9PIT | pdb_00009pit

HIV-1 bnAb 1-23 in complex with BG505 MD39 SOSIP and RM19R


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9PIT

This is version 1.1 of the entry. See complete history

Literature

Structural and immunogenetic signatures guide CD4-mimetic HIV vaccine development.

Bader, D.L.V.Flynn, C.T.Kalyuzhniy, O.Ozorowski, G.Corcoran, M.M.Burns, A.Altman, P.Rouzeau, R.Sincomb, T.Liguori, A.Fernandez-Quintero, M.L.Loeffler, J.R.Torres, J.L.Turner, H.L.Georgeson, E.Zhou, A.Voic, H.Goo, S.Shahin, L.Burton, I.Wu, M.Stanfield, R.L.Eskandarzadeh, S.Lu, D.Alavi, N.Phelps, N.Tingle, R.McKenney, K.Youhanna, J.Amirzehni, S.Schiffner, T.Steichen, J.M.Burton, D.R.Wilson, I.A.Karlsson Hedestam, G.B.Landais, E.Lee, J.H.Sok, D.Cottrell, C.A.Ward, A.B.Schief, W.R.

(2026) Cell Rep 45: 117180-117180

  • DOI: https://doi.org/10.1016/j.celrep.2026.117180
  • Primary Citation Related Structures: 
    9PIT, 9PIV

  • PubMed Abstract: 

    HIV vaccine strategies include aims to elicit broadly neutralizing antibodies (bnAbs) targeting the CD4-binding site, that are derived from immunoglobulin heavy-chain variable genes 1-2 (V H 1-2) and 1-46 (V H 1-46). Here, we present an integrated analysis of V H 1-46 bnAbs, including in vitro functional studies, cryo-electron microscopy structures of two V H 1-46 bnAbs (1-23 and 9-71) complexed with envelope trimers, and comprehensive structural and immunogenetic analyses, to help guide vaccine design. We show that V H 1-46-derived bnAbs use diverse light-chain variable (V K /V L ) genes and LCDR3 lengths commonly found in human antibody repertoires, which generate unique LCDR3 signatures that influence both the antibody paratope and approach angle. We identify three V H 1-46 bnAb classes, 1B2530 (V L 1-47), CH235 (V K 3-15), and 561 (V K 3-20), with the 561 class further subdivided into types I and II. Our findings indicate that V H 1-46 priming immunogens should be tailored to each bnAb class, with 561-class bnAbs presenting optimal targets for germline-targeting vaccine design.


  • Organizational Affiliation
    • Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 400.64 kDa 
  • Atom Count: 25,533 
  • Modeled Residue Count: 3,075 
  • Deposited Residue Count: 3,408 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
1-23 light chain FvA [auth L],
G [auth Q],
M [auth R]
109Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
1-23 heavy chain FvB [auth H],
H [auth M],
N
125Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160C [auth B],
I [auth E],
O [auth F]
512Human immunodeficiency virus 1Mutation(s): 12 
Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S5
Glycosylation
Glycosylation Sites: 15
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
RM19R light chain FvD [auth G],
J [auth I],
P [auth K]
107Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
RM19R heavy chain FvE [auth J],
K [auth O],
Q [auth P]
121Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41 - BG505 MD39F [auth A],
L [auth C],
R [auth D]
162Human immunodeficiency virus 1Mutation(s): 7 
Gene Names: env
UniProt
Find proteins for Q2N0S8 (Human immunodeficiency virus type 1)
Explore Q2N0S8 
Go to UniProtKB:  Q2N0S8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S8
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseDA [auth d],
OA [auth o],
S
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G56014GC
GlyCosmos: G56014GC
GlyGen: G56014GC
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
CA [auth c],
EA [auth e],
FA [auth f],
AA [auth a],
BA [auth b],
CA [auth c],
EA [auth e],
FA [auth f],
HA [auth h],
IA [auth i],
KA [auth k],
LA [auth l],
MA [auth m],
NA [auth n],
PA [auth p],
QA [auth q],
SA [auth s],
T,
TA [auth t],
U,
VA [auth v],
W,
WA [auth w],
X,
XA [auth x],
YA [auth y],
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 9
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-glucopyranose
GA [auth g],
JA [auth j],
RA [auth r],
UA [auth u],
V,
GA [auth g],
JA [auth j],
RA [auth r],
UA [auth u],
V,
Y
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

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 A]
EB [auth A]
AB [auth B],
BB [auth B],
CB [auth B],
DB [auth A],
EB [auth A],
FB [auth A],
GB [auth E],
HB [auth E],
IB [auth E],
JB [auth E],
KB [auth C],
LB [auth C],
MB [auth C],
NB [auth F],
OB [auth F],
PB [auth F],
QB [auth F],
RB [auth D],
SB [auth D],
TB [auth D],
ZA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv.4.7.0
MODEL REFINEMENTPHENIX1.21.1

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 StatesUM1 AI144462

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-04
    Type: Initial release
  • Version 1.1: 2026-04-29
    Changes: Data collection, Database references