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- PDB-4x11: JC Polyomavirus genotype 3 VP1 in complex with GD1a oligosaccharide -

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Basic information

Entry
Database: PDB / ID: 4x11
TitleJC Polyomavirus genotype 3 VP1 in complex with GD1a oligosaccharide
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / beta-sandwich / jelly-roll / viral major capsid protein
Function / homology
Function and homology information


T=7 icosahedral viral capsid / virion attachment to host cell / 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
: / N-acetyl-alpha-neuraminic acid / Capsid protein VP1
Similarity search - Component
Biological speciesJC polyomavirus type 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 2.0Jan 31, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / 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 / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Feb 14, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 2.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Major capsid protein
E: Major capsid protein
A: Major capsid protein
C: Major capsid protein
D: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,56932
Polymers150,1695
Non-polymers2,40027
Water14,574809
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29590 Å2
ΔGint-96 kcal/mol
Surface area44100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.140, 96.100, 127.950
Angle α, β, γ (deg.)90.00, 110.18, 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: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASPASPAC31 - 5114 - 34
21THRTHRASPASPBA31 - 5114 - 34
31THRTHRASPASPCD31 - 5114 - 34
41THRTHRASPASPDE31 - 5114 - 34
51THRTHRASPASPEB31 - 5114 - 34
12PROPROILEILEAC72 - 8555 - 68
22PROPROILEILEBA72 - 8555 - 68
32PROPROILEILECD72 - 8555 - 68
42PROPROILEILEDE72 - 8555 - 68
52PROPROILEILEEB72 - 8555 - 68
13METMETSERSERAC101 - 12284 - 105
23METMETSERSERBA101 - 12284 - 105
33METMETSERSERCD101 - 12284 - 105
43METMETSERSERDE101 - 12284 - 105
53METMETSERSEREB101 - 12284 - 105
14GLYGLYTHRTHRAC124 - 162107 - 145
24GLYGLYTHRTHRBA124 - 162107 - 145
34GLYGLYTHRTHRCD124 - 162107 - 145
44GLYGLYTHRTHRDE124 - 162107 - 145
54GLYGLYTHRTHREB124 - 162107 - 145
15GLNGLNLEULEUAC177 - 189160 - 172
25GLNGLNLEULEUBA177 - 189160 - 172
35GLNGLNLEULEUCD177 - 189160 - 172
45GLNGLNLEULEUDE177 - 189160 - 172
55GLNGLNLEULEUEB177 - 189160 - 172
16ALAALATHRTHRAC194 - 205177 - 188
26ALAALATHRTHRBA194 - 205177 - 188
36ALAALATHRTHRCD194 - 205177 - 188
46ALAALATHRTHRDE194 - 205177 - 188
56ALAALATHRTHREB194 - 205177 - 188
17LEULEUTHRTHRAC251 - 263234 - 246
27LEULEUTHRTHRBA251 - 263234 - 246
37LEULEUTHRTHRCD251 - 263234 - 246
47LEULEUTHRTHRDE251 - 263234 - 246
57LEULEUTHRTHREB251 - 263234 - 246
18SERSERVALVALAC266 - 280249 - 263
28SERSERVALVALBA266 - 280249 - 263
38SERSERVALVALCD266 - 280249 - 263
48SERSERVALVALDE266 - 280249 - 263
58SERSERVALVALEB266 - 280249 - 263
19ASNASNASPASPAC207 - 238190 - 221
29ASNASNASPASPBA207 - 238190 - 221
39ASNASNASPASPCD207 - 238190 - 221
49ASNASNASPASPDE207 - 238190 - 221
59ASNASNASPASPEB207 - 238190 - 221
110PHEPHEASPASPAC240 - 249223 - 232
210PHEPHEASPASPBA240 - 249223 - 232
310PHEPHEASPASPCD240 - 249223 - 232
410PHEPHEASPASPDE240 - 249223 - 232
510PHEPHEASPASPEB240 - 249223 - 232

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.451519, 0.845478, 0.285126), (-0.848758, 0.308422, 0.429519), (0.27521, -0.435939, 0.856865)11.17803, 19.80594, -5.59297
3given(-0.4413, 0.519369, 0.731786), (-0.531224, -0.808442, 0.253421), (0.723225, -0.276908, 0.632667)31.76874, 14.2523, -15.88011
4given(-0.439507, -0.527521, 0.727018), (0.514447, -0.811317, -0.277687), (0.736327, 0.251967, 0.627961)32.88104, -9.09463, -16.85301
5given(0.450289, -0.847718, 0.280383), (0.845695, 0.304183, -0.43849), (0.286428, 0.434566, 0.85388)13.22305, -17.86649, -7.04965

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Components

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Protein / Sugars , 2 types, 8 molecules BEACD

#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: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 833 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
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: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 12, 2013
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 81125 / % possible obs: 98.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 24.9 Å2 / Net I/σ(I): 16.1
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.5

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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: 2.3→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.6 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20148 3823 5 %RANDOM
Rwork0.1608 ---
obs0.16285 71920 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.879 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0.53 Å2
2--1.99 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9855 0 149 809 10813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910218
X-RAY DIFFRACTIONr_bond_other_d0.0010.029479
X-RAY DIFFRACTIONr_angle_refined_deg1.321.96213887
X-RAY DIFFRACTIONr_angle_other_deg0.754321820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50751273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61324.315445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.599151601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3251554
X-RAY DIFFRACTIONr_chiral_restr0.0790.21588
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022317
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_it1.3113.2655107
X-RAY DIFFRACTIONr_mcbond_other1.313.2655106
X-RAY DIFFRACTIONr_mcangle_it1.9174.3876366
X-RAY DIFFRACTIONr_mcangle_other1.9184.3886367
X-RAY DIFFRACTIONr_scbond_it2.574.0645111
X-RAY DIFFRACTIONr_scbond_other2.5674.0645111
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5375.1657519
X-RAY DIFFRACTIONr_long_range_B_refined5.1857.18411636
X-RAY DIFFRACTIONr_long_range_B_other5.1887.18511637
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 / Number: 2780 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.190.5
Bmedium positional0.280.5
Cmedium positional0.220.5
Dmedium positional0.210.5
Emedium positional0.190.5
Amedium thermal1.522
Bmedium thermal1.592
Cmedium thermal1.572
Dmedium thermal1.592
Emedium thermal1.582
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 251 -
Rwork0.226 5298 -
obs--99.95 %
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)
11.26850.13990.48510.99310.23441.06220.0107-0.1418-0.00860.08860.04820.06660.0064-0.455-0.0590.0120.0175-0.00880.23170.01340.075311.76948.870639.116
20.58820.00470.25021.0888-0.02360.9071-0.0206-0.03510.03490.08740.0179-0.0589-0.0614-0.07260.00270.0130.01630.00080.09560.00390.035318.39389.739239.8941
31.2865-0.06572.32630.17140.19517.67060.088-0.0234-0.16850.09450.02390.03310.31290.1266-0.11190.0846-0.02940.00280.08740.00540.099527.9009-25.212337.8643
41.1955-0.24640.13470.43240.08541.0203-0.0053-0.06690.00370.00270.02490.0560.054-0.0707-0.01960.0122-0.0224-0.00060.0535-0.01180.043523.0146-16.882935.6802
51.0157-0.60350.71431.4106-2.904810.9604-0.014-0.04340.00140.18280.0468-0.0979-0.16890.2609-0.03280.10740.00890.00070.09230.01090.144865.111-19.99639.8265
60.97380.3280.28920.6032-0.02711.0026-0.00270.0316-0.0372-0.0433-0.01170.01810.0530.03920.01440.0064-0.00030.00110.0644-0.02710.016148.0577-19.338622.0892
70.6517-0.49280.13130.813-0.2280.8788-0.01180.12920.0364-0.0277-0.0255-0.0514-0.05590.10190.03730.0137-0.0297-0.00180.09950.0230.016158.58516.395316.0435
81.8864-0.40371.49270.6512-0.39252.81060.0849-0.0134-0.11010.04220.0083-0.02840.08870.0057-0.09330.0264-0.019-0.0140.03040.01060.030357.05710.126725.0654
93.92320.25034.57180.39630.24946.2357-0.1598-0.16770.23760.119-0.0198-0.0637-0.3695-0.06140.17960.12790.0231-0.0080.10780.02990.133935.143830.135636.696
100.9064-0.0757-0.04420.2196-0.1841.0278-0.0442-0.06390.07180.04960.0037-0.018-0.1258-0.00530.04060.05510.0194-0.02040.06390.02230.0538.771524.826127.6976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 84
2X-RAY DIFFRACTION2A85 - 288
3X-RAY DIFFRACTION3B25 - 61
4X-RAY DIFFRACTION4B62 - 288
5X-RAY DIFFRACTION5C25 - 43
6X-RAY DIFFRACTION6C44 - 288
7X-RAY DIFFRACTION7D25 - 218
8X-RAY DIFFRACTION8D219 - 288
9X-RAY DIFFRACTION9E24 - 59
10X-RAY DIFFRACTION10E60 - 288

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