6VO1

BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20J


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates.

Cottrell, C.A.van Schooten, J.Bowman, C.A.Yuan, M.Oyen, D.Shin, M.Morpurgo, R.van der Woude, P.van Breemen, M.Torres, J.L.Patel, R.Gross, J.Sewall, L.M.Copps, J.Ozorowski, G.Nogal, B.Sok, D.Rakasz, E.G.Labranche, C.Vigdorovich, V.Christley, S.Carnathan, D.G.Sather, D.N.Montefiori, D.Silvestri, G.Burton, D.R.Moore, J.P.Wilson, I.A.Sanders, R.W.Ward, A.B.van Gils, M.J.

(2020) PLoS Pathog 16: e1008753-e1008753

  • DOI: 10.1371/journal.ppat.1008753
  • Primary Citation of Related Structures:  
    6VLR, 6VN0, 6VO1, 6VOR, 6VOS, 6VSR

  • PubMed Abstract: 
  • The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates ...

    The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.


    Related Citations: 
    • Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates
      Cottrell, C.A., van Schooten, J., Bowman, C.A., Yuan, M., Oyen, D., Shin, M., Morpurgo, R., van der Woude, P., van Breemen, M., Torres, J.L., Patel, R., Gross, J., Sewall, L.M., Copps, J., Ozorowski, G., Nogal, B., Sok, D., Rakasz, E.G., Labranche, C., Vigdorovich, V., Christley, S., Carnathan, D.G., Sather, D.N., Montefiori, D., Silvestri, G., Burton, D.R., Moore, J.P., Wilson, I.A., Sanders, R.W., Ward, A.B., van Gils, M.J.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp120A, E [auth C], I [auth D]475Human 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, F [auth E], J [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
RM20J Heavy chain FabG, C [auth H], K [auth I]118Macaca mulattaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RM20J Kappa light chainH [auth J], L [auth K], D [auth L]107Macaca mulattaMutation(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
AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], GA [auth g], HA [auth h], JA [auth j]
AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], GA [auth g], HA [auth h], JA [auth j], KA [auth k], LA [auth l], M, MA [auth m], O, P, R, S, T, U, V, 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-glucopyranoseFA [auth f], N, W3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
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-glucopyranoseIA [auth i], Q, Z6N-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 D] , BB [auth D] , CB [auth D] , DB [auth D] , EB [auth D] , NA [auth A] , OA [auth A] , PA [auth A] , 
AB [auth D],  BB [auth D],  CB [auth D],  DB [auth D],  EB [auth D],  NA [auth A],  OA [auth A],  PA [auth A],  QA [auth A],  RA [auth A],  SA [auth A],  TA [auth C],  UA [auth C],  VA [auth C],  WA [auth C],  XA [auth C],  YA [auth C],  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: 3.88 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 StatesF31 AI131873
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI100663
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI110657
National Institutes of Health/Office of the DirectorUnited StatesS10 OD021634
Bill & Melinda Gates FoundationUnited StatesOPP1115782
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI144462

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-09-16
    Changes: Database references, Structure summary