5VN8

Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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

Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike.

Ozorowski, G.Pallesen, J.de Val, N.Lyumkis, D.Cottrell, C.A.Torres, J.L.Copps, J.Stanfield, R.L.Cupo, A.Pugach, P.Moore, J.P.Wilson, I.A.Ward, A.B.

(2017) Nature 547: 360-363

  • DOI: 10.1038/nature23010
  • Primary Citation of Related Structures:  
    5VN3, 5VN8

  • PubMed Abstract: 
  • For many enveloped viruses, binding to a receptor(s) on a host cell acts as the first step in a series of events culminating in fusion with the host cell membrane and transfer of genetic material for replication. The envelope glycoprotein (Env) trimer on the surface of HIV is responsible for receptor binding and fusion ...

    For many enveloped viruses, binding to a receptor(s) on a host cell acts as the first step in a series of events culminating in fusion with the host cell membrane and transfer of genetic material for replication. The envelope glycoprotein (Env) trimer on the surface of HIV is responsible for receptor binding and fusion. Although Env can tolerate a high degree of mutation in five variable regions (V1-V5), and also at N-linked glycosylation sites that contribute roughly half the mass of Env, the functional sites for recognition of receptor CD4 and co-receptor CXCR4/CCR5 are conserved and essential for viral fitness. Soluble SOSIP Env trimers are structural and antigenic mimics of the pre-fusion native, surface-presented Env, and are targets of broadly neutralizing antibodies. Thus, they are attractive immunogens for vaccine development. Here we present high-resolution cryo-electron microscopy structures of subtype B B41 SOSIP Env trimers in complex with CD4 and antibody 17b, or with antibody b12, at resolutions of 3.7 Å and 3.6 Å, respectively. We compare these to cryo-electron microscopy reconstructions of B41 SOSIP Env trimers with no ligand or in complex with either CD4 or the CD4-binding-site antibody PGV04 at 5.6 Å, 5.2 Å and 7.4 Å resolution, respectively. Consequently, we present the most complete description yet, to our knowledge, of the CD4-17b-induced intermediate and provide the molecular basis of the receptor-binding-induced conformational change required for HIV-1 entry into host cells. Both CD4 and b12 induce large, previously uncharacterized conformational rearrangements in the gp41 subunits, and the fusion peptide becomes buried in a newly formed pocket. These structures provide key details on the biological function of the type I viral fusion machine from HIV-1 as well as new templates for inhibitor design.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160E [auth D], I [auth E], A [auth G]516Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
UniProt
Find proteins for B3UES2 (Human immunodeficiency virus 1)
Explore B3UES2 
Go to UniProtKB:  B3UES2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160B [auth A], F [auth B], J [auth C]153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for B3UEZ6 (Human immunodeficiency virus 1)
Explore B3UEZ6 
Go to UniProtKB:  B3UEZ6
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
b12 Fab heavy chainG [auth F], C [auth H], K [auth I]230Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
b12 Fab light chainH [auth J], L [auth K], D [auth L]215Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b], CA [auth c], DA [auth d], GA [auth g], HA [auth h], IA [auth i], JA [auth j], M
BA [auth b], CA [auth c], DA [auth d], GA [auth g], HA [auth h], IA [auth i], JA [auth j], M, MA [auth m], N, NA [auth n], OA [auth o], Q, R, RA [auth r], S, SA [auth s], V, W, X, Y
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
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
EA [auth e], FA [auth f], KA [auth k], O, PA [auth p], QA [auth q], T, U
EA [auth e], FA [auth f], KA [auth k], O, PA [auth p], QA [auth q], T, U, Z
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
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-glucopyranoseAA [auth a], LA [auth l], P4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
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 A] , BB [auth A] , CB [auth A] , DB [auth A] , EB [auth D] , FB [auth D] , GB [auth D] , HB [auth D] , 
AB [auth A],  BB [auth A],  CB [auth A],  DB [auth A],  EB [auth D],  FB [auth D],  GB [auth D],  HB [auth D],  IB [auth D],  JB [auth D],  KB [auth D],  LB [auth B],  MB [auth B],  NB [auth B],  OB [auth B],  PB [auth E],  QB [auth E],  RB [auth E],  SB [auth E],  TA [auth G],  TB [auth E],  UA [auth G],  UB [auth E],  VA [auth G],  VB [auth E],  WA [auth G],  WB [auth C],  XA [auth G],  XB [auth C],  YA [auth G],  YB [auth C],  ZA [auth G],  ZB [auth C]
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: 3.60 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 StatesUM1AI100663
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI110657

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary