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- PDB-4x0y: JC polyomavirus VP1 from a genotype 3 strain -

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Basic information

Entry
Database: PDB / ID: 4x0y
TitleJC polyomavirus VP1 from a genotype 3 strain
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / beta-sandwich / jelly-roll / viral capsid protein
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Capsid protein VP1
Similarity search - Component
Biological speciesJC polyomavirus type 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStroh, L.J. / Stehle, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: J.Virol. / Year: 2015
Title: The Greater Affinity of JC Polyomavirus Capsid for alpha 2,6-Linked Lactoseries Tetrasaccharide c than for Other Sialylated Glycans Is a Major Determinant of Infectivity.
Authors: Stroh, L.J. / Maginnis, M.S. / Blaum, B.S. / Nelson, C.D. / Neu, U. / Gee, G.V. / O'Hara, B.A. / Motamedi, N. / DiMaio, D. / Atwood, W.J. / Stehle, T.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 2.0Jan 31, 2018Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,00434
Polymers150,1695
Non-polymers1,83529
Water22,9511274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29040 Å2
ΔGint-80 kcal/mol
Surface area44270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.480, 96.830, 128.220
Angle α, β, γ (deg.)90.00, 110.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASPASPAA31 - 5114 - 34
21THRTHRASPASPBB31 - 5114 - 34
31THRTHRASPASPCC31 - 5114 - 34
41THRTHRASPASPDD31 - 5114 - 34
51THRTHRASPASPEE31 - 5114 - 34
12PROPROILEILEAA78 - 8561 - 68
22PROPROILEILEBB78 - 8561 - 68
32PROPROILEILECC78 - 8561 - 68
42PROPROILEILEDD78 - 8561 - 68
52PROPROILEILEEE78 - 8561 - 68
13METMETSERSERAA101 - 12284 - 105
23METMETSERSERBB101 - 12284 - 105
33METMETSERSERCC101 - 12284 - 105
43METMETSERSERDD101 - 12284 - 105
53METMETSERSEREE101 - 12284 - 105
14GLYGLYTHRTHRAA124 - 162107 - 145
24GLYGLYTHRTHRBB124 - 162107 - 145
34GLYGLYTHRTHRCC124 - 162107 - 145
44GLYGLYTHRTHRDD124 - 162107 - 145
54GLYGLYTHRTHREE124 - 162107 - 145
15GLNGLNLEULEUAA177 - 189160 - 172
25GLNGLNLEULEUBB177 - 189160 - 172
35GLNGLNLEULEUCC177 - 189160 - 172
45GLNGLNLEULEUDD177 - 189160 - 172
55GLNGLNLEULEUEE177 - 189160 - 172
16ALAALATHRTHRAA194 - 205177 - 188
26ALAALATHRTHRBB194 - 205177 - 188
36ALAALATHRTHRCC194 - 205177 - 188
46ALAALATHRTHRDD194 - 205177 - 188
56ALAALATHRTHREE194 - 205177 - 188
17LEULEUTHRTHRAA251 - 263234 - 246
27LEULEUTHRTHRBB251 - 263234 - 246
37LEULEUTHRTHRCC251 - 263234 - 246
47LEULEUTHRTHRDD251 - 263234 - 246
57LEULEUTHRTHREE251 - 263234 - 246
18SERSERVALVALAA266 - 280249 - 263
28SERSERVALVALBB266 - 280249 - 263
38SERSERVALVALCC266 - 280249 - 263
48SERSERVALVALDD266 - 280249 - 263
58SERSERVALVALEE266 - 280249 - 263
19ASNASNASPASPAA207 - 238190 - 221
29ASNASNASPASPBB207 - 238190 - 221
39ASNASNASPASPCC207 - 238190 - 221
49ASNASNASPASPDD207 - 238190 - 221
59ASNASNASPASPEE207 - 238190 - 221
110PHEPHEASPASPAA240 - 249223 - 232
210PHEPHEASPASPBB240 - 249223 - 232
310PHEPHEASPASPCC240 - 249223 - 232
410PHEPHEASPASPDD240 - 249223 - 232
510PHEPHEASPASPEE240 - 249223 - 232

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.4482, 0.848563, 0.281172), (-0.850315, 0.307642, 0.42699), (0.275828, -0.430462, 0.859431)11.36076, 19.84624, -5.68668
3given(-0.445032, 0.522259, 0.727456), (-0.531108, -0.807974, 0.255152), (0.721021, -0.272807, 0.63695)31.93232, 14.21638, -15.91972
4given(-0.4464, -0.527892, 0.722535), (0.516757, -0.811282, -0.273466), (0.73054, 0.2513, 0.634948)33.2321, -9.29441, -16.8096
5given(0.447671, -0.849486, 0.279221), (0.849137, 0.305979, -0.430516), (0.280281, 0.429826, 0.858308)13.27333, -18.23019, -6.88059

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Components

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


Mass: 30033.795 Da / Num. of mol.: 5 / Fragment: UNP residues 23-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus type 3 / Gene: VP1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P90498
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1274 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 187337 / % possible obs: 99.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 9.08
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.6 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Cootmodel building
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXG

3nxg


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.334 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17752 9417 5 %RANDOM
Rwork0.15683 ---
obs0.15788 177920 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.339 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å20.16 Å2
2---0.19 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9938 0 111 1274 11323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910458
X-RAY DIFFRACTIONr_bond_other_d0.0010.029717
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.95514246
X-RAY DIFFRACTIONr_angle_other_deg0.78322417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43651354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83224.594468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.893151665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7291554
X-RAY DIFFRACTIONr_chiral_restr0.0880.21617
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022395
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1251.8455230
X-RAY DIFFRACTIONr_mcbond_other1.121.8445229
X-RAY DIFFRACTIONr_mcangle_it1.6792.5746544
X-RAY DIFFRACTIONr_mcangle_other1.6792.5746545
X-RAY DIFFRACTIONr_scbond_it2.2082.5065228
X-RAY DIFFRACTIONr_scbond_other2.2082.5065228
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1073.2417669
X-RAY DIFFRACTIONr_long_range_B_refined6.8176.10212484
X-RAY DIFFRACTIONr_long_range_B_other6.8166.10412485
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1082medium positional0.080.5
B1082medium positional0.090.5
C1082medium positional0.080.5
D1082medium positional0.090.5
E1082medium positional0.070.5
A1641loose positional0.175
B1641loose positional0.275
C1641loose positional0.175
D1641loose positional0.185
E1641loose positional0.25
A1082medium thermal0.572
B1082medium thermal0.642
C1082medium thermal0.92
D1082medium thermal0.742
E1082medium thermal0.62
A1641loose thermal1.0110
B1641loose thermal0.9910
C1641loose thermal1.4710
D1641loose thermal110
E1641loose thermal0.9510
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 682 -
Rwork0.258 12932 -
obs--98.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.34570.55092.6440.95161.02585.92740.0917-0.237-0.02280.1566-0.01290.02350.0912-0.2709-0.07880.0980.02070.00630.1988-0.01370.075314.05174.487748.5637
20.45420.0250.11961.1982-0.06310.48220.016-0.0060.04140.03290.0028-0.0087-0.0438-0.0552-0.01880.04640.0109-0.00630.1301-0.00430.017617.21710.442938.5027
30.9236-0.18871.1990.3870.22035.32130.0518-0.106-0.07510.11750.0143-0.00150.28640.0381-0.06620.1241-0.0352-0.01370.12560.0150.062728.5817-25.650139.5771
40.9998-0.2546-0.0920.45420.17740.6849-0.0003-0.0520.01060.02090.01620.04680.0169-0.0509-0.01580.0705-0.0224-0.01960.0843-0.00110.017122.892-16.899135.6143
50.63350.25160.06670.496-0.07660.86820.00050.0255-0.0612-0.0219-0.0133-0.04460.0880.0910.01270.07330.0163-0.01150.0887-0.01190.011648.0702-21.37221.161
61.16490.04840.70080.8549-0.221.9878-0.0175-0.0786-0.00720.06070.01580.0429-0.0354-0.04250.00170.04040.0001-0.00420.0787-0.0040.004551.7282-15.239527.7119
71.1511-0.26290.97050.5055-0.29911.9158-0.0698-0.00750.03540.0871-0.0046-0.1115-0.11180.12420.07440.0794-0.0128-0.02070.12480.02570.035760.694513.546319.3772
80.3823-0.29340.08330.8836-0.00050.6302-0.02290.023-0.0176-0.0011-0.0014-0.0454-0.01490.05530.02440.0586-0.0224-0.01250.10230.0170.013457.97756.434218.6946
92.67630.2412.73560.37110.24354.2641-0.1077-0.23930.16310.09450.0054-0.0743-0.3017-0.14350.10220.16250.0176-0.02920.13640.00370.090935.006430.129936.8084
100.8378-0.0153-0.27790.2558-0.18450.9594-0.0169-0.0550.0440.03730.0117-0.0127-0.0916-0.00920.00520.0980.0136-0.03230.07640.00450.020139.003224.974427.9504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 57
2X-RAY DIFFRACTION2A58 - 288
3X-RAY DIFFRACTION3B25 - 59
4X-RAY DIFFRACTION4B60 - 288
5X-RAY DIFFRACTION5C25 - 207
6X-RAY DIFFRACTION6C208 - 288
7X-RAY DIFFRACTION7D25 - 65
8X-RAY DIFFRACTION8D66 - 288
9X-RAY DIFFRACTION9E24 - 59
10X-RAY DIFFRACTION10E60 - 288

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