8SW4

BG505 GT1.1 SOSIP in complex with NHP Fabs 21N13, 21M20 and RM20A3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 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

Germline-targeting HIV vaccination induces neutralizing antibodies to the CD4 binding site.

Caniels, T.G.Medina-Ramirez, M.Zhang, S.Kratochvil, S.Xian, Y.Koo, J.H.Derking, R.Samsel, J.van Schooten, J.Pecetta, S.Lamperti, E.Yuan, M.Carrasco, M.R.Del Moral Sanchez, I.Allen, J.D.Bouhuijs, J.H.Yasmeen, A.Ketas, T.J.Snitselaar, J.L.Bijl, T.P.L.Martin, I.C.Torres, J.L.Cupo, A.Shirreff, L.Rogers, K.Mason, R.D.Roederer, M.Greene, K.M.Gao, H.Silva, C.M.Baken, I.J.L.Tian, M.Alt, F.W.Pulendran, B.Seaman, M.S.Crispin, M.van Gils, M.J.Montefiori, D.C.McDermott, A.B.Villinger, F.J.Koup, R.A.Moore, J.P.Klasse, P.J.Ozorowski, G.Batista, F.D.Wilson, I.A.Ward, A.B.Sanders, R.W.

(2024) Sci Immunol 9: eadk9550-eadk9550

  • DOI: https://doi.org/10.1126/sciimmunol.adk9550
  • Primary Citation of Related Structures:  
    8SW3, 8SW4

  • PubMed Abstract: 

    Eliciting potent and broadly neutralizing antibodies (bnAbs) is a major goal in HIV-1 vaccine development. Here, we describe how germline-targeting immunogen BG505 SOSIP germline trimer 1.1 (GT1.1), generated through structure-based design, engages a diverse range of VRC01-class bnAb precursors. A single immunization with GT1.1 expands CD4 binding site (CD4bs)-specific VRC01-class B cells in knock-in mice and drives VRC01-class maturation. In nonhuman primates (NHPs), GT1.1 primes CD4bs-specific neutralizing serum responses. Selected monoclonal antibodies (mAbs) isolated from GT1.1-immunized NHPs neutralize fully glycosylated BG505 virus. Two mAbs, 12C11 and 21N13, neutralize subsets of diverse heterologous neutralization-resistant viruses. High-resolution structures revealed that 21N13 targets the same conserved residues in the CD4bs as VRC01-class and CH235-class bnAbs despite its low sequence similarity (~40%), whereas mAb 12C11 binds predominantly through its heavy chain complementarity-determining region 3. These preclinical data underpin the ongoing evaluation of GT1.1 in a phase 1 clinical trial in healthy volunteers.


  • Organizational Affiliation

    Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
21M20 heavy chain variable regionA [auth H]125MacacaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
8SW4_1
0102030405060708090100110120
8SW4_1
EVQLVESGGGLAKPGGSLRLSCAASGFTFSRSIMHWVRQAPGKGLEWVSTINYAGSTYYADSVRGRFVISRDNSKNTLSLQMNSVRPEDRAVYHCAKDKEGYYSGGYPLWYFDLWGPGTPVTISS
UNMODELED
HYDROPATHY
DISORDER
DISORDERED BINDING
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
21M20 light chain variable regionB [auth L]107MacacaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
8SW4_2
0102030405060708090100
8SW4_2
DVQMTQSPSSLSASVGDKVSITCRASQGIADALAWYQQKPGKAPKLLIYGASNLESGVPSRFSGSGSGTDFSLTISSLQAEDFAVYYCQQRNSHPPTFGQGTRVEVK
UNMODELED
HYDROPATHY
DISORDER
DISORDERED BINDING
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BG505 GT1.1 SOSIP gp120C [auth A],
G [auth C],
K [auth D]
509Human immunodeficiency virus 1Mutation(s): 0 
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: 10
Sequence Annotations
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  • Reference Sequence
8SW4_3
050100150200250300350400450500
8SW4_3
UNIPROT Q2N0S6
UNMODELED
HYDROPATHY
DISORDER
DISORDERED BINDING
PFAM
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41D [auth B],
H [auth G],
L [auth I]
153Human 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: 3
Sequence Annotations
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  • Reference Sequence
8SW4_4
020406080100120140
8SW4_4
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
UNIPROT Q2N0S6
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICTTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD
UNMODELED
MUTATION
HYDROPATHY
DISORDER
DISORDERED BINDING
PFAM
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RM20A3 heavy chain variable regionE,
I [auth J],
M [auth K]
124MacacaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
8SW4_5
0102030405060708090100110120
8SW4_5
EVQLVETGGGLVQPGGSLKLSCRASGYTFSSFAMSWVRQAPGKGLEWVSLINDRGGLTFYVDSVKGRFTISRDNSKNTLSLQMHSLRDGDTAVYYCATGGMSSALQSSKYYFDFWGQGALVTVS
UNMODELED
HYDROPATHY
DISORDER
DISORDERED BINDING
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RM20A3 light chain variable regionF,
J [auth M],
N
111MacacaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
8SW4_6
0102030405060708090100110
8SW4_6
QSALTQPPSVSGSPGQSVTISCTGTSSDIGSYNYVSWYQQHPGKAPKLMIYDVTQRPSGVSDRFSGSKSGNTASLTISGLQADDEADYYCSAYAGRQTFYIFGGGTRLTVL
UNMODELED
HYDROPATHY
DISORDER
DISORDERED BINDING
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
21N13 heavy chain variable region
O, Q, S
130MacacaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
8SW4_7
0102030405060708090100110120130
8SW4_7
QVQLQESGPGRVKPSETLSLTCAVSDDSFGSSYFYWSWIRQAPGKGLEWIGYIAYSGGVRYNPSLSSRVTISRNIHERQFYLRLTSMTAADTAVYYCARHCEDDYGYYSAAQSYGLDSWGQGIAVTVSPS
UNMODELED
HYDROPATHY
DISORDER
DISORDERED BINDING
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
21N13 light chain variable region
P, R, T
107MacacaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
8SW4_8
0102030405060708090100
8SW4_8
DIQMTQSPSSLSASVGDRVTITCRTSENVNNCLNWYQQKPGKAPKLLIYRTSTLQRGVPSRFSGTGSGTDYTLTISSLQSEDFGTYYCQHYYGTPLTFGGGTMVDIK
UNMODELED
HYDROPATHY
DISORDER
DISORDERED BINDING
Oligosaccharides

Help

Entity ID: 9
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
U, W, X
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
V
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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 D]
BA [auth A]
BB [auth D]
CA [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4

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 StatesP01 AI110657

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary