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- PDB-9pz3: Crystal structure of HIV Apex targeting neutralizing antibody Q12... -

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Basic information

Entry
Database: PDB / ID: 9pz3
TitleCrystal structure of HIV Apex targeting neutralizing antibody Q12BBM-069
Components
  • Fab Q12BBM-069 heavy chain
  • Fab Q12BBM-069 light chain
KeywordsIMMUNE SYSTEM / HIV / Apex neutralizing antibody
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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) United States
CitationJournal: Nature / Year: 2026
Title: Vaccination generates broadly cross-neutralizing antibodies to the HIV Env apex.
Authors: Javier Guenaga / Monika Ádori / Shridhar Bale / Swastik Phulera / Ioannis Zygouras / Fabian-Alexander Schleich / Xaquin Castro Dopico / Sashank Agrawal / Miyo Ota / Richard Wilson / Jocelyn ...Authors: Javier Guenaga / Monika Ádori / Shridhar Bale / Swastik Phulera / Ioannis Zygouras / Fabian-Alexander Schleich / Xaquin Castro Dopico / Sashank Agrawal / Miyo Ota / Richard Wilson / Jocelyn Cluff / Tamar Dzvelaia / Marco Mandolesi / Wen-Hsin Lee / Agnes A Walsh / Mariane B Melo / Laurent Verkoczy / Darrell J Irvine / Martin Corcoran / Ian A Wilson / Diane Carnathan / Guido Silvestri / Andrew B Ward / Gabriel Ozorowski / Gunilla B Karlsson Hedestam / Richard T Wyatt /
Abstract: As a chronically replicating virus, HIV has evolved extreme sequence variability and effective shielding of functionally constrained spike protein determinants by host-derived glycans. Broadly ...As a chronically replicating virus, HIV has evolved extreme sequence variability and effective shielding of functionally constrained spike protein determinants by host-derived glycans. Broadly neutralizing antibodies, although rare, can be isolated from people living with HIV, revealing conserved envelope glycoprotein (Env) sites as key targets for vaccine development. One such target is the apex of the Env spike. Here we identify a vaccination strategy using heterologous HIV Env trimers covalently coupled to liposomes for multivalent display that resulted in the elicitation of cross-neutralizing HIV serum antibody responses in all trimer-liposome-immunized non-human primates. Critically, we isolated monoclonal antibodies from multiple macaques that cross-neutralize divergent HIV clinical isolates. High-resolution cryogenic electron microscopy structural analyses of monoclonal antibodies from four different macaques demonstrate that they target the Env trimer apex in a manner highly similar to that of the human-infection-elicited, apex-directed broadly neutralizing antibody PG9, representing a substantial advance in HIV vaccine development.
History
DepositionAug 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab Q12BBM-069 heavy chain
B: Fab Q12BBM-069 light chain


Theoretical massNumber of molelcules
Total (without water)48,3212
Polymers48,3212
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-23 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.419, 72.502, 175.215
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 Fab Q12BBM-069 heavy chain


Mass: 25164.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody Fab Q12BBM-069 light chain


Mass: 23155.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
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: 3.71 Å3/Da / Density % sol: 66.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.26 M NH4-sulfate, 0.1 M cacodylate pH 6.5

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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: 0.91972 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91972 Å / Relative weight: 1
ReflectionResolution: 1.787→33.497 Å / Num. obs: 68718 / % possible obs: 99.6 % / Redundancy: 13.8 % / CC1/2: 0.999 / Net I/σ(I): 13.9
Reflection shellResolution: 1.787→1.818 Å / Num. unique obs: 3389 / CC1/2: 0.392

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→33.497 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 3407 4.96 %
Rwork0.2111 --
obs0.2125 68711 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→33.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3355 0 0 221 3576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133432
X-RAY DIFFRACTIONf_angle_d1.3234672
X-RAY DIFFRACTIONf_dihedral_angle_d16.0581221
X-RAY DIFFRACTIONf_chiral_restr0.091531
X-RAY DIFFRACTIONf_plane_restr0.01598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.810.34121450.31482696X-RAY DIFFRACTION99
1.81-1.840.33851190.30472659X-RAY DIFFRACTION99
1.84-1.870.31391430.29372662X-RAY DIFFRACTION99
1.87-1.90.32781450.27882684X-RAY DIFFRACTION99
1.9-1.930.25851410.26372643X-RAY DIFFRACTION99
1.93-1.970.27531420.24652699X-RAY DIFFRACTION99
1.97-20.24971360.24182682X-RAY DIFFRACTION100
2-2.050.27581290.23072690X-RAY DIFFRACTION99
2.05-2.090.2681290.22392715X-RAY DIFFRACTION99
2.09-2.140.25051440.22462687X-RAY DIFFRACTION100
2.14-2.190.26291460.22332702X-RAY DIFFRACTION100
2.19-2.250.29991330.22662712X-RAY DIFFRACTION100
2.25-2.320.27621380.22172668X-RAY DIFFRACTION100
2.32-2.390.25291490.22292713X-RAY DIFFRACTION100
2.39-2.480.25441340.22382727X-RAY DIFFRACTION100
2.48-2.580.25381580.22812707X-RAY DIFFRACTION100
2.58-2.690.27471340.23082739X-RAY DIFFRACTION100
2.69-2.840.2641580.22352701X-RAY DIFFRACTION100
2.84-3.010.24011440.23312744X-RAY DIFFRACTION100
3.01-3.250.25731630.23772732X-RAY DIFFRACTION100
3.25-3.570.23911400.20982766X-RAY DIFFRACTION100
3.57-4.090.21891390.19142805X-RAY DIFFRACTION100
4.09-5.150.1871320.15272832X-RAY DIFFRACTION100
5.15-33.4970.19711660.18882939X-RAY DIFFRACTION100

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