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- PDB-6mqr: Vaccine-elicited NHP FP-targeting neutralizing antibody 0PV-a.01 ... -

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Basic information

Entry
Database: PDB / ID: 6mqr
TitleVaccine-elicited NHP FP-targeting neutralizing antibody 0PV-a.01 in complex with FP (residue 512-519)
Components
  • (antibody 0PV-A.01 Fab ...) x 2
  • HIV fusion peptide residue 512-519
KeywordsIMMUNE SYSTEM / HIV / neutralizing / NHP / FP / Fusion Peptide / vaccine
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsXu, K. / Wang, Y. / Kwong, P.D.
CitationJournal: Cell / Year: 2019
Title: Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.
Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / ...Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Gwo-Yu Chuang / Cara W Chao / Ying Gu / Alexander J Jafari / Mark K Louder / Sijy O'Dell / Ariana P Rowshan / Elise G Viox / Yiran Wang / Chang W Choi / Martin M Corcoran / Angela R Corrigan / Venkata P Dandey / Edward T Eng / Hui Geng / Kathryn E Foulds / Yicheng Guo / Young D Kwon / Bob Lin / Kevin Liu / Rosemarie D Mason / Martha C Nason / Tiffany Y Ohr / Li Ou / Reda Rawi / Edward K Sarfo / Arne Schön / John P Todd / Shuishu Wang / Hui Wei / Winston Wu / / James C Mullikin / Robert T Bailer / Nicole A Doria-Rose / Gunilla B Karlsson Hedestam / Diana G Scorpio / Julie Overbaugh / Jesse D Bloom / Bridget Carragher / Clinton S Potter / Lawrence Shapiro / Peter D Kwong / John R Mascola /
Abstract: The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be ...The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization.
History
DepositionOct 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2019Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: antibody 0PV-A.01 Fab heavy chain
L: antibody 0PV-A.01 Fab light chain
A: HIV fusion peptide residue 512-519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0776
Polymers48,8443
Non-polymers2323
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-67 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.250, 159.250, 159.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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Protein/peptide , 1 types, 1 molecules A

#3: Protein/peptide HIV fusion peptide residue 512-519


Mass: 732.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS

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Antibody , 2 types, 2 molecules HL

#1: Antibody antibody 0PV-A.01 Fab heavy chain


Mass: 24624.574 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 antibody 0PV-A.01 Fab light chain


Mass: 23486.994 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)

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Non-polymers , 3 types, 134 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.17 M NH4CH3CO2, 0.085 M acetate pH 4.6, 25.5% w/v PEG 4000, and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 24735 / % possible obs: 99.6 % / Redundancy: 8.5 % / Biso Wilson estimate: 50.31 Å2 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.059 / Rrim(I) all: 0.165 / Χ2: 1.502 / Net I/σ(I): 4.7 / Num. measured all: 210137
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.499.50.87212410.8050.2970.9220.56100
2.49-2.549.40.75712290.8270.260.8010.557100
2.54-2.599.20.65412270.8690.2270.6930.596100
2.59-2.6490.60612080.8740.2130.6430.628100
2.64-2.78.60.51912530.8850.1880.5530.7100
2.7-2.767.80.43912260.9170.1640.470.67599.8
2.76-2.838.60.40212160.9270.1450.4280.772100
2.83-2.99.80.37912180.9350.1280.40.907100
2.9-2.999.80.32712480.9540.110.3451.094100
2.99-3.099.70.27912360.9590.0950.2951.301100
3.09-3.29.40.2512280.9670.0870.2651.532100
3.2-3.329.20.21812250.9730.0770.2321.837100
3.32-3.488.80.19412570.9790.070.2062.18699.9
3.48-3.668.30.16712290.9820.0630.1792.434100
3.66-3.897.40.15412510.980.0620.1672.53599.8
3.89-4.196.20.1212290.9850.0520.1312.5897.5
4.19-4.616.90.11112200.9850.0470.1212.94698.9
4.61-5.286.60.10212350.9870.0450.1122.6798.4
5.28-6.657.90.09312560.9910.0370.12.13999.2
6.65-507.70.08313030.9950.0330.0893.08699.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→42.561 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.14
RfactorNum. reflection% reflection
Rfree0.2085 1256 5.08 %
Rwork0.1752 --
obs0.1769 24733 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→42.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 11 131 3562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143511
X-RAY DIFFRACTIONf_angle_d1.3724787
X-RAY DIFFRACTIONf_dihedral_angle_d13.642079
X-RAY DIFFRACTIONf_chiral_restr0.073548
X-RAY DIFFRACTIONf_plane_restr0.007608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4497-2.54780.28191550.22392569X-RAY DIFFRACTION100
2.5478-2.66370.28271420.20982585X-RAY DIFFRACTION100
2.6637-2.80410.2741390.20462612X-RAY DIFFRACTION100
2.8041-2.97980.25731220.20382597X-RAY DIFFRACTION100
2.9798-3.20980.23871290.19532638X-RAY DIFFRACTION100
3.2098-3.53260.23421390.18262602X-RAY DIFFRACTION100
3.5326-4.04350.21031470.16972571X-RAY DIFFRACTION99
4.0435-5.0930.16231330.1412621X-RAY DIFFRACTION99
5.093-42.56780.18051500.17132682X-RAY DIFFRACTION99

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