9YMK | pdb_00009ymk

RVz20_wk72_08 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9YMK

This is version 1.1 of the entry. See complete history

Literature

Vaccination elicits HIV broadly neutralizing antibodies in primates.

Steichen, J.M.Madden, P.J.Flynn, C.T.Phulera, S.Shil, M.Kalyuzhniy, O.Liguori, A.Kifude, C.Sewall, L.M.Cottrell, C.A.Ma, K.M.Baboo, S.Diedrich, J.K.McKenney, K.deCamp, A.C.Carnathan, D.G.Phung, I.Ramezani-Rad, P.Marina-Zarate, E.Freeman, B.Xie, Z.Lee, J.H.Sincomb, T.Phelps, N.Lu, D.Goodwin, D.Tingle, R.Adachi, Y.Alavi, N.Tran, J.Tran, A.S.Nascimento, A.Sovie, C.Bader, D.L.V.Voic, H.Zhou, X.Pixton, G.Walsh, A.Melo, M.B.Schiffner, T.Batista, F.D.Burton, D.R.Irvine, D.J.Paulson, J.C.Yates 3rd, J.R.Ozorowski, G.Ward, A.B.Silvestri, G.Crotty, S.Schief, W.R.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10837-5
  • Primary Citation Related Structures: 
    9YMJ, 9YMK, 9YML

  • PubMed Abstract: 

    The high antigenic diversity of HIV has been a major obstacle to development of a broadly protective vaccine. Nevertheless, protective HIV broadly neutralizing antibodies (bnAbs) exist and have been proposed as templates for vaccine development 1-6 . Germline-targeting is a conceptually radical vaccine design approach to elicit bnAbs, aiming to prime rare bnAb-precursor B cells possessing pre-determined human genetic and structural features shared with template bnAbs, and then guide B cell affinity maturation to potent bnAb evolution with heterologous boosters 7-11 . Although the approach has shown promise in clinical 12-17 and pre-clinical 18-34 studies, it faces many immunological challenges and, to date, has not succeeded in generating bnAbs in humans or nontransgenic animals. Here, we report an adjuvanted protein germline-targeting vaccine tested in outbred nonhuman primates that generated bnAb-class memory B cells and sera capable of neutralizing diverse HIV clinical isolates. bnAb lineages were generated in ≥50% of animals, achieving up to 67% neutralization breadth compared to the reference bnAb. Vaccine-induced bnAbs exhibited precise structural mimicry of human bnAb interactions with HIV envelope (Env), matching the germline-targeting predictions. Furthermore, serum bnAb activity developed in 44% of animals and in the most striking instance reached titers expected to confer protection against diverse HIV isolates. These results demonstrate proof of principle that germline-targeting vaccines can reproducibly elicit prespecified classes of bnAbs to prespecified epitopes under endogenous conditions, supporting further optimization of this approach for HIV vaccine development.


  • Organizational Affiliation
    • Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 529.69 kDa 
  • Atom Count: 25,272 
  • Modeled Residue Count: 3,081 
  • Deposited Residue Count: 4,671 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RM20A3 Fab heavy chainA [auth G],
G [auth J],
M [auth O]
229Macaca 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
RM20A3 light chainB [auth I],
H [auth M],
N [auth Q]
215Macaca mulattaMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505 MD39 SOSIP gp120C [auth A],
I [auth C],
O [auth E]
513Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 15
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
BG505 MD39 SOSIP gp41D [auth B],
J [auth D],
P [auth F]
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
RVz20_wk72_08 Fab heavy chainE [auth H],
K,
Q [auth P]
230Macaca 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: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
RVz20_wk72_08 light chainF [auth L],
L [auth N],
R
217Macaca mulattaMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseCA [auth c],
S,
X
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G46836GH
GlyCosmos: G46836GH
GlyGen: G46836GH
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseDA [auth d],
T,
Y
9N-Glycosylation
Glycosylation Resources
GlyTouCan: G83161QT
GlyCosmos: G83161QT
GlyGen: G83161QT
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
EA [auth e],
GA [auth g],
U,
W,
BA [auth b],
EA [auth e],
GA [auth g],
U,
W,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 10
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-glucopyranoseAA [auth a],
FA [auth f],
V
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 C]
BB [auth C]
CB [auth C]
DB [auth D]
EB [auth D]
AB [auth C],
BB [auth C],
CB [auth C],
DB [auth D],
EB [auth D],
FB [auth E],
GB [auth E],
HA [auth A],
HB [auth E],
IA [auth A],
IB [auth E],
JA [auth A],
JB [auth E],
KA [auth A],
KB [auth E],
LA [auth A],
LB [auth E],
MA [auth A],
MB [auth E],
NA [auth A],
NB [auth E],
OA [auth A],
OB [auth E],
PA [auth A],
PB [auth F],
QA [auth A],
QB [auth F],
RA [auth B],
SA [auth B],
TA [auth C],
UA [auth C],
VA [auth C],
WA [auth C],
XA [auth C],
YA [auth C],
ZA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC

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: 2026-07-08
    Type: Initial release
  • Version 1.1: 2026-07-15
    Changes: Data collection, Database references