6PW6

The HIV-1 Envelope Glycoprotein Clone BG505 SOSIP.664 in Complex with Three Copies of the Bovine Broadly Neutralizing Antibody, NC-Cow1, Fragment Antigen Binding Domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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

Structural basis of broad HIV neutralization by a vaccine-induced cow antibody.

Stanfield, R.L.Berndsen, Z.T.Huang, R.Sok, D.Warner, G.Torres, J.L.Burton, D.R.Ward, A.B.Wilson, I.A.Smider, V.V.

(2020) Sci Adv 6: eaba0468-eaba0468

  • DOI: 10.1126/sciadv.aba0468
  • Primary Citation of Related Structures:  
    6OO0, 6OPA, 6PW6

  • PubMed Abstract: 
  • Potent broadly neutralizing antibodies (bnAbs) to HIV have been very challenging to elicit by vaccination in wild-type animals. Here, by x-ray crystallography, cryo-electron microscopy, and site-directed mutagenesis, we structurally and functionally elucidate the mode of binding of a potent bnAb (NC-Cow1) elicited in cows by immunization with the HIV envelope (Env) trimer BG505 SOSIP ...

    Potent broadly neutralizing antibodies (bnAbs) to HIV have been very challenging to elicit by vaccination in wild-type animals. Here, by x-ray crystallography, cryo-electron microscopy, and site-directed mutagenesis, we structurally and functionally elucidate the mode of binding of a potent bnAb (NC-Cow1) elicited in cows by immunization with the HIV envelope (Env) trimer BG505 SOSIP.664. The exceptionally long (60 residues) third complementarity-determining region of the heavy chain (CDR H3) of NC-Cow1 forms a mini domain (knob) on an extended stalk that navigates through the dense glycan shield on Env to target a small footprint on the gp120 CD4 receptor binding site with no contact of the other CDRs to the rest of the Env trimer. These findings illustrate, in molecular detail, how an unusual vaccine-induced cow bnAb to HIV Env can neutralize with high potency and breadth.


    Organizational Affiliation

    Taurus Biosciences LLC, San Diego, CA 92127, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A, D [auth C], G [auth E]516Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp41B, E [auth D], H [auth F]153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Broadly Neutralizing Antibody NC-Cow1 Heavy ChainC [auth G], F [auth H], I268Bos taurusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a], CA [auth c], DA [auth d], EA [auth e], GA [auth g], HA [auth h], IA [auth i], J
AA [auth a], CA [auth c], DA [auth d], EA [auth e], GA [auth g], HA [auth h], IA [auth i], J, JA [auth j], K, KA [auth k], M, MA [auth m], N, O, P, Q, S, T, U, W, X, Y, Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseBA [auth b], FA [auth f], L, LA [auth l], R, V4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
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 C] , BB [auth C] , CB [auth C] , DB [auth C] , EB [auth C] , FB [auth C] , GB [auth C] , HB [auth D] , 
AB [auth C],  BB [auth C],  CB [auth C],  DB [auth C],  EB [auth C],  FB [auth C],  GB [auth C],  HB [auth D],  IB [auth D],  JB [auth D],  KB [auth D],  LB [auth E],  MB [auth E],  NA [auth A],  NB [auth E],  OA [auth A],  OB [auth E],  PA [auth A],  PB [auth E],  QA [auth A],  QB [auth E],  RA [auth A],  RB [auth E],  SA [auth A],  SB [auth E],  TA [auth A],  TB [auth F],  UA [auth A],  UB [auth F],  VA [auth B],  VB [auth F],  WA [auth B],  WB [auth F],  XA [auth B],  YA [auth B],  ZA [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: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
International AIDS Vaccine InitiativeUnited StatesOPP1084519
Bill & Melinda Gates FoundationUnited StatesOPP1115782
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1AI100663

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary