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- PDB-7paa: JC polyomavirus VP1 in complex with scFv 29B1 -

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Basic information

Entry
Database: PDB / ID: 7paa
TitleJC polyomavirus VP1 in complex with scFv 29B1
Components
  • Major capsid protein VP1
  • scFv 29B1
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 speciesHomo sapiens (human)
JC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.102 Å
AuthorsHarprecht, C. / Stroeh, L.J. / 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 1.2Nov 6, 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
ZZZ: scFv 29B1
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
KKK: scFv 29B1
aaa: scFv 29B1
bbb: scFv 29B1
ccc: scFv 29B1
ddd: scFv 29B1
eee: scFv 29B1
WWW: scFv 29B1
XXX: scFv 29B1
YYY: scFv 29B1


Theoretical massNumber of molelcules
Total (without water)570,23620
Polymers570,23620
Non-polymers00
Water41423
1
ZZZ: scFv 29B1
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
KKK: scFv 29B1
WWW: scFv 29B1
XXX: scFv 29B1
YYY: scFv 29B1


Theoretical massNumber of molelcules
Total (without water)285,11810
Polymers285,11810
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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
aaa: scFv 29B1
bbb: scFv 29B1
ccc: scFv 29B1
ddd: scFv 29B1
eee: scFv 29B1


Theoretical massNumber of molelcules
Total (without water)285,11810
Polymers285,11810
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.127, 172.530, 159.710
Angle α, β, γ (deg.)90.000, 104.527, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
scFv 29B1


Mass: 26947.736 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#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 (E. coli) / References: UniProt: P03089
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M trimethanolamine N-oxide, 0.1 M Tris (pH 8.5), 20% PEG 2000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→48.5 Å / Num. obs: 129715 / % possible obs: 99.8 % / Redundancy: 7.06 % / CC1/2: 0.99 / Rrim(I) all: 0.23 / Net I/σ(I): 10.37
Reflection shellResolution: 3→3.18 Å / Mean I/σ(I) obs: 2.21 / Num. unique obs: 20801 / CC1/2: 0.72 / Rrim(I) all: 0.95

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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: 3.102→48.507 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.869 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.195 / Average fsc free: 0.9053 / Average fsc work: 0.9098 / Cross valid method: FREE R-VALUE / ESU R Free: 0.441
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.24 5881 5 %
Rwork0.2246 111728 -
all0.225 --
obs-117609 99.926 %
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: 44.614 Å2
Baniso -1Baniso -2Baniso -3
1-1.331 Å20 Å2-0.675 Å2
2--0.489 Å20 Å2
3----1.296 Å2
Refinement stepCycle: LAST / Resolution: 3.102→48.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37635 0 0 23 37658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01338800
X-RAY DIFFRACTIONr_bond_other_d0.0360.01734362
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.64752867
X-RAY DIFFRACTIONr_angle_other_deg2.3941.57379813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21854978
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27922.0931954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.381155967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.84615240
X-RAY DIFFRACTIONr_chiral_restr0.0490.25038
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0244244
X-RAY DIFFRACTIONr_gen_planes_other0.0040.028344
X-RAY DIFFRACTIONr_nbd_refined0.1810.25838
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.231328
X-RAY DIFFRACTIONr_nbtor_refined0.1580.218054
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.217013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2606
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0180.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.350.270
X-RAY DIFFRACTIONr_nbd_other0.4180.2129
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3480.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2080.21
X-RAY DIFFRACTIONr_mcbond_it2.6594.94119756
X-RAY DIFFRACTIONr_mcbond_other2.6594.94119755
X-RAY DIFFRACTIONr_mcangle_it4.147.40424648
X-RAY DIFFRACTIONr_mcangle_other4.147.40424649
X-RAY DIFFRACTIONr_scbond_it1.4744.85919044
X-RAY DIFFRACTIONr_scbond_other1.4744.85919045
X-RAY DIFFRACTIONr_scangle_it2.5177.27428173
X-RAY DIFFRACTIONr_scangle_other2.5177.27428174
X-RAY DIFFRACTIONr_lrange_it4.38554.27139515
X-RAY DIFFRACTIONr_lrange_other4.38354.27239515
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
3.102-3.1830.3354320.32382060.32386780.7960.80499.53910.306
3.183-3.2690.3034220.28880150.28984370.850.8531000.269
3.269-3.3640.2784100.27277840.27381950.880.87899.98780.25
3.364-3.4670.2543970.2675530.2679500.8930.8941000.237
3.467-3.580.2663830.25172760.25276590.8950.8971000.229
3.58-3.7050.2633750.24871150.24974910.8950.89999.98660.223
3.705-3.8440.2643610.23368510.23572120.8950.9151000.207
3.844-40.2463490.22166270.22369770.9130.92499.98570.194
4-4.1760.2063330.20163220.20266550.9410.941000.176
4.176-4.3790.2063170.18460210.18563380.9410.9471000.161
4.379-4.6130.1883030.17157650.17260690.9570.9699.98350.149
4.613-4.890.1842880.17454790.17557670.9580.9571000.149
4.89-5.2240.1862700.17451290.17553990.9540.9581000.148
5.224-5.6370.2292520.19747910.19850440.9360.94599.98020.168
5.637-6.1670.2322340.22444320.22446670.9330.93499.97860.19
6.167-6.8810.2252100.22839950.22842070.9280.92799.95250.195
6.881-7.9190.2231860.20835450.20937310.9390.9411000.178
7.919-9.6350.241590.20930210.2131800.9240.9421000.189
9.635-13.3650.2491260.22423770.22625030.9290.9381000.213
13.365-48.5070.344750.32414240.32515000.8520.84399.93330.32

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