9PNU | pdb_00009pnu

Cryo-EM structure of K001-A1 Fab in complex with HIV-1 459C-OPT RnS DS-SOSIP Env trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Vaccine elicitation of HIV-1 neutralizing antibodies against both V2 apex and fusion peptide in rhesus macaques.

Duan, H.Nkolola, J.P.Wang, S.Chaudhari, J.Teng, I.T.Lavine, C.Parchment, D.K.Sellers, G.S.McKee, K.O'Dell, S.Choe, M.Du, H.Zhang, B.Perez, A.A.E.Rossler, A.Lasrado, N.Biju, A.Becker, J.E.Carroll, R.Carson, A.S.Henry, A.R.Morano, N.C.Mughal, M.Rawi, R.Roark, R.S.Schramm, C.A.Shen, C.H.Smith, S.C.Stephens, T.Tsybovsky, Y.Van Wazer, D.J.Wang, H.Yang, Y.Rutten, L.Langedijk, J.P.M.Cheng, C.Wang, L.Douek, D.C.Koup, R.A.Mascola, J.R.Shapiro, L.Zhou, T.Doria-Rose, N.A.Korber, B.Seaman, M.S.Pierson, T.C.Kwong, P.D.Barouch, D.H.

(2026) Cell Rep 45: 116905-116905

  • DOI: https://doi.org/10.1016/j.celrep.2025.116905
  • Primary Citation of Related Structures:  
    9PNI, 9PNN, 9PNU, 9PQ2, 9PQ3

  • PubMed Abstract: 

    Broadly neutralizing antibodies (bNAbs) targeting multiple sites of HIV-1 Env vulnerability can be induced by infection, but simultaneous elicitation of bNAbs against multiple epitopes has not been achieved by vaccination. In this study, we designed a dual-epitope vaccine targeting both the fusion peptide (FP) and the V2 apex and evaluated its capacity to induce bNAbs against both epitopes in rhesus macaques. This vaccine combined an FP conjugate with a cocktail of engineered Env trimers with enhanced V2 apex recognition and increased antigen retention in lymph nodes. Macaque immunization with the dual-epitope vaccine elicited >1,000-fold higher autologous tier 2-neutralizing titers than wild-type Env trimers and enhanced heterologous neutralization. Both FP- and V2 apex-monoclonal antibodies were isolated from immunized macaques and showed heterologous neutralization with genetic and structural signatures similar to well-characterized FP and V2 apex bNAbs. These results demonstrate proof of concept for simultaneous vaccine elicitation of neutralizing antibodies against multiple sites of Env vulnerability.


  • Organizational Affiliation
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
K001-A1 Fab heavy chainA [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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
K001-A1 Fab light chainB [auth L]220Macaca mulattaMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
459C-OPT probe RnS DS-SOSIP gp41C [auth A],
E [auth B],
G [auth F]
179Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for A0A866DY39 (Human immunodeficiency virus type 1)
Explore A0A866DY39 
Go to UniProtKB:  A0A866DY39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A866DY39
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
459C-OPT probe RnS DS-SOSIP gp120D [auth C],
F [auth G],
H [auth I]
470Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for A0A0K1H7M8 (Human immunodeficiency virus type 1)
Explore A0A0K1H7M8 
Go to UniProtKB:  A0A0K1H7M8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K1H7M8
Glycosylation
Glycosylation Sites: 19
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
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-glucopyranoseGA [auth g],
I [auth D],
MA [auth m],
Q
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 7
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-glucopyranoseBA [auth b],
M,
QA [auth q],
T
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
EA [auth e],
HA [auth h],
LA [auth l],
R,
SA [auth s],
EA [auth e],
HA [auth h],
LA [auth l],
R,
SA [auth s],
U,
V,
VA [auth v],
W,
X,
XA [auth x],
YA [auth y]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 9
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-glucopyranoseJA [auth j],
UA [auth u]
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth A]
BB [auth A]
CB [auth A]
DB [auth C]
EB [auth C]
AB [auth A],
BB [auth A],
CB [auth A],
DB [auth C],
EB [auth C],
FB [auth C],
GB [auth C],
HB [auth C],
IB [auth B],
JB [auth B],
KB [auth B],
LB [auth G],
MB [auth G],
NB [auth G],
OB [auth F],
PB [auth F],
QB [auth F],
RB [auth F],
SB [auth I],
TB [auth I],
UB [auth I],
VB [auth I],
WB [auth I],
ZA [auth A]
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
A [auth H]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1
MODEL REFINEMENTPHENIX1.21.2_5419

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Data collection, Database references