6V8Z

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


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 of 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.


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 1)
Explore Q2N0S6 
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 1)
Go to UniProtKB:  Q2N0S7
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)
Explore Q6N089 
Go to UniProtKB:  Q6N089
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N089
Sequence Annotations
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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)
Explore Q8N5F4 
Go to UniProtKB:  Q8N5F4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N5F4
Sequence Annotations
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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)
Go to UniProtKB:  P0DOX5
Sequence Annotations
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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 
Go to UniProtKB:  Q6P5S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P5S8
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D 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 Glycosylation3D 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 Glycosylation3D 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 Glycosylation3D 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