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- PDB-6pdr: Vaccine-elicited murine FP-targeting antibody vFP25.18 in complex... -

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Basic information

Entry
Database: PDB / ID: 6pdr
TitleVaccine-elicited murine FP-targeting antibody vFP25.18 in complex with HIV fusion peptide (residue 512-519)
Components
  • HIV fusion peptide residue 512-519
  • antibody vFP25.18 heavy chain
  • antibody vFP25.18 light chain
KeywordsIMMUNE SYSTEM / HIV / neutralizing / antibody / murine / FP / Fusion Peptide / vaccine / mouse
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 speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.555 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 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: antibody vFP25.18 light chain
H: antibody vFP25.18 heavy chain
A: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)48,2143
Polymers48,2143
Non-polymers00
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-32 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.124, 51.189, 75.258
Angle α, β, γ (deg.)90.000, 114.470, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-491-

HOH

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Components

#1: Antibody antibody vFP25.18 light chain


Mass: 24162.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody antibody vFP25.18 heavy chain


Mass: 23317.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH 8.0, 28% PEG 4000

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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 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 61868 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.047 / Rrim(I) all: 0.087 / Χ2: 2.068 / Net I/σ(I): 9.5 / Num. measured all: 214926
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.612.60.46229210.7080.3340.5730.71994.8
1.61-1.643.10.4430790.7920.2910.5290.76699.4
1.64-1.673.30.41731310.7860.2670.4960.8398.9
1.67-1.73.40.3930910.8660.2450.4620.91999.9
1.7-1.743.50.35930780.8770.2230.4230.99799.2
1.74-1.783.50.32131250.9120.1970.3781.10299.6
1.78-1.823.60.28531050.910.1740.3351.28499.8
1.82-1.873.60.24431270.9380.1490.2871.46199.7
1.87-1.933.60.20130720.960.1230.2361.68699.4
1.93-1.993.60.17431310.9580.1080.2051.93199.1
1.99-2.063.70.15231210.9730.0930.1792.13898.9
2.06-2.143.60.13330460.9780.0820.1572.4198.4
2.14-2.243.60.1231020.9790.0750.1422.57598.4
2.24-2.363.70.10730560.9820.0660.1262.6297.9
2.36-2.513.60.09430700.9860.0590.1122.68597.9
2.51-2.73.60.08430880.9870.0530.12.83897.9
2.7-2.973.60.07630820.990.0480.093.16698.1
2.97-3.43.50.06631130.9910.0420.0793.43998.7
3.4-4.293.40.05631660.9920.0370.0673.38499.2
4.29-503.20.05531640.9910.0370.0673.68197

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.555→34.25 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.02
RfactorNum. reflection% reflection
Rfree0.1997 3034 4.9 %
Rwork0.1748 --
obs0.176 61865 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.22 Å2 / Biso mean: 27.7551 Å2 / Biso min: 14.35 Å2
Refinement stepCycle: final / Resolution: 1.555→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 0 489 3826
Biso mean---38.37 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043433
X-RAY DIFFRACTIONf_angle_d0.814684
X-RAY DIFFRACTIONf_chiral_restr0.053539
X-RAY DIFFRACTIONf_plane_restr0.005593
X-RAY DIFFRACTIONf_dihedral_angle_d10.2212373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.555-1.57930.3035690.25771468153753
1.5793-1.60520.27711460.23642715286197
1.6052-1.63290.28291350.228327082843100
1.6329-1.66260.26851300.22132707283799
1.6626-1.69460.25241370.213627542891100
1.6946-1.72920.2351510.20362713286499
1.7292-1.76680.25251510.205727622913100
1.7668-1.80790.24361230.198527382861100
1.8079-1.85310.2381600.204227322892100
1.8531-1.90320.21981500.19122738288899
1.9032-1.95920.22241310.18252759289099
1.9592-2.02240.21381140.17852712282699
2.0224-2.09470.20061430.18372726286999
2.0947-2.17850.21471550.18352696285198
2.1785-2.27770.20281530.18012700285398
2.2777-2.39770.2161190.18712735285498
2.3977-2.54790.21141540.18572696285098
2.5479-2.74450.19411480.1792701284998
2.7445-3.02060.18721560.17612732288898
3.0206-3.45730.18591320.1622760289299
3.4573-4.35440.17541200.15052806292699
4.3544-34.25850.18141570.16452773293097

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