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- PDB-7pa6: JC polyomavirus VP1 in complex with scFv 27C11 -

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Basic information

Entry
Database: PDB / ID: 7pa6
TitleJC polyomavirus VP1 in complex with scFv 27C11
Components
  • Major capsid protein VP1
  • scFv 27C11 antibody heavy chain
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 / host cell nucleus / virion attachment to host cell / 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 speciesHomo sapiens (human)
JC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHarprecht, C. / Stroeh, L.J. / Nagel, F. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
KKK: scFv 27C11 antibody heavy chain
LLL: scFv 27C11 antibody heavy chain
MMM: scFv 27C11 antibody heavy chain
NNN: scFv 27C11 antibody heavy chain
OOO: scFv 27C11 antibody heavy chain
PPP: scFv 27C11 antibody heavy chain
QQQ: scFv 27C11 antibody heavy chain
RRR: scFv 27C11 antibody heavy chain
SSS: scFv 27C11 antibody heavy chain
TTT: scFv 27C11 antibody heavy chain
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: Major capsid protein VP1
GGG: Major capsid protein VP1
HHH: Major capsid protein VP1
III: Major capsid protein VP1
JJJ: Major capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)570,49720
Polymers570,49720
Non-polymers00
Water40,5162249
1
KKK: scFv 27C11 antibody heavy chain
LLL: scFv 27C11 antibody heavy chain
MMM: scFv 27C11 antibody heavy chain
NNN: scFv 27C11 antibody heavy chain
OOO: scFv 27C11 antibody heavy chain
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


  • defined by author&software
  • Evidence: gel filtration
  • 285 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)285,24810
Polymers285,24810
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34990 Å2
ΔGint-165 kcal/mol
Surface area85520 Å2
MethodPISA
2
PPP: scFv 27C11 antibody heavy chain
QQQ: scFv 27C11 antibody heavy chain
RRR: scFv 27C11 antibody heavy chain
SSS: scFv 27C11 antibody heavy chain
TTT: scFv 27C11 antibody heavy chain
FFF: Major capsid protein VP1
GGG: Major capsid protein VP1
HHH: Major capsid protein VP1
III: Major capsid protein VP1
JJJ: Major capsid protein VP1


  • defined by author&software
  • 285 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)285,24810
Polymers285,24810
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34900 Å2
ΔGint-164 kcal/mol
Surface area85610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.090, 96.110, 190.410
Angle α, β, γ (deg.)100.913, 93.012, 113.835
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
scFv 27C11 antibody heavy chain


Mass: 26973.826 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#2: Protein
Major capsid protein VP1 / Major structural protein VP1


Mass: 30075.861 Da / Num. of mol.: 10 / Fragment: UNP residues 23-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P03089
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2249 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM potassium phosphate monohydrate / potassium phosphate dihydrate pH 6.0, 10% (w/v) PEG 8000, 686 mM NaCl

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.9→48.5 Å / Num. obs: 465782 / % possible obs: 89.9 % / Redundancy: 3.83 % / CC1/2: 0.99 / Rrim(I) all: 0.1 / Net I/σ(I): 9.27
Reflection shellResolution: 1.9→2.01 Å / Mean I/σ(I) obs: 1.15 / Num. unique obs: 252959 / CC1/2: 0.5 / Rrim(I) all: 1.19

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXG, 4KQ3

3nxg

4kq3


Resolution: 1.9→47.809 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.183 / Average fsc free: 0.8975 / Average fsc work: 0.9075 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2164 23290 5 %
Rwork0.1835 442492 -
all0.185 --
obs-465782 97.59 %
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: 36.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.146 Å21.239 Å2-0.33 Å2
2---0.626 Å2-0.557 Å2
3----0.758 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37890 0 0 2249 40139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01339019
X-RAY DIFFRACTIONr_bond_other_d0.0370.01734360
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.64653144
X-RAY DIFFRACTIONr_angle_other_deg2.361.5779899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7454993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25322.3931851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.666156044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.82415208
X-RAY DIFFRACTIONr_chiral_restr0.0730.25146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0244139
X-RAY DIFFRACTIONr_gen_planes_other0.0090.028267
X-RAY DIFFRACTIONr_nbd_refined0.1950.26607
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2310.233500
X-RAY DIFFRACTIONr_nbtor_refined0.1770.218952
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.218416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.22232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1380.224
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.226
X-RAY DIFFRACTIONr_nbd_other0.2290.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.29
X-RAY DIFFRACTIONr_mcbond_it3.2483.74619901
X-RAY DIFFRACTIONr_mcbond_other3.2493.74519900
X-RAY DIFFRACTIONr_mcangle_it4.5165.58924813
X-RAY DIFFRACTIONr_mcangle_other4.5165.5924814
X-RAY DIFFRACTIONr_scbond_it4.3814.04119118
X-RAY DIFFRACTIONr_scbond_other4.3814.04119119
X-RAY DIFFRACTIONr_scangle_it6.3735.90928301
X-RAY DIFFRACTIONr_scangle_other6.3735.90928301
X-RAY DIFFRACTIONr_lrange_it8.46371.097161247
X-RAY DIFFRACTIONr_lrange_other8.45271.051159686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.32916530.30731404X-RAY DIFFRACTION93.6088
1.949-2.0030.28916660.26131652X-RAY DIFFRACTION96.6355
2.003-2.0610.26516220.24130812X-RAY DIFFRACTION96.8989
2.061-2.1240.25815750.22229929X-RAY DIFFRACTION97.013
2.124-2.1940.25415320.21529099X-RAY DIFFRACTION97.2289
2.194-2.2710.24814840.20428207X-RAY DIFFRACTION97.3475
2.271-2.3570.23614340.19327240X-RAY DIFFRACTION97.5937
2.357-2.4530.2313860.1926326X-RAY DIFFRACTION97.7289
2.453-2.5620.23113260.18425207X-RAY DIFFRACTION97.9258
2.562-2.6870.23412740.18824208X-RAY DIFFRACTION98.1209
2.687-2.8320.23312140.1923058X-RAY DIFFRACTION98.2473
2.832-3.0040.22211490.18521825X-RAY DIFFRACTION98.4403
3.004-3.2110.22510790.1820508X-RAY DIFFRACTION98.6158
3.211-3.4680.21310050.17819089X-RAY DIFFRACTION98.7323
3.468-3.7990.2019270.1717624X-RAY DIFFRACTION98.9439
3.799-4.2480.1768420.14715990X-RAY DIFFRACTION99.1342
4.248-4.9040.1477430.13114117X-RAY DIFFRACTION99.2586
4.904-6.0050.1946290.16411947X-RAY DIFFRACTION99.3757
6.005-8.4890.214850.1899218X-RAY DIFFRACTION99.5282
8.489-47.8090.2132650.2065033X-RAY DIFFRACTION98.954

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