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- PDB-9mpb: Crystal structure of the HIV V2-apex-targeting antibody RM038, de... -

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Basic information

Entry
Database: PDB / ID: 9mpb
TitleCrystal structure of the HIV V2-apex-targeting antibody RM038, derived from macaque ApexGT6 immunization
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: 1.98 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


Theoretical massNumber of molelcules
Total (without water)49,4322
Polymers49,4322
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-22 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.251, 66.512, 53.405
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody Fab heavy chain


Mass: 25336.232 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: 24095.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca (macaques) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Imidazole pH 8.0 1.0 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 40445 / % possible obs: 94.1 % / Redundancy: 5.9 % / Biso Wilson estimate: 26.33 Å2 / CC1/2: 0.999 / Net I/σ(I): 28.72
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 1989 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→41.58 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 1997 4.94 %
Rwork0.1855 --
obs0.1873 40421 93.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 0 165 3549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022
X-RAY DIFFRACTIONf_angle_d1.653
X-RAY DIFFRACTIONf_dihedral_angle_d19.8651243
X-RAY DIFFRACTIONf_chiral_restr0.108521
X-RAY DIFFRACTIONf_plane_restr0.014608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.19421260.16832674X-RAY DIFFRACTION91
2.03-2.090.23141610.17552752X-RAY DIFFRACTION96
2.09-2.150.21751340.17682816X-RAY DIFFRACTION96
2.15-2.220.25061530.18892815X-RAY DIFFRACTION97
2.22-2.30.26241460.19952791X-RAY DIFFRACTION96
2.3-2.390.2541440.20042773X-RAY DIFFRACTION96
2.39-2.50.27041330.20212692X-RAY DIFFRACTION92
2.5-2.630.23851410.19082705X-RAY DIFFRACTION93
2.63-2.790.23941460.20312831X-RAY DIFFRACTION97
2.79-3.010.25231450.2072833X-RAY DIFFRACTION97
3.01-3.310.2151440.19692756X-RAY DIFFRACTION94
3.31-3.790.20721300.19332506X-RAY DIFFRACTION86
3.79-4.780.1961440.15682673X-RAY DIFFRACTION90
4.78-41.580.19481500.1752807X-RAY DIFFRACTION93

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