8TQ1

HIV-1 BG505 Env SOSIP in complex with bovine Fab Bess4 and non-human primate Fab RM20A3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire.

Altman, P.X.Ozorowski, G.Stanfield, R.L.Haakenson, J.Appel, M.Parren, M.Lee, W.H.Sang, H.Woehl, J.Saye-Francisco, K.Sewall, L.M.Joyce, C.Song, G.Porter, K.Landais, E.Andrabi, R.Wilson, I.A.Ward, A.B.Mwangi, W.Smider, V.V.Burton, D.R.Sok, D.

(2024) PLoS Pathog 20: e1012042-e1012042

  • DOI: https://doi.org/10.1371/journal.ppat.1012042
  • Primary Citation of Related Structures:  
    8TQ1, 8VBJ, 8VBK, 8VBL, 8VBM, 8VBN, 8VBO, 8VBP, 8VBQ, 8VBR

  • PubMed Abstract: 

    The generation of broadly neutralizing antibodies (bnAbs) to conserved epitopes on HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The animal models commonly used for HIV do not reliably produce a potent broadly neutralizing serum antibody response, with the exception of cows. Cows have previously produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models, other engineered immunogens were shown to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n = 4) with two regimens of V2-apex focusing Env immunogens to investigate whether antibody responses could be generated to the V2-apex on Env. Group 1 was immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 was immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows, respectively, and showed moderate breadth and potency. Potent and broad responses in this study developed much later than previous cow immunizations that elicited CD4bs bnAbs responses and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target more than one broadly neutralizing epitope on the HIV surface reveals the generality of elongated structures for the recognition of highly glycosylated proteins. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response.


  • Organizational Affiliation

    Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120A,
E [auth J],
I [auth E]
516Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 17
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein gp41B,
F [auth K],
J [auth F]
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S5
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NHP RM20A3 Fab heavy chainC,
G [auth M],
K [auth G]
125Macaca mulattaMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NHP RM20A3 Fab light chainD,
H [auth N],
L [auth I]
128Macaca mulattaMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Bovine Bess4 Fab heavy chainM [auth H]163Bos taurusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N [auth L],
O,
P,
R,
S,
N [auth L],
O,
P,
R,
S,
T,
W,
Y
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranose
Q, U
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranose
V, X
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth J]
BA [auth A]
BB [auth K]
CA [auth A]
AA [auth A],
AB [auth J],
BA [auth A],
BB [auth K],
CA [auth A],
CB [auth K],
DA [auth A],
DB [auth E],
EA [auth A],
EB [auth E],
FA [auth A],
FB [auth E],
GA [auth A],
GB [auth E],
HA [auth A],
HB [auth E],
IA [auth A],
IB [auth E],
JA [auth A],
JB [auth E],
KA [auth A],
KB [auth E],
LA [auth B],
LB [auth E],
MA [auth B],
MB [auth E],
NA [auth J],
NB [auth E],
OA [auth J],
OB [auth E],
PA [auth J],
PB [auth E],
QA [auth J],
QB [auth F],
RA [auth J],
RB [auth F],
SA [auth J],
TA [auth J],
UA [auth J],
VA [auth J],
WA [auth J],
XA [auth J],
YA [auth J],
Z [auth A],
ZA [auth J]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-034657

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary