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- PDB-3nxg: JC polyomavirus VP1 -

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Basic information

Entry
Database: PDB / ID: 3nxg
TitleJC polyomavirus VP1
ComponentsMajor capsid protein VP1
KeywordsVIRAL PROTEIN / beta-sandwich jelly roll
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 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: 1.95 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 1.2Feb 21, 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,15015
Polymers150,3795
Non-polymers77110
Water17,781987
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25230 Å2
ΔGint-112 kcal/mol
Surface area46430 Å2
MethodPISA
2
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
D: Major capsid protein VP1
E: Major capsid protein VP1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)302,30030
Polymers300,75910
Non-polymers1,54220
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area53460 Å2
ΔGint-223 kcal/mol
Surface area89860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.570, 96.020, 128.550
Angle α, β, γ (deg.)90.00, 110.44, 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
11VALVALVALVALAA26 - 299 - 12
21VALVALVALVALBB26 - 299 - 12
31VALVALVALVALCC26 - 299 - 12
41VALVALVALVALDD26 - 299 - 12
51VALVALVALVALEE26 - 299 - 12
12PROPROILEILEAA78 - 8561 - 68
22PROPROILEILEBB78 - 8561 - 68
32PROPROILEILECC78 - 8561 - 68
42PROPROILEILEDD78 - 8561 - 68
52PROPROILEILEEE78 - 8561 - 68
13THRTHRASPASPAA31 - 5114 - 34
23THRTHRASPASPBB31 - 5114 - 34
33THRTHRASPASPCC31 - 5114 - 34
43THRTHRASPASPDD31 - 5114 - 34
53THRTHRASPASPEE31 - 5114 - 34
14HISHISPHEPHEAA53 - 5736 - 40
24HISHISPHEPHEBB53 - 5736 - 40
34HISHISPHEPHECC53 - 5736 - 40
44HISHISPHEPHEDD53 - 5736 - 40
54HISHISPHEPHEEE53 - 5736 - 40
15LEULEUPROPROAA87 - 8870 - 71
25LEULEUPROPROBB87 - 8870 - 71
35LEULEUPROPROCC87 - 8870 - 71
45LEULEUPROPRODD87 - 8870 - 71
55LEULEUPROPROEE87 - 8870 - 71
16METMETSERSERAA101 - 12284 - 105
26METMETSERSERBB101 - 12284 - 105
36METMETSERSERCC101 - 12284 - 105
46METMETSERSERDD101 - 12284 - 105
56METMETSERSEREE101 - 12284 - 105
17GLYGLYTHRTHRAA124 - 162107 - 145
27GLYGLYTHRTHRBB124 - 162107 - 145
37GLYGLYTHRTHRCC124 - 162107 - 145
47GLYGLYTHRTHRDD124 - 162107 - 145
57GLYGLYTHRTHREE124 - 162107 - 145
18TYRTYRPROPROAA164 - 165147 - 148
28TYRTYRPROPROBB164 - 165147 - 148
38TYRTYRPROPROCC164 - 165147 - 148
48TYRTYRPROPRODD164 - 165147 - 148
58TYRTYRPROPROEE164 - 165147 - 148
19ASNASNTHRTHRAA173 - 175156 - 158
29ASNASNTHRTHRBB173 - 175156 - 158
39ASNASNTHRTHRCC173 - 175156 - 158
49ASNASNTHRTHRDD173 - 175156 - 158
59ASNASNTHRTHREE173 - 175156 - 158
110GLNGLNLEULEUAA177 - 189160 - 172
210GLNGLNLEULEUBB177 - 189160 - 172
310GLNGLNLEULEUCC177 - 189160 - 172
410GLNGLNLEULEUDD177 - 189160 - 172
510GLNGLNLEULEUEE177 - 189160 - 172
111ALAALATHRTHRAA194 - 205177 - 188
211ALAALATHRTHRBB194 - 205177 - 188
311ALAALATHRTHRCC194 - 205177 - 188
411ALAALATHRTHRDD194 - 205177 - 188
511ALAALATHRTHREE194 - 205177 - 188
112LEULEUTHRTHRAA251 - 263234 - 246
212LEULEUTHRTHRBB251 - 263234 - 246
312LEULEUTHRTHRCC251 - 263234 - 246
412LEULEUTHRTHRDD251 - 263234 - 246
512LEULEUTHRTHREE251 - 263234 - 246
113SERSERVALVALAA266 - 280249 - 263
213SERSERVALVALBB266 - 280249 - 263
313SERSERVALVALCC266 - 280249 - 263
413SERSERVALVALDD266 - 280249 - 263
513SERSERVALVALEE266 - 280249 - 263
114ASNASNASPASPAA207 - 238190 - 221
214ASNASNASPASPBB207 - 238190 - 221
314ASNASNASPASPCC207 - 238190 - 221
414ASNASNASPASPDD207 - 238190 - 221
514ASNASNASPASPEE207 - 238190 - 221
115GLYGLYPROPROAA167 - 171150 - 154
215GLYGLYPROPROBB167 - 171150 - 154
315GLYGLYPROPROCC167 - 171150 - 154
415GLYGLYPROPRODD167 - 171150 - 154
515GLYGLYPROPROEE167 - 171150 - 154
116PHEPHEASPASPAA240 - 249223 - 232
216PHEPHEASPASPBB240 - 249223 - 232
316PHEPHEASPASPCC240 - 249223 - 232
416PHEPHEASPASPDD240 - 249223 - 232
516PHEPHEASPASPEE240 - 249223 - 232
117LEULEUVALVALAA282 - 287265 - 270
217LEULEUVALVALBB282 - 287265 - 270
317LEULEUVALVALCC282 - 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: 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 987 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.23 %
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: 0.9506 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 30, 2008
RadiationMonochromator: Bartels monochromator (DCCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9506 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 124178 / Num. obs: 119853 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.9
Reflection shellResolution: 1.95→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.5 / % possible all: 91.7

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.83 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.842 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20658 6089 5.1 %RANDOM
Rwork0.17379 ---
obs0.17545 113760 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.349 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-0.59 Å2
2--0.19 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10044 0 50 987 11081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210440
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.95714196
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98551327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23324.283474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.834151719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1811562
X-RAY DIFFRACTIONr_chiral_restr0.0780.21588
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217970
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_it1.60256484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.545710551
X-RAY DIFFRACTIONr_scbond_it2.11753956
X-RAY DIFFRACTIONr_scangle_it3.1873622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1622 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.145
2BLOOSE POSITIONAL0.175
3CLOOSE POSITIONAL0.155
4DLOOSE POSITIONAL0.135
5ELOOSE POSITIONAL0.155
1ALOOSE THERMAL1.2510
2BLOOSE THERMAL1.5610
3CLOOSE THERMAL1.2410
4DLOOSE THERMAL1.1610
5ELOOSE THERMAL1.5310
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 418 -
Rwork0.226 7923 -
obs--91.69 %

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