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- PDB-6p8d: Vaccine-elicited murine FP-targeting antibody vFP6.01 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6p8d
TitleVaccine-elicited murine FP-targeting antibody vFP6.01 in complex with HIV fusion peptide (residue 512-519)
Components
  • Antibody VFP6.01 heavy chain
  • Antibody VFP6.01 light chain
  • HIV fusion peptide residue 512-519
KeywordsIMMUNE SYSTEM / HIV / neutralizing / antibody / murine / FP / Fusion Peptide / vaccine / mouse
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsXu, K. / Liu, K. / Wang, Y. / Kwong, P.D.
CitationJournal: To Be Published
Title: Modular recognition of antigens provides a mechanism that improves vaccine-elicited antibody-class frequencies
Authors: Xu, K. / Liu, K. / Wang, Y. / Kwong, P.D.
History
DepositionJun 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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: Antibody VFP6.01 heavy chain
B: Antibody VFP6.01 light chain
D: Antibody VFP6.01 heavy chain
E: Antibody VFP6.01 light chain
F: HIV fusion peptide residue 512-519
C: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)97,2296
Polymers97,2296
Non-polymers00
Water2,450136
1
A: Antibody VFP6.01 heavy chain
B: Antibody VFP6.01 light chain
C: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)48,6143
Polymers48,6143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-35 kcal/mol
Surface area19440 Å2
MethodPISA
2
D: Antibody VFP6.01 heavy chain
E: Antibody VFP6.01 light chain
F: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)48,6143
Polymers48,6143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-37 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.311, 119.777, 185.503
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 Antibody VFP6.01 heavy chain


Mass: 23580.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Antibody VFP6.01 light chain


Mass: 24300.912 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#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.: 136 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.5M NaCl, 0.2M Li2SO4, 0.1M acetate pH 4.5

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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: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 53466 / % possible obs: 95.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.042 / Rrim(I) all: 0.101 / Χ2: 1.085 / Net I/σ(I): 6.4 / Num. measured all: 275912
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1440.48121530.8850.2280.5350.55578.5
2.14-2.184.30.46121660.9140.2130.510.57279.9
2.18-2.224.50.42624180.9180.1960.4710.61186.4
2.22-2.264.50.43625570.9150.2020.4830.60892.7
2.26-2.314.80.38226360.9450.1730.4210.61596.1
2.31-2.3750.35527110.960.1590.390.62797.9
2.37-2.425.10.35827120.9570.1610.3940.62599.1
2.42-2.495.30.2828100.9660.1250.3080.66399.8
2.49-2.565.40.27427270.9750.1230.3010.73299.9
2.56-2.655.50.23528140.9830.1050.2580.793100
2.65-2.745.50.20327070.9840.0910.2230.827100
2.74-2.855.60.16428180.9880.0740.180.919100
2.85-2.985.60.14227870.990.0640.1561.036100
2.98-3.145.60.12527730.9920.0570.1381.16399.9
3.14-3.335.60.10728220.9910.0490.1181.29399.7
3.33-3.595.50.08727800.9920.040.0961.54699
3.59-3.955.30.0827570.9940.0370.0891.92497.4
3.95-4.525.30.06526700.9960.030.0722.11193.5
4.52-5.75.20.05426500.9970.0250.061.84191.7
5.7-5050.04929980.9960.0240.0551.89197.1

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.102→41.252 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3093 2652 4.97 %
Rwork0.2705 --
obs0.2724 53354 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.102→41.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6689 0 0 136 6825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056845
X-RAY DIFFRACTIONf_angle_d0.8269311
X-RAY DIFFRACTIONf_dihedral_angle_d13.6474102
X-RAY DIFFRACTIONf_chiral_restr0.0521051
X-RAY DIFFRACTIONf_plane_restr0.0061185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1025-2.14070.42721020.34192115X-RAY DIFFRACTION76
2.1407-2.18190.37831350.31712174X-RAY DIFFRACTION80
2.1819-2.22640.35061190.31012449X-RAY DIFFRACTION87
2.2264-2.27480.34381380.31842497X-RAY DIFFRACTION93
2.2748-2.32770.35341370.31332686X-RAY DIFFRACTION96
2.3277-2.38590.35641440.3252708X-RAY DIFFRACTION98
2.3859-2.45040.35891330.3232767X-RAY DIFFRACTION99
2.4504-2.52250.35941360.31332757X-RAY DIFFRACTION100
2.5225-2.60390.36881490.32822773X-RAY DIFFRACTION100
2.6039-2.6970.37211540.30142760X-RAY DIFFRACTION100
2.697-2.80490.31161510.29822820X-RAY DIFFRACTION100
2.8049-2.93260.36151410.28992761X-RAY DIFFRACTION100
2.9326-3.08710.32591420.29322796X-RAY DIFFRACTION100
3.0871-3.28050.28911450.29032803X-RAY DIFFRACTION100
3.2805-3.53360.29981630.27762802X-RAY DIFFRACTION99
3.5336-3.8890.28251300.25132768X-RAY DIFFRACTION98
3.889-4.45120.28041380.23782669X-RAY DIFFRACTION94
4.4512-5.60580.27191200.21592665X-RAY DIFFRACTION91
5.6058-41.25950.28761750.25422932X-RAY DIFFRACTION97

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