9ZRY | pdb_00009zry

Cryo-EM structure of SHIV-elicited CN81-2029 Fab in complex with HIV Env trimer Q23-SCT27


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9ZRY

This is version 1.1 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 

  • 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 novel 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 >90% of macaques - neutralization breadth that includes N130-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 post-infection or immunization, and neutralization breadth in 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, ID 50 ). 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 N130 glycan. Further, rhesus bNAbs were not restricted to IGHD3-15*01 heavy chain alleles. These results expand the utility 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: 298.18 kDa 
  • Atom Count: 17,248 
  • Modeled Residue Count: 1,961 
  • Deposited Residue Count: 2,431 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CN81-2029 heavy chain243Macaca 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
CN81-2029 light chain220Macaca mulattaMutation(s): 0 
Entity Groups
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Sequence Annotations
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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: 20
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],
KA [auth k],
L [auth F],
MA [auth m],
N [auth H],
NA [auth n],
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],
U [auth O],
X [auth R],
Y [auth S],
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-glucopyranoseIA [auth i],
J [auth D],
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-glucopyranoseJA [auth j],
K [auth E],
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-glucopyranoseM [auth G]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-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-glucopyranoseLA [auth l]7N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL
GlyCosmos: G55220VL
GlyGen: G55220VL

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 c]
CB [auth c]
DB [auth c]
EB [auth d]
AB [auth b],
BB [auth c],
CB [auth c],
DB [auth c],
EB [auth d],
FB [auth d],
GB [auth d],
HB [auth d],
IB [auth d],
JB [auth d],
KB [auth d],
LB [auth e],
MB [auth e],
NB [auth e],
OB [auth f],
PB [auth f],
QB [auth f],
RB [auth f],
SB [auth f],
TA [auth b],
TB [auth f],
UA [auth b],
UB [auth f],
VA [auth b],
VB [auth f],
WA [auth b],
WB [auth g],
XA [auth b],
XB [auth g],
YA [auth b],
YB [auth g],
ZA [auth b]
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
L-PEPTIDE LINKINGC9 H11 N O6 STYR

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 Å
  • Resolution: 2.90 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