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 9ZRX | pdb_00009zrx

Cryo-EM structure of SHIV-elicited CE79-1571 Fab in complex with HIV Env trimer Q23-SCT27


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9ZRX

This is version 1.2 of the entry. See complete history. 

Literature

Enhanced B cell priming induces broadly neutralizing HIV-1 apex antibodies.

Marchitto, L., Wagh, K., Roark, R.S., Coleon, S., Li, H., Skelly, A.N., Hogarty, M.P., Habib, R., Ding, W., Ayyanathan, K., Liu, W., Sheng, Z., Guo, Y., Bal, J., Smith, L.M., Sutherland, L.L., Park, Y., Connell, A.J., Bibollet-Ruche, F., Lewis, E., Plante, S.J., Akeley, M.J., Lora, J., Zhao, C., Carey, J.W., Martella, C.L., Li, Y., Campion, M.S., Lituchy, M.G., Osbaldeston, R.A., Gordon, C.G., Albertus, A., Su, J., Noguchi, C., Tam, Y.K., Barbosa, C., Liang, B., Amereh, K., Li, X., Walsh, A.A., Irvine, D.J., Andrabi, R., Edwards, R.J., Kreider, E.F., Weissman, D., Shapiro, L., Kwong, P.D., Korber, B.T., Haynes, B.F., Saunders, K.O., Hahn, B.H., Shaw, G.M.

(2026) Nature 656: 712-722

  • DOI: https://doi.org/10.1038/s41586-026-10838-4
  • Primary Citation Related Structures: 
    9ZRX, 9ZRY, 9ZRZ

  • PubMed Abstract: 

    Efficient priming of B cell precursors is a rate-limiting step in the induction of V2 apex broadly neutralizing antibodies (bnAbs) 1,2 . Here we describe a germline-targeted HIV-1 Env (CAP256.OPT4) that increases the efficiency of V2 apex bnAb precursor priming by 30-400-fold compared with wild-type HIV-1 Envs and induces, in over 90% of macaques, neutralization breadth that includes Asn130-containing viruses. Using three different delivery platforms-persistently replicating simian human immunodeficiency viruses (SHIVs), protein nanoparticles and mRNA-we show bnAb priming as early as 4 weeks after infection or immunization, and neutralization breadth in the plasma by 12 weeks. In 14 SHIV-infected macaques, neutralization breadth reached as high as 90% on a 21-virus panel with potency as great as 1:20,000 (50% inhibitory dilution). Monoclonal bnAbs isolated from these animals were similarly broad and potent, with cryo-EM structures representing three distinct lineages revealing canonical needle-like HCDR3 binding. Env-Ab coevolution and structural analyses identified five key residues and loop features under positive selection and temporally associated with neutralization breadth. Importantly, prime-boost immunogens designed to capture these features induced broad and potent neutralization of globally diverse viruses including those containing Asn130 glycan. Furthermore, rhesus bnAbs were not restricted to IGHD3-15*01 heavy-chain alleles. These results expand the use of the rhesus model for HIV-1 vaccine design and provide a molecular blueprint for inducing V2 apex bnAbs in rhesus and humans.


  • Organizational Affiliation: 
    • Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

Macromolecule Content 

  • Total Structure Weight: 299.01 kDa 
  • Atom Count: 17,291 
  • Modeled Residue Count: 1,965 
  • Deposited Residue Count: 2,437 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CE79-1571 heavy chain248Macaca mulattaMutation(s): 0 
Entity Groups
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Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CE79-1571 light chain221Macaca mulattaMutation(s): 0 
Entity Groups
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope gp120C [auth b],
E [auth d],
G [auth f]
503Human immunodeficiency virusMutation(s): 0 
Gene Names: env
UniProt
Find proteins for O55774 (Human immunodeficiency virus type 1)
Explore O55774 
Go to UniProtKB:  O55774
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO55774
Glycosylation
Glycosylation Sites: 18
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope gp41 ectodomainD [auth c],
F [auth e],
H [auth g]
153Human immunodeficiency virusMutation(s): 0 
Gene Names: env
UniProt
Find proteins for O55774 (Human immunodeficiency virus type 1)
Explore O55774 
Go to UniProtKB:  O55774
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO55774
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth U],
BA [auth V],
CA [auth W],
DA [auth X],
EA [auth Y],
AA [auth U],
BA [auth V],
CA [auth W],
DA [auth X],
EA [auth Y],
FA [auth Z],
GA [auth a],
HA [auth h],
I [auth C],
JA [auth j],
L [auth F],
M [auth G],
MA [auth m],
N [auth H],
O [auth I],
OA [auth o],
PA [auth p],
Q [auth K],
QA [auth q],
R [auth L],
RA [auth r],
S [auth M],
SA [auth s],
T [auth N],
TA [auth t],
U [auth O],
UA [auth u],
X [auth R],
Z [auth T]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth D],
KA [auth k],
P [auth J],
V [auth P]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseK [auth E],
LA [auth l],
NA [auth n],
W [auth Q]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseY [auth S]4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranoseIA [auth i]3N/A
Glycosylation Resources
GlyTouCan: G00619DD
GlyCosmos: G00619DD
GlyGen: G00619DD

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AB [auth b]
BB [auth b]
CB [auth b]
DB [auth c]
EB [auth c]
AB [auth b],
BB [auth b],
CB [auth b],
DB [auth c],
EB [auth c],
FB [auth c],
GB [auth d],
HB [auth d],
IB [auth d],
JB [auth d],
KB [auth d],
LB [auth d],
MB [auth e],
NB [auth e],
OB [auth e],
PB [auth f],
QB [auth f],
RB [auth f],
SB [auth f],
TB [auth f],
UB [auth f],
VA [auth b],
VB [auth f],
WA [auth b],
WB [auth f],
XA [auth b],
XB [auth g],
YA [auth b],
YB [auth g],
ZA [auth b],
ZB [auth g]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Modified Residues  1 Unique
IDChains Modified ResidueModification TypeFormula2D Diagram
TYS
Query on TYS
TYRSulfationC9 H11 N O6 S

Experimental Data & Validation

Experimental Data

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

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: 2026-06-03
    Type: Initial release
  • Version 1.1: 2026-07-22
    Changes: Data collection, Database references
  • Version 1.2: 2026-09-02
    Changes: Data collection, Database references