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- PDB-7pa9: JC polyomavirus VP1 in complex with Fab 98D3 -

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Basic information

Entry
Database: PDB / ID: 7pa9
TitleJC polyomavirus VP1 in complex with Fab 98D3
Components
  • Fab 98D3 VH
  • Fab 98D3 VL
  • 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: 2.75 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: 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: Fab 98D3 VH
LLL: Fab 98D3 VL
MMM: Fab 98D3 VH
NNN: Fab 98D3 VL
OOO: Fab 98D3 VH
PPP: Fab 98D3 VL
QQQ: Fab 98D3 VH
RRR: Fab 98D3 VL
SSS: Fab 98D3 VL
TTT: Fab 98D3 VH
UUU: Fab 98D3 VL
VVV: Fab 98D3 VH
WWW: Fab 98D3 VL
XXX: Fab 98D3 VH
YYY: Fab 98D3 VH
ZZZ: Fab 98D3 VL
aaa: Fab 98D3 VL
bbb: Fab 98D3 VH
ccc: Fab 98D3 VH
ddd: Fab 98D3 VL


Theoretical massNumber of molelcules
Total (without water)971,32930
Polymers971,32930
Non-polymers00
Water6,233346
1
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: Fab 98D3 VH
LLL: Fab 98D3 VL
MMM: Fab 98D3 VH
NNN: Fab 98D3 VL
OOO: Fab 98D3 VH
PPP: Fab 98D3 VL
QQQ: Fab 98D3 VH
RRR: Fab 98D3 VL
ccc: Fab 98D3 VH
ddd: Fab 98D3 VL


Theoretical massNumber of molelcules
Total (without water)485,66415
Polymers485,66415
Non-polymers00
Water27015
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
SSS: Fab 98D3 VL
TTT: Fab 98D3 VH
UUU: Fab 98D3 VL
VVV: Fab 98D3 VH
WWW: Fab 98D3 VL
XXX: Fab 98D3 VH
YYY: Fab 98D3 VH
ZZZ: Fab 98D3 VL
aaa: Fab 98D3 VL
bbb: Fab 98D3 VH


Theoretical massNumber of molelcules
Total (without water)485,66415
Polymers485,66415
Non-polymers00
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.970, 202.310, 251.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: 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
#2: Antibody
Fab 98D3 VH


Mass: 43939.391 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
Fab 98D3 VL


Mass: 23117.639 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Ammonium tartrate dibasic 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: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 225685 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.99 / Net I/σ(I): 11.99
Reflection shellResolution: 2.75→2.85 Å / Num. unique obs: 16539 / CC1/2: 0.68

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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: 2.75→49.153 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.88 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.177 / Average fsc free: 0.863 / Average fsc work: 0.8829 / Cross valid method: FREE R-VALUE / ESU R: 1.287 / ESU R Free: 0.359
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2628 11285 5 %
Rwork0.2068 214400 -
all0.21 --
obs-225685 99.957 %
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: 45.959 Å2
Baniso -1Baniso -2Baniso -3
1--0.966 Å20 Å20 Å2
2--5.19 Å2-0 Å2
3----4.224 Å2
Refinement stepCycle: LAST / Resolution: 2.75→49.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50676 0 0 346 51022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01351864
X-RAY DIFFRACTIONr_bond_other_d0.0360.01746099
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.64470637
X-RAY DIFFRACTIONr_angle_other_deg2.4411.569107317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70956607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29822.942401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.705157987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.46715236
X-RAY DIFFRACTIONr_chiral_restr0.0660.26861
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0258429
X-RAY DIFFRACTIONr_gen_planes_other0.0060.0210675
X-RAY DIFFRACTIONr_nbd_refined0.1960.28540
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.243006
X-RAY DIFFRACTIONr_nbtor_refined0.1650.223993
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.222643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.21213
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0820.233
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.222
X-RAY DIFFRACTIONr_nbd_other0.2320.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2390.24
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_mcbond_it2.8634.98126623
X-RAY DIFFRACTIONr_mcbond_other2.8634.98126622
X-RAY DIFFRACTIONr_mcangle_it4.5847.45733165
X-RAY DIFFRACTIONr_mcangle_other4.5847.45733166
X-RAY DIFFRACTIONr_scbond_it2.7295.07325241
X-RAY DIFFRACTIONr_scbond_other2.7295.07325242
X-RAY DIFFRACTIONr_scangle_it4.4167.55137472
X-RAY DIFFRACTIONr_scangle_other4.4167.55137472
X-RAY DIFFRACTIONr_lrange_it7.97392.626201779
X-RAY DIFFRACTIONr_lrange_other7.97392.631201734
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
2.75-2.8210.398250.331156630.334164940.6770.71399.96360.305
2.821-2.8980.3418060.3153240.302161320.7640.77299.98760.265
2.898-2.9820.3267820.281148470.283156320.7950.80899.98080.244
2.982-3.0730.3227640.261145150.264152820.8090.83699.98040.222
3.073-3.1740.2947370.24140050.243147440.8450.86699.98640.204
3.174-3.2850.3057120.227135370.231142500.8490.88199.9930.192
3.285-3.4080.2886910.221131190.224138140.8710.89899.9710.19
3.408-3.5470.2826650.214126380.217133050.8830.91299.9850.188
3.547-3.7030.2636370.206121160.208127550.90.91999.98430.182
3.703-3.8830.2476130.192116300.195122430.9130.931000.169
3.883-4.0920.2385800.171110260.175116070.9220.94399.99140.149
4.092-4.3380.225520.158104900.161110450.9360.95199.97280.136
4.338-4.6350.195200.14298780.145104010.9540.96399.97120.124
4.635-5.0030.2134840.15292050.15496910.9410.95699.97940.132
5.003-5.4740.2184480.16485090.16789570.9420.9541000.143
5.474-6.1110.2614080.19777520.281600.910.9341000.171
6.111-7.0380.2733600.19868450.20272050.9180.9351000.171
7.038-8.5760.2383090.19558650.19761750.9310.9499.98380.175
8.576-11.9480.2072440.19246290.19348780.9480.95399.89750.185
11.948-49.1530.3271480.3128070.31129580.8840.88699.89860.309

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