6NF5

BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP1 fragmentantigen binding and base-binding RM20A3 fragment antigen binding


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.71 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

A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses.

Steichen, J.M.Lin, Y.C.Havenar-Daughton, C.Pecetta, S.Ozorowski, G.Willis, J.R.Toy, L.Sok, D.Liguori, A.Kratochvil, S.Torres, J.L.Kalyuzhniy, O.Melzi, E.Kulp, D.W.Raemisch, S.Hu, X.Bernard, S.M.Georgeson, E.Phelps, N.Adachi, Y.Kubitz, M.Landais, E.Umotoy, J.Robinson, A.Briney, B.Wilson, I.A.Burton, D.R.Ward, A.B.Crotty, S.Batista, F.D.Schief, W.R.

(2019) Science 366

  • DOI: 10.1126/science.aax4380
  • Primary Citation of Related Structures:  
    6DFG, 6DFH, 6NF5, 6NFC, 6OC7

  • PubMed Abstract: 
  • Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity-determining region 3 (HCDR3) is a major barrier ...

    Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity-determining region 3 (HCDR3) is a major barrier. Exploiting ultradeep human antibody sequencing data, we identified a diverse set of potential antibody precursors for a bnAb with dominant HCDR3 contacts. We then developed HIV envelope trimer-based immunogens that primed responses from rare bnAb-precursor B cells in a mouse model and bound a range of potential bnAb-precursor human naïve B cells in ex vivo screens. Our repertoire-guided germline-targeting approach provides a framework for priming the induction of many HIV bnAbs and could be applied to most HCDR3-dominant antibodies from other pathogens.


    Organizational Affiliation

    The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 Env BG505 MD64 N332-GT5 SOSIP gp120A, G [auth C], M [auth J]481Human 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
HIV-1 Env BG505 MD64 N332-GT5 SOSIP gp41B, H [auth D], N [auth M]162Human 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
BG18-like precursor HMP1 fragment antigen binding heavy chainI [auth E], C [auth H], O131Homo sapiensMutation(s): 0 
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
BG18-like precursor HMP1 fragment antigen binding light chainJ [auth F], D [auth L], P106Homo sapiensMutation(s): 0 
Gene Names: V2-17
Protein Feature View
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
base-binding RM20A3 fragment antigen binding heavy chainK [auth G], E [auth K], Q125Macaca mulattaMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
base-binding RM20A3 fragment antigen binding light chainL [auth I], F [auth N], R128Macaca mulattaMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b], DA [auth d], EA [auth e], FA [auth f], GA [auth g], IA [auth i], KA [auth k], LA [auth l]
BA [auth b], DA [auth d], EA [auth e], FA [auth f], GA [auth g], IA [auth i], KA [auth k], LA [auth l], MA [auth m], S, U, W, X, Y, Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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], HA [auth h], T5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42227JK
GlyCosmos:  G42227JK
GlyGen:  G42227JK
Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-glucopyranoseCA [auth c], JA [auth j], V6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
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 J],  KB [auth J],  LB [auth J],  MB [auth J],  NA [auth A],  NB [auth J],  OA [auth A],  OB [auth J],  PA [auth A],  PB [auth J],  QA [auth A],  QB [auth J],  RA [auth A],  RB [auth J],  SA [auth A],  SB [auth M],  TA [auth A],  TB [auth M],  UA [auth A],  VA [auth A],  WA [auth B],  XA [auth B],  YA [auth C],  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: 3.71 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 StatesUM1 AI100663
Bill & Melinda Gates FoundationUnited StatesOPP1115782
Bill & Melinda Gates FoundationUnited StatesOPP1084519

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary