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- PDB-3nxd: JC polyomavirus VP1 in complex with LSTc -

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Basic information

Entry
Database: PDB / ID: 3nxd
TitleJC polyomavirus VP1 in complex with LSTc
ComponentsMajor capsid protein VP1
KeywordsVIRAL PROTEIN / beta-sandwich with jelly roll topology / major capsid protein
Function / homology
Function and homology information


T=7 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / 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
Major capsid protein VP1
Similarity search - Component
Biological speciesJC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNeu, U. / Stroeh, L.J. / Stehle, T.
CitationJournal: Cell Host Microbe / Year: 2010
Title: Structure-function analysis of the human JC polyomavirus establishes the LSTc pentasaccharide as a functional receptor motif.
Authors: Neu, U. / Maginnis, M.S. / Palma, A.S. / Stroh, L.J. / Nelson, C.D. / Feizi, T. / Atwood, W.J. / Stehle, T.
History
DepositionJul 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 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 / 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
C: Major capsid protein VP1
B: Major capsid protein VP1
A: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,21018
Polymers150,3795
Non-polymers2,83113
Water17,042946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28750 Å2
ΔGint-92 kcal/mol
Surface area47410 Å2
MethodPISA
2
C: Major capsid protein VP1
B: Major capsid protein VP1
A: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
hetero molecules

C: Major capsid protein VP1
B: Major capsid protein VP1
A: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,42036
Polymers300,75910
Non-polymers5,66126
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area60310 Å2
ΔGint-188 kcal/mol
Surface area92020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.670, 96.340, 128.220
Angle α, β, γ (deg.)90.00, 110.28, 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: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVALAC26 - 299 - 12
21VALVALVALVALBB26 - 299 - 12
31VALVALVALVALCA26 - 299 - 12
41VALVALVALVALDD26 - 299 - 12
51VALVALVALVALEE26 - 299 - 12
12PROPROILEILEAC78 - 8561 - 68
22PROPROILEILEBB78 - 8561 - 68
32PROPROILEILECA78 - 8561 - 68
42PROPROILEILEDD78 - 8561 - 68
52PROPROILEILEEE78 - 8561 - 68
13THRTHRASPASPAC31 - 5114 - 34
23THRTHRASPASPBB31 - 5114 - 34
33THRTHRASPASPCA31 - 5114 - 34
43THRTHRASPASPDD31 - 5114 - 34
53THRTHRASPASPEE31 - 5114 - 34
14HISHISPHEPHEAC53 - 5736 - 40
24HISHISPHEPHEBB53 - 5736 - 40
34HISHISPHEPHECA53 - 5736 - 40
44HISHISPHEPHEDD53 - 5736 - 40
54HISHISPHEPHEEE53 - 5736 - 40
15LEULEUPROPROAC87 - 8870 - 71
25LEULEUPROPROBB87 - 8870 - 71
35LEULEUPROPROCA87 - 8870 - 71
45LEULEUPROPRODD87 - 8870 - 71
55LEULEUPROPROEE87 - 8870 - 71
16METMETSERSERAC101 - 12284 - 105
26METMETSERSERBB101 - 12284 - 105
36METMETSERSERCA101 - 12284 - 105
46METMETSERSERDD101 - 12284 - 105
56METMETSERSEREE101 - 12284 - 105
17GLYGLYTHRTHRAC124 - 162107 - 145
27GLYGLYTHRTHRBB124 - 162107 - 145
37GLYGLYTHRTHRCA124 - 162107 - 145
47GLYGLYTHRTHRDD124 - 162107 - 145
57GLYGLYTHRTHREE124 - 162107 - 145
18TYRTYRPROPROAC164 - 165147 - 148
28TYRTYRPROPROBB164 - 165147 - 148
38TYRTYRPROPROCA164 - 165147 - 148
48TYRTYRPROPRODD164 - 165147 - 148
58TYRTYRPROPROEE164 - 165147 - 148
19ASNASNTHRTHRAC173 - 175156 - 158
29ASNASNTHRTHRBB173 - 175156 - 158
39ASNASNTHRTHRCA173 - 175156 - 158
49ASNASNTHRTHRDD173 - 175156 - 158
59ASNASNTHRTHREE173 - 175156 - 158
110GLNGLNLEULEUAC177 - 189160 - 172
210GLNGLNLEULEUBB177 - 189160 - 172
310GLNGLNLEULEUCA177 - 189160 - 172
410GLNGLNLEULEUDD177 - 189160 - 172
510GLNGLNLEULEUEE177 - 189160 - 172
111ALAALATHRTHRAC194 - 205177 - 188
211ALAALATHRTHRBB194 - 205177 - 188
311ALAALATHRTHRCA194 - 205177 - 188
411ALAALATHRTHRDD194 - 205177 - 188
511ALAALATHRTHREE194 - 205177 - 188
112LEULEUTHRTHRAC251 - 263234 - 246
212LEULEUTHRTHRBB251 - 263234 - 246
312LEULEUTHRTHRCA251 - 263234 - 246
412LEULEUTHRTHRDD251 - 263234 - 246
512LEULEUTHRTHREE251 - 263234 - 246
113SERSERVALVALAC266 - 280249 - 263
213SERSERVALVALBB266 - 280249 - 263
313SERSERVALVALCA266 - 280249 - 263
413SERSERVALVALDD266 - 280249 - 263
513SERSERVALVALEE266 - 280249 - 263
114ASNASNASPASPAC207 - 238190 - 221
214ASNASNASPASPBB207 - 238190 - 221
314ASNASNASPASPCA207 - 238190 - 221
414ASNASNASPASPDD207 - 238190 - 221
514ASNASNASPASPEE207 - 238190 - 221
115GLYGLYPROPROAC167 - 171150 - 154
215GLYGLYPROPROBB167 - 171150 - 154
315GLYGLYPROPROCA167 - 171150 - 154
415GLYGLYPROPRODD167 - 171150 - 154
515GLYGLYPROPROEE167 - 171150 - 154
116PHEPHEASPASPAC240 - 249223 - 232
216PHEPHEASPASPBB240 - 249223 - 232
316PHEPHEASPASPCA240 - 249223 - 232
416PHEPHEASPASPDD240 - 249223 - 232
516PHEPHEASPASPEE240 - 249223 - 232
117LEULEUVALVALAC282 - 287265 - 270
217LEULEUVALVALBB282 - 287265 - 270
317LEULEUVALVALCA282 - 287265 - 270
417LEULEUVALVALDD282 - 287265 - 270
517LEULEUVALVALEE282 - 287265 - 270

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Components

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


Mass: 30075.861 Da / Num. of mol.: 5 / Fragment: UNP residues 23-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Strain: Mad-1 / Gene: VP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03089
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-2-4/a4-b1_b3-c1_c4-d1_d6-e2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 946 / 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: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12 % PEG 3,350, 0.1 M HEPES, 0.2 M KSCN, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2010
RadiationMonochromator: Bartels monochromator (DCCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 115472 / Num. obs: 114938 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8302 / % possible all: 97.5

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.27 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.138 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20608 5769 5 %RANDOM
Rwork0.17818 ---
obs0.17958 109159 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20.11 Å2
2---0.01 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2→35.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10109 0 190 946 11245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02210634
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.981.97414475
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60451331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72924.396480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.812151732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0781562
X-RAY DIFFRACTIONr_chiral_restr0.0650.21648
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218036
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.16656511
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.935710599
X-RAY DIFFRACTIONr_scbond_it1.44154123
X-RAY DIFFRACTIONr_scangle_it2.22473854
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: 1630 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.115
Bloose positional0.135
Cloose positional0.135
Dloose positional0.115
Eloose positional0.15
Aloose thermal0.9510
Bloose thermal1.6510
Cloose thermal1.0510
Dloose thermal1.1410
Eloose thermal1.3810
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 422 -
Rwork0.213 7842 -
obs--97.22 %

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