6DFH

BG505 MD64 N332-GT2 SOSIP trimer in complex with germline-reverted BG18 fragment antigen binding


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160A, E [auth C], I [auth D]476Human 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 gp160B, F [auth E], J [auth F]162Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
germline-reverted BG18 fragment antigen binding heavy chainG, C [auth H], K [auth I]233Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
germline-reverted BG18 fragment antigen binding light chainH [auth J], L [auth K], D [auth L]214Homo 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], EA [auth e], FA [auth f], GA [auth g], JA [auth j], M
BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], JA [auth j], M, N, O, P, Q, T, U, V, W, X, Y
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
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-glucopyranoseHA [auth h], R, Z5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42227JK
GlyCosmos:  G42227JK
GlyGen:  G42227JK
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseAA [auth a], IA [auth i], S7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G46836GH
GlyCosmos:  G46836GH
GlyGen:  G46836GH
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 D] , BB [auth F] , KA [auth A] , LA [auth A] , MA [auth A] , NA [auth A] , OA [auth A] , PA [auth B] , 
AB [auth D],  BB [auth F],  KA [auth A],  LA [auth A],  MA [auth A],  NA [auth A],  OA [auth A],  PA [auth B],  QA [auth C],  RA [auth C],  SA [auth C],  TA [auth C],  UA [auth C],  VA [auth E],  WA [auth D],  XA [auth D],  YA [auth D],  ZA [auth D]
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: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




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, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary