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- PDB-9mif: Crystal structure of the VRC01-class antibody 9C09, derived from ... -

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Basic information

Entry
Database: PDB / ID: 9mif
TitleCrystal structure of the VRC01-class antibody 9C09, derived from GT1.1 vaccination, in complex with eOD-GT8
Components
  • 9C09 Fab heavy chain
  • 9C09 Fab light chain
  • eOD-GT8 engineered mutant of gp120
KeywordsIMMUNE SYSTEM / Fab / Germline-targeting vaccination / CD4bs mAb / HIV-1
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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, 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.
History
DepositionDec 12, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 9C09 Fab heavy chain
L: 9C09 Fab light chain
C: eOD-GT8 engineered mutant of gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7295
Polymers67,2873
Non-polymers4422
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.005, 74.440, 208.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 9C09 Fab heavy chain


Mass: 24512.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 9C09 Fab light chain


Mass: 22885.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein eOD-GT8 engineered mutant of gp120


Mass: 19889.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 20% PEG-300, 10% glycerol, 5% (w/v) PEG-8000, 0.1M Tris pH 8.5, final pH 8.7

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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: Sep 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.93→33.23 Å / Num. obs: 62686 / % possible obs: 99.4 % / Redundancy: 13.7 % / CC1/2: 0.99 / Net I/σ(I): 10.6
Reflection shellResolution: 1.93→1.96 Å / Num. unique obs: 2862 / CC1/2: 0.32

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PHASERphasing
autoPROCdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→33.23 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 3096 4.97 %
Rwork0.2334 --
obs0.2354 62338 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 28 126 4750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.128
X-RAY DIFFRACTIONf_dihedral_angle_d16.1211722
X-RAY DIFFRACTIONf_chiral_restr0.066723
X-RAY DIFFRACTIONf_plane_restr0.009826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.960.41731200.36932557X-RAY DIFFRACTION94
1.96-20.40351510.35712540X-RAY DIFFRACTION97
2-2.030.37831170.33682689X-RAY DIFFRACTION99
2.03-2.070.36331390.32362624X-RAY DIFFRACTION100
2.07-2.110.38811320.32152671X-RAY DIFFRACTION100
2.11-2.150.37421510.30652646X-RAY DIFFRACTION100
2.15-2.20.35031450.29922682X-RAY DIFFRACTION100
2.2-2.250.33421400.29392661X-RAY DIFFRACTION100
2.25-2.30.29721490.27872680X-RAY DIFFRACTION100
2.3-2.370.2851160.28552677X-RAY DIFFRACTION100
2.37-2.440.35821460.27592684X-RAY DIFFRACTION100
2.44-2.510.30781230.26382722X-RAY DIFFRACTION100
2.51-2.60.32741380.25522676X-RAY DIFFRACTION100
2.6-2.710.33191390.25752697X-RAY DIFFRACTION100
2.71-2.830.2991570.26452699X-RAY DIFFRACTION100
2.83-2.980.30071460.26342720X-RAY DIFFRACTION100
2.98-3.170.28011460.25712705X-RAY DIFFRACTION100
3.17-3.410.30811520.24152715X-RAY DIFFRACTION100
3.41-3.750.3021510.22892715X-RAY DIFFRACTION99
3.75-4.30.21811340.19942758X-RAY DIFFRACTION100
4.3-5.410.20731460.16342797X-RAY DIFFRACTION100
5.41-33.230.19491580.18262927X-RAY DIFFRACTION100

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