[English] 日本語
Yorodumi
- PDB-4x11: JC Polyomavirus genotype 3 VP1 in complex with GD1a oligosaccharide -

+
Open data


ID or keywords:

Loading...

-
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 / 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
: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more