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- PDB-9mj6: Crystal structure of the VRC01-class antibody 7A03 derived from G... -

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Basic information

Entry
Database: PDB / ID: 9mj6
TitleCrystal structure of the VRC01-class antibody 7A03 derived from GT1.1 vaccination
Components
  • 7A03 Fab heavy chain
  • 7A03 Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 / Germline-targeting vaccination / CD4bs mAb
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsAgrawal, S. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5P01AI110657 United States
CitationJournal: Science / Year: 2025
Title: Precise targeting of HIV broadly neutralizing antibody precursors in humans.
Authors: Tom G Caniels / Madhu Prabhakaran / Gabriel Ozorowski / Kellie J MacPhee / Weiwei Wu / Karlijn van der Straten / Sashank Agrawal / Ronald Derking / Emma I M M Reiss / Katrina Millard / ...Authors: Tom G Caniels / Madhu Prabhakaran / Gabriel Ozorowski / Kellie J MacPhee / Weiwei Wu / Karlijn van der Straten / Sashank Agrawal / Ronald Derking / Emma I M M Reiss / Katrina Millard / Martina Turroja / Aimee Desrosiers / Jeffrey Bethony / Elissa Malkin / Marinus H Liesdek / Annelou van der Veen / Michelle Klouwens / Jonne L Snitselaar / Joey H Bouhuijs / Rhianna Bronson / Jalen Jean-Baptiste / Suprabhath Gajjala / Zahra Rikhtegaran Tehrani / Alison Benner / Mukundhan Ramaswami / Michael O Duff / Yung-Wen Liu / Alicia H Sato / Ju Yeong Kim / Isabel J L Baken / Catarina Mendes Silva / Tom P L Bijl / Jacqueline van Rijswijk / Judith A Burger / Albert Cupo / Anila Yasmeen / Swastik Phulera / Wen-Hsin Lee / Kipchoge N Randall / Shiyu Zhang / Martin M Corcoran / Isabel Regadas / Alex C Sullivan / David M Brown / Jennifer A Bohl / Kelli M Greene / Hongmei Gao / Nicole L Yates / Sheetal Sawant / Jan M Prins / Neeltje A Kootstra / Stephen M Kaminsky / Burc Barin / Farhad Rahaman / Margaret Meller / Vince Philiponis / Dagna S Laufer / Angela Lombardo / Lindsey Mwoga / Solmaz Shotorbani / Drienna Holman / Richard A Koup / Per Johan Klasse / Gunilla B Karlsson Hedestam / Georgia D Tomaras / Marit J van Gils / David C Montefiori / Adrian B McDermott / Ollivier Hyrien / John P Moore / Ian A Wilson / Andrew B Ward / David J Diemert / Godelieve J de Bree / Sarah F Andrews / Marina Caskey / Rogier W Sanders /
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 ...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, induced bnAb precursors of the VRC01-class at a high frequency in the majority of vaccine recipients. These bnAb precursors, which 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.
History
DepositionDec 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 7A03 Fab heavy chain
L: 7A03 Fab light chain
E: 7A03 Fab heavy chain
F: 7A03 Fab light chain


Theoretical massNumber of molelcules
Total (without water)91,3384
Polymers91,3384
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-52 kcal/mol
Surface area35770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.483, 137.866, 62.983
Angle α, β, γ (deg.)90.00, 108.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 7A03 Fab heavy chain


Mass: 23995.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 7A03 Fab light chain


Mass: 21673.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG-1000, 0.2 M Lithium sulfate, phosphate-citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.06→34.47 Å / Num. obs: 15508 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.91 / Net I/σ(I): 3.37
Reflection shellResolution: 3.06→3.11 Å / Num. unique obs: 3080 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PHASERphasing
autoPROCdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→34.47 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3236 744 4.81 %
Rwork0.2644 --
obs0.2672 15483 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.06→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6199 0 0 0 6199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.478
X-RAY DIFFRACTIONf_dihedral_angle_d10.632260
X-RAY DIFFRACTIONf_chiral_restr0.042963
X-RAY DIFFRACTIONf_plane_restr0.0051112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.290.37811540.32192906X-RAY DIFFRACTION99
3.29-3.620.37071470.29542936X-RAY DIFFRACTION100
3.62-4.150.35621510.27142957X-RAY DIFFRACTION100
4.15-5.220.2711400.23052964X-RAY DIFFRACTION100
5.22-34.470.28851520.24372976X-RAY DIFFRACTION100

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