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- PDB-6mqc: Vaccine-elicited NHP FP-targeting neutralizing antibody 0PV-c.01 ... -

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Basic information

Entry
Database: PDB / ID: 6mqc
TitleVaccine-elicited NHP FP-targeting neutralizing antibody 0PV-c.01 in complex with FP (residue 512-519)
Components
  • 0PV-C.01 antibody Fab heavy chain
  • 0PV-C.01 antibody Fab light chain
  • 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 / Resolution: 1.99 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 9, 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 1.3Oct 16, 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
A: 0PV-C.01 antibody Fab heavy chain
B: 0PV-C.01 antibody Fab light chain
H: 0PV-C.01 antibody Fab heavy chain
L: 0PV-C.01 antibody Fab light chain
C: HIV fusion peptide residue 512-519
D: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)98,0306
Polymers98,0306
Non-polymers00
Water8,017445
1
A: 0PV-C.01 antibody Fab heavy chain
B: 0PV-C.01 antibody Fab light chain
D: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)49,0153
Polymers49,0153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-30 kcal/mol
Surface area20250 Å2
MethodPISA
2
H: 0PV-C.01 antibody Fab heavy chain
L: 0PV-C.01 antibody Fab light chain
C: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)49,0153
Polymers49,0153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-33 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.122, 72.898, 169.305
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 0PV-C.01 antibody Fab heavy chain


Mass: 24398.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody 0PV-C.01 antibody Fab light chain


Mass: 23883.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV fusion peptide residue 512-519


Mass: 732.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaNO3 and 20% w/v PEG 3350

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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: Apr 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 62096 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 33.78 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.05 / Rrim(I) all: 0.122 / Χ2: 1.186 / Net I/σ(I): 6.1 / Num. measured all: 358892
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.035.10.80831050.7920.3810.8960.45499.9
2.03-2.075.20.7430520.8080.3470.8190.48199.9
2.07-2.115.30.65730600.8120.3060.7270.48899.9
2.11-2.155.20.55130950.8510.2580.610.52899.6
2.15-2.24.80.51230150.8460.2520.5730.54798.9
2.2-2.255.40.46130460.8960.2130.5090.61199.5
2.25-2.316.40.43631070.9240.1850.4750.64399.9
2.31-2.376.50.38330740.9470.1610.4160.665100
2.37-2.446.60.33230890.9510.1390.360.71999.9
2.44-2.526.40.27330920.9660.1160.2980.82799.9
2.52-2.616.40.23230870.970.0990.2530.934100
2.61-2.716.30.19530890.9770.0840.2121.01399.9
2.71-2.846.10.16731160.980.0730.1821.14899.9
2.84-2.995.90.13930740.9830.0630.1531.39199.6
2.99-3.175.10.11331000.9840.0550.1271.66898.8
3.17-3.4260.09631070.9910.0430.1061.88399.4
3.42-3.766.30.08331330.9920.0360.0912.15899.7
3.76-4.3160.07431580.9940.0330.0812.4299
4.31-5.435.40.06731390.9950.0310.0752.61398.7
5.43-505.30.06433580.9950.030.0712.25199.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 1.99→44.625 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 3060 4.93 %
Rwork0.1987 --
obs0.2005 62023 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→44.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 0 445 7169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066886
X-RAY DIFFRACTIONf_angle_d1.0539398
X-RAY DIFFRACTIONf_dihedral_angle_d13.4174096
X-RAY DIFFRACTIONf_chiral_restr0.061091
X-RAY DIFFRACTIONf_plane_restr0.0061203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9905-2.02160.27191040.25172170X-RAY DIFFRACTION80
2.0216-2.05470.3091070.24722647X-RAY DIFFRACTION100
2.0547-2.09010.28691510.24422715X-RAY DIFFRACTION100
2.0901-2.12820.2991290.2342632X-RAY DIFFRACTION100
2.1282-2.16910.31641120.23252706X-RAY DIFFRACTION99
2.1691-2.21340.24541320.22642679X-RAY DIFFRACTION99
2.2134-2.26150.27831580.21992640X-RAY DIFFRACTION100
2.2615-2.31410.26181720.22632641X-RAY DIFFRACTION100
2.3141-2.3720.24681280.22692714X-RAY DIFFRACTION100
2.372-2.43610.26341220.22742727X-RAY DIFFRACTION100
2.4361-2.50780.26811470.22132684X-RAY DIFFRACTION100
2.5078-2.58870.26731400.21692691X-RAY DIFFRACTION100
2.5887-2.68120.29561730.21122666X-RAY DIFFRACTION100
2.6812-2.78850.28191240.21572716X-RAY DIFFRACTION100
2.7885-2.91540.23571300.21462730X-RAY DIFFRACTION100
2.9154-3.06910.2661290.21212695X-RAY DIFFRACTION99
3.0691-3.26130.27971230.20012695X-RAY DIFFRACTION99
3.2613-3.51310.2451490.19452726X-RAY DIFFRACTION100
3.5131-3.86640.22121530.18052735X-RAY DIFFRACTION100
3.8664-4.42550.20661430.16782715X-RAY DIFFRACTION99
4.4255-5.57390.17861720.16422742X-RAY DIFFRACTION99
5.5739-44.63630.18961620.19762897X-RAY DIFFRACTION99

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