9MIB | pdb_00009mib

206-9C09 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9MIB

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 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.

Macromolecule Content 

  • Total Structure Weight: 399.26 kDa 
  • Atom Count: 25,266 
  • Modeled Residue Count: 3,075 
  • Deposited Residue Count: 3,423 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RM20A3 heavy chain FvA [auth G],
G [auth J],
M [auth O]
125Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RM20A3 light chain FvB [auth I],
H [auth M],
N [auth Q]
128Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
GT1.1 v4.1 SOSIP gp120C [auth A],
I [auth C],
O [auth E]
509Human immunodeficiency virus 1Mutation(s): 0 
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: 13
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160D [auth B],
J [auth D],
P [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: 2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
206-9C09 heavy chain FvE [auth H],
K,
Q [auth P]
123Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
206-9C09 kappa chain FvF [auth L],
L [auth N],
R
103Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 8
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
AA [auth a],
DA [auth d],
FA [auth f],
KA [auth k],
NA [auth n],
AA [auth a],
DA [auth d],
FA [auth f],
KA [auth k],
NA [auth n],
PA [auth p],
T,
UA [auth u],
V
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-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-glucopyranoseIA [auth i],
SA [auth s],
Y
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G42984ZU
GlyCosmos: G42984ZU
GlyGen: G42984ZU

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 E],
HB [auth E],
IB [auth E],
JB [auth F],
KB [auth F],
WA [auth A],
XA [auth A],
YA [auth A],
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: 2.80 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