTERrefinement
cctbx.primedata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NIH/NIAIDUnited StatesP01 AI100148
Bill and Melinda Gates FoundationUnited StatesOPP1124068
NIHUnited StatesP41GM103393

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release