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- PDB-7pa8: JC polyomavirus VP1 in complex with Fab 27C2 -

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Basic information

Entry
Database: PDB / ID: 7pa8
TitleJC polyomavirus VP1 in complex with Fab 27C2
Components
  • Fab 27C2 heavy chain
  • Fab 27C2 light chain
  • Major capsid protein VP1
KeywordsVIRAL PROTEIN / antibody / polyomavirus / VP1 / neutralization
Function / homology
Function and homology information


T=7 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein VP1
Similarity search - Component
Biological speciesJC polyomavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsStroeh, L.J. / Harprecht, C. / Freytag, J. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: To Be Published
Title: Structural characterization of human neutralizing antibodies against JC and BK polyomavirus
Authors: Harprecht, C. / Stroeh, L.J. / Senn, L. / O'Hara, B.A. / Nagel, F. / Freytag, J. / Stiehrof, Y.D. / Atwood, W.J. / Combaluzier, B. / Stehle, T.
History
DepositionJul 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Major capsid protein VP1
BBB: Major capsid protein VP1
CCC: Major capsid protein VP1
DDD: Major capsid protein VP1
EEE: Major capsid protein VP1
FFF: Fab 27C2 light chain
GGG: Fab 27C2 light chain
HHH: Fab 27C2 heavy chain
III: Fab 27C2 light chain
JJJ: Fab 27C2 heavy chain
KKK: Fab 27C2 light chain
LLL: Fab 27C2 heavy chain
MMM: Fab 27C2 light chain
NNN: Fab 27C2 heavy chain
YYY: Fab 27C2 heavy chain


Theoretical massNumber of molelcules
Total (without water)479,14215
Polymers479,14215
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.070, 110.440, 158.210
Angle α, β, γ (deg.)90.000, 93.115, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Major capsid protein VP1 / Major structural protein VP1


Mass: 30075.861 Da / Num. of mol.: 5 / Fragment: UNP residues 23-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03089
#2: Antibody
Fab 27C2 light chain


Mass: 22227.623 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
Fab 27C2 heavy chain


Mass: 43524.938 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium citrate tribasic pH 7.0, 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.15→49.007 Å / Num. obs: 81593 / % possible obs: 99.6 % / Redundancy: 7.03 % / CC1/2: 0.98 / Rrim(I) all: 0.32 / Net I/σ(I): 9.49
Reflection shellResolution: 3.15→3.34 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 12843 / CC1/2: 0.53 / Rrim(I) all: 1.05

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXG, 5BVJ

3nxg

5bvj


Resolution: 3.15→49.007 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.872 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.193 / Average fsc free: 0.8945 / Average fsc work: 0.9052 / Cross valid method: FREE R-VALUE / ESU R Free: 0.405
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2407 4079 5.001 %
Rwork0.212 77491 -
all0.213 --
obs-81570 99.682 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.462 Å2
Baniso -1Baniso -2Baniso -3
1-6.326 Å2-0 Å20.325 Å2
2---2.023 Å20 Å2
3----4.313 Å2
Refinement stepCycle: LAST / Resolution: 3.15→49.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21270 0 0 0 21270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01321774
X-RAY DIFFRACTIONr_bond_other_d0.0370.01719268
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.64229671
X-RAY DIFFRACTIONr_angle_other_deg2.4441.56944756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85952803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41122.653965
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.348153202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.89115104
X-RAY DIFFRACTIONr_chiral_restr0.0690.22872
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0224617
X-RAY DIFFRACTIONr_gen_planes_other0.0080.024507
X-RAY DIFFRACTIONr_nbd_refined0.2070.23734
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2240.217795
X-RAY DIFFRACTIONr_nbtor_refined0.1680.210335
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.29343
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2401
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.050.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2730.213
X-RAY DIFFRACTIONr_nbd_other0.2930.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.25
X-RAY DIFFRACTIONr_mcbond_it4.6895.03611341
X-RAY DIFFRACTIONr_mcbond_other4.6895.03611340
X-RAY DIFFRACTIONr_mcangle_it7.4037.52514101
X-RAY DIFFRACTIONr_mcangle_other7.4037.52514102
X-RAY DIFFRACTIONr_scbond_it4.6284.92310433
X-RAY DIFFRACTIONr_scbond_other4.6284.92410434
X-RAY DIFFRACTIONr_scangle_it7.2857.37915570
X-RAY DIFFRACTIONr_scangle_other7.2857.37915571
X-RAY DIFFRACTIONr_lrange_it11.54990.88684636
X-RAY DIFFRACTIONr_lrange_other11.54990.88684637
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.15-3.2320.352880.3354750.33159840.7460.76296.30680.312
3.232-3.320.3272930.27855720.2858690.7980.82599.93180.262
3.32-3.4150.3012820.26153560.26356380.8410.8511000.241
3.415-3.520.2652790.24353000.24455790.8730.8821000.223
3.52-3.6350.2362670.21650670.21753350.9140.91699.98130.194
3.635-3.7620.2542590.21449130.21651720.9010.9131000.192
3.762-3.9030.2342500.19547630.19750130.9160.9351000.174
3.903-4.0610.2262420.18945910.19148330.9230.9351000.167
4.061-4.240.1982300.16943820.17146130.9450.95199.97830.15
4.24-4.4460.1782220.1642050.16144270.9570.9581000.141
4.446-4.6840.1872110.15540060.15642170.9550.9631000.137
4.684-4.9650.1831990.15837960.15939950.9520.9581000.139
4.965-5.3040.2011890.17135800.17337690.940.9541000.151
5.304-5.7240.2781750.20433290.20835040.8950.9241000.18
5.724-6.2610.2481620.22730850.22832490.9210.91799.93840.2
6.261-6.9860.2811480.22227970.22529450.9030.9231000.198
6.986-8.040.2291300.22124780.22126080.9250.9291000.199
8.04-9.7810.2311120.22921190.22922310.930.9331000.215
9.781-13.5650.242880.24616720.24617610.9370.92799.94320.239
13.565-49.0070.337530.36310060.36210620.850.8699.71750.361

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