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 6V8Z | pdb_00006v8z

VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6V8Z

This is version 2.1 of the entry. See complete history. 

Literature

Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements.

Henderson, R., Lu, M., Zhou, Y., Mu, Z., Parks, R., Han, Q., Hsu, A.L., Carter, E., Blanchard, S.C., Edwards, R.J., Wiehe, K., Saunders, K.O., Borgnia, M.J., Bartesaghi, A., Mothes, W., Haynes, B.F., Acharya, P., Munir Alam, S.

(2020) Nat Commun 11: 520-520

  • DOI: https://doi.org/10.1038/s41467-019-14196-w
  • Primary Citation Related Structures: 
    6V8X, 6V8Z

  • PubMed Abstract: 

    The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of conformational transitions, with allosteric elements in each protomer orchestrating host receptor-induced exposure of the co-receptor binding site and fusion elements. To understand the molecular details of this allostery, here, we introduce Env mutations aimed to prevent CD4-induced rearrangements in the HIV-1 BG505 Env trimer. Binding analysis and single-molecule Förster Resonance Energy Transfer confirm that these mutations prevent CD4-induced transitions of the HIV-1 Env. Structural analysis by single-particle cryo-electron microscopy performed on the BG505 SOSIP mutant Env proteins shows rearrangements in the gp120 topological layer contacts with gp41. Displacement of a conserved tryptophan (W571) from its typical pocket in these Env mutants renders the Env insensitive to CD4 binding. These results reveal the critical function of W571 as a conformational switch in Env allostery and receptor-mediated viral entry and provide insights on Env conformation that are relevant for vaccine design.


  • Organizational Affiliation: 
    • Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA. rory.henderson@duke.edu.

Macromolecule Content 

  • Total Structure Weight: 522.12 kDa 
  • Atom Count: 35,877 
  • Modeled Residue Count: 4,416 
  • Deposited Residue Count: 4,512 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120
A, G, M
472Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
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Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 16
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
envelope glycoprotein gp41
B, H, N
147Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus type 1)
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Go to UniProtKB:  Q2N0S7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S7
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
10-1074 Fab Heavy ChainC [auth D],
I [auth J],
O [auth P]
235Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6N089 (Homo sapiens)
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Entity Groups
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UniProt GroupQ6N089
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
10-1074 Fab Light ChainD [auth E],
J [auth K],
P [auth Q]
211Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8N5F4 (Homo sapiens)
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Entity Groups
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UniProt GroupQ8N5F4
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC03 Fab Heavy ChainE [auth C],
K [auth I],
Q [auth O]
231Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
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UniProt GroupP0DOX5
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
VRC03 Fab Light Chain
F, L, R
208Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6P5S8 (Homo sapiens)
Explore Q6P5S8 
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UniProt GroupQ6P5S8
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
DA [auth d],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
DA [auth d],
EA [auth e],
GA [auth g],
HA [auth h],
IA [auth i],
JA [auth j],
KA [auth k],
NA [auth n],
OA [auth o],
PA [auth p],
QA [auth q],
S,
SA [auth s],
TA [auth t],
U,
UA [auth u],
V,
VA [auth v],
W,
WA [auth w],
X,
Y,
ZA [auth z]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseFA [auth f],
RA [auth r],
T
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseLA [auth l],
XA [auth x],
Z
8N-Glycosylation
Glycosylation Resources
GlyTouCan: G81980VO
GlyCosmos: G81980VO
GlyGen: G81980VO
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a],
MA [auth m],
YA [auth y]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
CB [auth A]
DB [auth A]
EB [auth A]
FB [auth A]
GB [auth B]
CB [auth A],
DB [auth A],
EB [auth A],
FB [auth A],
GB [auth B],
HB [auth B],
IB [auth B],
JB [auth G],
KB [auth G],
LB [auth G],
MB [auth G],
NB [auth H],
OB [auth H],
PB [auth H],
QB [auth M],
RB [auth M],
SB [auth M],
TB [auth M],
UB [auth N],
VB [auth N],
WB [auth N]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI145687-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary