9MSD | pdb_00009msd

G002-293-0536 Fab in complex with 001428_T278M_L14 SOSIP and RM20A3 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Vaccination with mRNA-encoded nanoparticles drives early maturation of HIV bnAb precursors in humans.

Willis, J.R.Prabhakaran, M.Muthui, M.Naidoo, A.Sincomb, T.Wu, W.Cottrell, C.A.Landais, E.deCamp, A.C.Keshavarzi, N.R.Kalyuzhniy, O.Lee, J.H.Murungi, L.M.Ogonda, W.A.Yates, N.L.Corcoran, M.M.Phulera, S.Musando, J.Tsai, A.Lemire, G.Sein, Y.Muteti, M.Alamuri, P.Bohl, J.A.Holman, D.Himansu, S.Leav, B.Reuter, C.Lin, L.A.Ding, B.He, C.Straus, W.L.MacPhee, K.J.Regadas, I.Nyabundi, D.V.Chirchir, R.Anzala, O.Kimotho, J.N.Kibet, C.Greene, K.Gao, H.Beatman, E.Benson, K.Laddy, D.Brown, D.M.Bronson, R.Jean-Baptiste, J.Gajjala, S.Rikhtegaran-Tehrani, Z.Benner, A.Ramaswami, M.Lu, D.Alavi, N.Amirzehni, S.Kubitz, M.Tingle, R.Georgeson, E.Phelps, N.Adachi, Y.Liguori, A.Flynn, C.McKenney, K.Zhou, X.Owuor, D.C.Owuor, S.A.Kim, S.Y.Duff, M.Kim, J.Y.Gibson, G.Baboo, S.Diedrich, J.Schiffner, T.Shields, M.Matsoso, M.Santos, J.Syvertsen, K.Kennedy, A.Schroeter, M.Vekemans, J.Yates 3rd, J.R.Paulson, J.C.Hyrien, O.McDermott, A.B.Maenetje, P.Nyombayire, J.Karita, E.Ingabire, R.Edward, V.Muturi-Kioi, V.Maenza, J.Shapiro, A.E.McElrath, M.J.Edupuganti, S.Taylor, B.S.Diemert, D.Ozorowski, G.Koup, R.A.Montefiori, D.Ward, A.B.Karlsson Hedestam, G.B.Tomaras, G.Hunt, D.J.Muema, D.Sok, D.Laufer, D.S.Andrews, S.F.Nduati, E.W.Schief, W.R.

(2025) Science 389: eadr8382-eadr8382

  • DOI: https://doi.org/10.1126/science.adr8382
  • Primary Citation of Related Structures:  
    9MSD, 9MSY

  • PubMed Abstract: 

    A leading HIV vaccine strategy requires a priming immunogen to induce broadly neutralizing antibody (bnAb) precursors, followed by a series of heterologous boosters to elicit somatic hypermutation (SHM) and produce bnAbs. In two randomized, open-label phase 1 human clinical trials, IAVI-G002 in the United States and IAVI-G003 in Rwanda and South Africa, we evaluated the safety and immunogenicity of mRNA-encoded nanoparticles as priming immunogens (both trials) and first-boosting immunogens (IAVI-G002). The vaccines were generally safe and well tolerated, except 18% of IAVI-G002 participants experienced skin reactions. Priming induced bnAb precursors with substantial frequencies and SHM, and heterologous boosting elicited increased SHM, affinity, and neutralization activity toward bnAb development. The results establish clinical proof of concept that heterologous boosting can advance bnAb-precursor maturation and demonstrate bnAb priming in Africa where the HIV burden is highest.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
001428_T278M_L14 SOSIP gp140A,
F [auth G],
K [auth B]
650Human immunodeficiency virus 1Mutation(s): 16 
Gene Names: env
UniProt
Find proteins for A0A0B5KZH3 (Human immunodeficiency virus type 1)
Explore A0A0B5KZH3 
Go to UniProtKB:  A0A0B5KZH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B5KZH3
Glycosylation
Glycosylation Sites: 12
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
G002-293-0536 Fab heavy chainB [auth H],
G [auth I],
L [auth N]
224Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
G002-293-0536 Fab light chainC [auth L],
H [auth M],
M [auth O]
210Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RM20A3 Fab light chainD,
I [auth F],
N [auth K]
215Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RM20A3 Rab heavy chainE [auth C],
J [auth E],
O [auth J]
228Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
P, Q, S, T, V
P, Q, S, T, V, W
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
R, U, X
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 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth G],
IA [auth G],
JA [auth G],
KA [auth G],
LA [auth G],
MA [auth G],
NA [auth G],
OA [auth G],
PA [auth G],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B],
Y [auth A],
YA [auth B],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-002916

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Data collection, Database references