9MII | pdb_00009mii

253-7A03 Fab in complex with HIV-1 BG505 SOSIP Env trimer and RM20A3 Fab


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Precise targeting of HIV broadly neutralizing antibody precursors in humans.

Caniels, T.G.Prabhakaran, M.Ozorowski, G.MacPhee, K.J.Wu, W.van der Straten, K.Agrawal, S.Derking, R.Reiss, E.I.M.M.Millard, K.Turroja, M.Desrosiers, A.Bethony, J.Malkin, E.Liesdek, M.H.van der Veen, A.Klouwens, M.Snitselaar, J.L.Bouhuijs, J.H.Bronson, R.Jean-Baptiste, J.Gajjala, S.Rikhtegaran Tehrani, Z.Benner, A.Ramaswami, M.Duff, M.O.Liu, Y.W.Sato, A.H.Kim, J.Y.Baken, I.J.L.Mendes Silva, C.Bijl, T.P.L.van Rijswijk, J.Burger, J.A.Cupo, A.Yasmeen, A.Phulera, S.Lee, W.H.Randall Jr., K.N.Zhang, S.Corcoran, M.M.Regadas, I.Sullivan, A.C.Brown, D.M.Bohl, J.A.Greene, K.M.Gao, H.Yates, N.L.Sawant, S.Prins, J.M.Kootstra, N.A.Kaminsky, S.M.Barin, B.Rahaman, F.Meller, M.Philiponis, V.Laufer, D.S.Lombardo, A.Mwoga, L.Shotorbani, S.Holman, D.Koup, R.A.Klasse, P.J.Karlsson Hedestam, G.B.Tomaras, G.D.van Gils, M.J.Montefiori, D.C.McDermott, A.B.Hyrien, O.Moore, J.P.Wilson, I.A.Ward, A.B.Diemert, D.J.de Bree, G.J.Andrews, S.F.Caskey, M.Sanders, R.W.

(2025) Science 389: eadv5572-eadv5572

  • DOI: https://doi.org/10.1126/science.adv5572
  • Primary Citation of Related Structures:  
    9MI0, 9MIA, 9MIB, 9MIC, 9MID, 9MIF, 9MIH, 9MII, 9MJ3, 9MJ6, 9MJC, 9MJD, 9MJI, 9MK4

  • PubMed Abstract: 

    A protective HIV vaccine will need to induce broadly neutralizing antibodies (bnAbs) in humans, but priming rare bnAb precursor B cells has been challenging. In a double-blinded, placebo-controlled phase 1 human clinical trial, the recombinant, germline-targeting envelope glycoprotein (Env) trimer BG505 SOSIP.v4.1-GT1.1, adjuvanted with AS01 B , induced bnAb precursors of the VRC01-class at a high frequency in the majority of vaccine recipients. These bnAb precursors, that target the CD4 receptor binding site, had undergone somatic hypermutation characteristic of the VRC01-class. A subset of isolated VRC01-class monoclonal antibodies neutralized wild-type pseudoviruses and was structurally extremely similar to bnAb VRC01. These results further support germline-targeting approaches for human HIV vaccine design and demonstrate atomic-level manipulation of B cell responses with rational vaccine design.


  • Organizational Affiliation
    • Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, location AMC, Amsterdam, Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120A,
E [auth C],
I [auth E]
516Human immunodeficiency virus 1Mutation(s): 2 
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: 16
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160B,
F [auth D],
J [auth F]
153Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for D0PUM0 (Human immunodeficiency virus type 1)
Explore D0PUM0 
Go to UniProtKB:  D0PUM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0PUM0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RM20A3 heavy chain FvC [auth G],
G [auth J],
K [auth M]
125Macaca mulattaMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RM20A3 light chain FvD [auth I],
H [auth K],
L [auth N]
128Macaca mulattaMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
253-7A03 heavy chain FvM [auth H]119Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
253-7A03 lambda chain FvN [auth L]100Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O, P, Q, S, T
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
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
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranose
U
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranose
V
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth E]
BA [auth A]
BB [auth E]
CA [auth A]
AA [auth A],
AB [auth E],
BA [auth A],
BB [auth E],
CA [auth A],
CB [auth E],
DA [auth A],
DB [auth E],
EA [auth A],
EB [auth E],
FA [auth A],
FB [auth E],
GA [auth A],
GB [auth E],
HA [auth B],
HB [auth E],
IA [auth C],
IB [auth E],
JA [auth C],
JB [auth E],
KA [auth C],
KB [auth E],
LA [auth C],
LB [auth F],
MA [auth C],
MB [auth F],
NA [auth C],
NB [auth F],
OA [auth C],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C],
W [auth A],
WA [auth C],
X [auth A],
XA [auth D],
Y [auth A],
YA [auth D],
Z [auth A],
ZA [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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
Bill & Melinda Gates FoundationUnited StatesINV-002916

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection, Database references
  • Version 1.2: 2025-08-13
    Changes: Data collection, Database references