6V8X

VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: 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 ...

    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 Pathology, Duke University School of Medicine, Durham, NC, 27710, USA. munir.alam@duke.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A, E, I471Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q2N0S6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp41B, F, J145Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S9 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q2N0S9
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
VRC01 Fab Heavy ChainC, G, K224Homo sapiensMutation(s): 0 
Gene Names: DKFZp686K03196
UniProt
Find proteins for Q6N095 (Homo sapiens)
Explore Q6N095 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
VRC01 Fab Light ChainD, H, L208Homo sapiensMutation(s): 0 
Gene Names: IGK@
UniProt
Find proteins for Q6PIL8 (Homo sapiens)
Explore Q6PIL8 
Go to UniProtKB:  Q6PIL8
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseKA [auth k], M, Y4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DA [auth d], EA [auth e], GA [auth g], HA [auth h], IA [auth i], JA [auth j], LA [auth l], N
DA [auth d], EA [auth e], GA [auth g], HA [auth h], IA [auth i], JA [auth j], LA [auth l], N, PA [auth p], QA [auth q], R, S, SA [auth s], TA [auth t], U, UA [auth u], V, VA [auth v], W, X, Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a], BA [auth b], CA [auth c], FA [auth f], MA [auth m], NA [auth n], O, OA [auth o]
AA [auth a], BA [auth b], CA [auth c], FA [auth f], MA [auth m], NA [auth n], O, OA [auth o], P, Q, RA [auth r], T
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth B] , BB [auth E] , CB [auth E] , DB [auth E] , EB [auth E] , FB [auth F] , GB [auth I] , HB [auth I] , 
AB [auth B],  BB [auth E],  CB [auth E],  DB [auth E],  EB [auth E],  FB [auth F],  GB [auth I],  HB [auth I],  IB [auth I],  JB [auth I],  KB [auth J],  WA [auth A],  XA [auth A],  YA [auth A],  ZA [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary