6VO0

BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 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

HIV envelope trimer-elicited autologous neutralizing antibodies bind a region overlapping the N332 glycan supersite.

Nogal, B.McCoy, L.E.van Gils, M.J.Cottrell, C.A.Voss, J.E.Andrabi, R.Pauthner, M.Liang, C.H.Messmer, T.Nedellec, R.Shin, M.Turner, H.L.Ozorowski, G.Sanders, R.W.Burton, D.R.Ward, A.B.

(2020) Sci Adv 6: eaba0512-eaba0512

  • DOI: https://doi.org/10.1126/sciadv.aba0512
  • Primary Citation of Related Structures:  
    6VO0

  • PubMed Abstract: 

    To date, immunization studies of rabbits with the BG505 SOSIP.664 HIV envelope glycoprotein trimers have revealed the 241/289 glycan hole as the dominant neutralizing antibody epitope. Here, we isolated monoclonal antibodies from a rabbit that did not exhibit glycan hole-dependent autologous serum neutralization. The antibodies did not compete with a previously isolated glycan hole-specific antibody but did compete with N332 glycan supersite broadly neutralizing antibodies. A 3.5-Å cryoEM structure of one of the antibodies in complex with the BG505 SOSIP.v5.2 trimer demonstrated that while the epitope recognized overlapped the N332 glycan supersite by contacting the GDIR motif at the base of V3, primary contacts were located in the variable V1 loop. These data suggest that strain-specific responses to V1 may interfere with broadly neutralizing responses to the N332 glycan supersite and vaccine immunogens may require engineering to minimize these off-target responses or steer them toward a more desirable pathway.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
43A2 light chainA [auth L],
E [auth J],
I [auth K]
113Oryctolagus cuniculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
43A2 heavy chainB [auth H],
F [auth G],
J [auth I]
120Oryctolagus cuniculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120C [auth A],
G [auth C],
K [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
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UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 16
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41D [auth B],
H [auth E],
L [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
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseCA [auth c],
O,
V
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth D]
BB [auth D]
CB [auth D]
DB [auth D]
EB [auth D]
AB [auth D],
BB [auth D],
CB [auth D],
DB [auth D],
EB [auth D],
FB [auth D],
GB [auth D],
HA [auth A],
HB [auth D],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth C],
RA [auth C],
SA [auth C],
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC1
MODEL REFINEMENTRosettaEM
MODEL REFINEMENTCoot

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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1 AI144462
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesF31 AI131873

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: 2024-10-16
    Changes: Data collection, Database references, Structure summary