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- PDB-9mpc: Crystal structure of the HIV V2-apex-targeting antibody RM018 fro... -

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Basic information

Entry
Database: PDB / ID: 9mpc
TitleCrystal structure of the HIV V2-apex-targeting antibody RM018 from macaque
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 / Germline-targeting vaccination / ApexGT6 / V2-apex antibody
Biological speciesMacaca (macaques)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAgrawal, S. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
International AIDS Vaccine InitiativeINV-034657 United States
International AIDS Vaccine InitiativeINV-064772 United States
CitationJournal: Sci Immunol / Year: 2025
Title: HIV broadly neutralizing antibody precursors to the Apex epitope induced in nonhuman primates.
Authors: Krystal M Ma / Henry J Sutton / Payal P Pratap / Jon M Steichen / Diane Carnathan / James Quinn / Oleksandr Kalyuzhniy / Alessia Liguori / Sashank Agrawal / Sabyasachi Baboo / Patrick Madden ...Authors: Krystal M Ma / Henry J Sutton / Payal P Pratap / Jon M Steichen / Diane Carnathan / James Quinn / Oleksandr Kalyuzhniy / Alessia Liguori / Sashank Agrawal / Sabyasachi Baboo / Patrick Madden / Christopher A Cottrell / Jordan R Willis / Jeong-Hyun Lee / Elise Landais / Xiaozhen Hu / Parham Ramezani-Rad / Gabriel Ozorowski / Vanessa R Lewis / Jolene K Diedrich / Xiaoya Zhou / Tasha K Altheide / Nicole Phelps / Erik Georgeson / Nushin B Alavi / Danny Lu / Saman Eskandarzadeh / Michael Kubitz / Yumiko Adachi / Tina-Marie Mullen / Murillo Silva / Mariane B Melo / Sunny Himansu / Darrell J Irvine / Dennis R Burton / John R Yates / James C Paulson / Devin Sok / Ian A Wilson / Guido Silvestri / Andrew B Ward / Shane Crotty / William R Schief /
Abstract: An effective prophylactic HIV vaccine will likely need to induce broadly neutralizing antibodies (bnAbs). bnAbs to the Apex region of the HIV envelope glycoprotein (Env) are promising targets for ...An effective prophylactic HIV vaccine will likely need to induce broadly neutralizing antibodies (bnAbs). bnAbs to the Apex region of the HIV envelope glycoprotein (Env) are promising targets for vaccination because of their relatively low somatic hypermutation compared with other bnAbs. Most Apex bnAbs engage Env using an exceptionally long heavy-chain complementarity-determining region 3 (HCDR3) containing specific binding motifs, which reduces bnAb precursor frequency and makes priming of rare bnAb precursors a likely limiting step in the path to Apex bnAb induction. We found that adjuvanted protein or mRNA lipid nanoparticle (LNP) immunization of rhesus macaques with ApexGT6, an Env trimer engineered to bind Apex bnAb precursors, consistently induced Apex bnAb-related precursors with long HCDR3s bearing bnAb-like sequence motifs. Cryo-electron microscopy revealed that elicited Apex bnAb-related HCDR3s had structures combining elements of several prototype Apex bnAbs. These results achieve a critical HIV vaccine development milestone in outbred primates.
History
DepositionDec 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6385
Polymers48,3622
Non-polymers2763
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-21 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.702, 118.702, 194.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42

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Components

#1: Antibody Fab heavy chain


Mass: 25377.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca (macaques) / Production host: Homo sapiens (human)
#2: Antibody Fab light chain


Mass: 22984.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca (macaques) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
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: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.16 M Zinc acetate 0.108 M Sodium cacodylate pH 6.5 14.4% PEG 8000, 20% Glycerol

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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: Aug 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 10810 / % possible obs: 100 % / Redundancy: 15.5 % / CC1/2: 0.997 / Net I/σ(I): 7.6
Reflection shellResolution: 3.3→3.36 Å / Num. unique obs: 519 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→29.71 Å / SU ML: 0.4925 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 28.8901
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3073 1067 10 %
Rwork0.249 9601 -
obs0.2547 10668 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.02 Å2
Refinement stepCycle: LAST / Resolution: 3.3→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 18 0 3299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223374
X-RAY DIFFRACTIONf_angle_d0.49024604
X-RAY DIFFRACTIONf_chiral_restr0.0422528
X-RAY DIFFRACTIONf_plane_restr0.004581
X-RAY DIFFRACTIONf_dihedral_angle_d11.64721188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.450.37671270.33651143X-RAY DIFFRACTION97.47
3.45-3.630.31581280.3051156X-RAY DIFFRACTION97.49
3.63-3.860.34171320.28621182X-RAY DIFFRACTION98.21
3.86-4.150.3041320.25761185X-RAY DIFFRACTION98.8
4.16-4.570.25741330.22471198X-RAY DIFFRACTION99.18
4.57-5.230.29061330.20871195X-RAY DIFFRACTION99.03
5.23-6.570.32931370.24631236X-RAY DIFFRACTION99.64
6.58-29.710.29761450.23441306X-RAY DIFFRACTION99.59

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