9BTJ | pdb_00009btj

Rhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and genetic basis of HIV-1 envelope V2 apex recognition by rhesus broadly neutralizing antibodies.

Roark, R.S.Habib, R.Gorman, J.Li, H.Connell, A.J.Bonsignori, M.Guo, Y.Hogarty, M.P.Olia, A.S.Sowers, K.J.Zhang, B.Bibollet-Ruche, F.Bylund, T.Callaghan, S.Carey, J.W.Cerutti, G.Harris, D.R.He, W.Lewis, E.Liu, T.Mason, R.D.Qiao, Y.Park, Y.Rando, J.M.Singh, A.Wolff, J.J.Lei, Q.P.Louder, M.K.Andrabi, R.Doria-Rose, N.A.Saunders, K.O.Seaman, M.S.Haynes, B.F.Kulp, D.W.Mascola, J.R.Roederer, M.Pierson, T.C.Sheng, Z.Hahn, B.H.Shaw, G.M.Kwong, P.D.Shapiro, L.

(2025) J Exp Medicine 222

  • DOI: https://doi.org/10.1084/jem.20250638
  • Primary Citation of Related Structures:  
    9BNK, 9BNL, 9BNM, 9BNP, 9BTH, 9BTI, 9BTJ, 9BTL, 9BTV

  • PubMed Abstract: 

    Broadly neutralizing antibodies targeting the V2 apex of HIV-1 envelope are desired as vaccine design templates, but few have been described. Here, we report 11 lineages of V2 apex-neutralizing antibodies from simian-human immunodeficiency virus (SHIV)-infected rhesus macaques and determine cryo-EM structures for 9. A single V2 apex-neutralizing lineage accounted for cross-clade breadth in most macaques, and somatic hypermutation relative to breadth was generally low, exemplified by antibody V033-a.01 with <5% nucleotide mutation and 37% breadth (208-strain panel). Envelope complex structures revealed eight different antibody classes (one multi-donor) and the complete repertoire of all five possible recognition topologies, recapitulating canonical human modes of apex insertion and C-strand hydrogen bonding. Despite this diversity in recognition, all rhesus-V2 apex antibodies were derived from reading frame two of the DH3-15*01 gene. Collectively, these results define-in rhesus-the structural and genetic basis of HIV-1 V2 apex recognition and demonstrate unprecedented structural plasticity of a highly selected immunogenetic element.


  • Organizational Affiliation
    • Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons , New York, NY, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 6561-a.01 light chainA [auth L]217Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 6561-a.01 heavy chainB [auth H]246Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120C [auth G],
E [auth A],
G [auth D]
477Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for C6G0D7 (Human immunodeficiency virus type 1)
Explore C6G0D7 
Go to UniProtKB:  C6G0D7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6G0D7
Glycosylation
Glycosylation Sites: 17
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41D [auth B],
F [auth C],
H [auth E]
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for C6G0E7 (Human immunodeficiency virus type 1)
Explore C6G0E7 
Go to UniProtKB:  C6G0E7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6G0E7
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
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-glucopyranoseDA [auth d],
J [auth I],
N,
NA [auth n],
T
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 7
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-glucopyranoseK [auth J],
MA [auth m],
X
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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
O
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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
P
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ
GlyCosmos:  G80966KZ
GlyGen:  G80966KZ
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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-glucopyranose
U
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83161QT
GlyCosmos:  G83161QT
GlyGen:  G83161QT
Entity ID: 11
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-glucopyranoseEA [auth e]4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranoseFA [auth f]6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth G]
AC [auth D]
BB [auth G]
BC [auth D]
CB [auth G]
AB [auth G],
AC [auth D],
BB [auth G],
BC [auth D],
CB [auth G],
CC [auth D],
DB [auth G],
DC [auth D],
EB [auth G],
EC [auth D],
FB [auth B],
FC [auth D],
GB [auth B],
GC [auth D],
HB [auth B],
HC [auth D],
IB [auth A],
IC [auth D],
JB [auth A],
JC [auth D],
KB [auth A],
KC [auth D],
LB [auth A],
LC [auth E],
MB [auth A],
MC [auth E],
NB [auth A],
NC [auth E],
OB [auth A],
PA [auth G],
PB [auth A],
QA [auth G],
QB [auth A],
RA [auth G],
RB [auth A],
SA [auth G],
SB [auth A],
TA [auth G],
TB [auth A],
UA [auth G],
UB [auth A],
VA [auth G],
VB [auth A],
WA [auth G],
WB [auth A],
XA [auth G],
XB [auth C],
YA [auth G],
YB [auth C],
ZA [auth G],
ZB [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
B [auth H]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev_5278

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310
Simons FoundationUnited StatesSF349247

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Data collection, Database references