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- PDB-5cpu: Crystal structure of murine polyomavirus PTA strain VP1 -

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Basic information

Entry
Database: PDB / ID: 5cpu
TitleCrystal structure of murine polyomavirus PTA strain VP1
ComponentsVP1
KeywordsVIRAL PROTEIN / Murine Polyomavirus / carbohydrate complex / virus-host interaction
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / 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 / Capsid protein VP1
Similarity search - Component
Biological speciesMurine polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsLiaci, A.M. / Buch, M.H.C. / Neu, U. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 685 Germany
CitationJournal: Plos Pathog. / Year: 2015
Title: Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity.
Authors: Buch, M.H. / Liaci, A.M. / O'Hara, S.D. / Garcea, R.L. / Neu, U. / Stehle, T.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,79812
Polymers158,1545
Non-polymers6457
Water32,6431812
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.610, 219.610, 99.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11E-754-

HOH

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
11ASPASPVALVALAA44 - 4612 - 14
21ASPASPVALVALBB44 - 4612 - 14
31ASPASPVALVALCC44 - 4612 - 14
41ASPASPVALVALDD44 - 4612 - 14
51ASPASPVALVALEE44 - 4612 - 14
12GLUGLUILEILEAA48 - 4916 - 17
22GLUGLUILEILEBB48 - 4916 - 17
32GLUGLUILEILECC48 - 4916 - 17
42GLUGLUILEILEDD48 - 4916 - 17
52GLUGLUILEILEEE48 - 4916 - 17
13ALAALAALAALAAA5119
23ALAALAALAALABB5119
33ALAALAALAALACC5119
43ALAALAALAALADD5119
53ALAALAALAALAEE5119
14GLYGLYTHRTHRAA69 - 8337 - 51
24GLYGLYTHRTHRBB69 - 8337 - 51
34GLYGLYTHRTHRCC69 - 8337 - 51
44GLYGLYTHRTHRDD69 - 8337 - 51
54GLYGLYTHRTHREE69 - 8337 - 51
15ASPASPTHRTHRAA85 - 8653 - 54
25ASPASPTHRTHRBB85 - 8653 - 54
35ASPASPTHRTHRCC85 - 8653 - 54
45ASPASPTHRTHRDD85 - 8653 - 54
55ASPASPTHRTHREE85 - 8653 - 54
16ASPASPASPASPAA8856
26ASPASPASPASPBB8856
36ASPASPASPASPCC8856
46ASPASPASPASPDD8856
56ASPASPASPASPEE8856
17PROPROSERSERAA90 - 9958 - 67
27PROPROSERSERBB90 - 9958 - 67
37PROPROSERSERCC90 - 9958 - 67
47PROPROSERSERDD90 - 9958 - 67
57PROPROSERSEREE90 - 9958 - 67
18ALAALAASNASNAA101 - 10969 - 77
28ALAALAASNASNBB101 - 10969 - 77
38ALAALAASNASNCC101 - 10969 - 77
48ALAALAASNASNDD101 - 10969 - 77
58ALAALAASNASNEE101 - 10969 - 77
19GLNGLNASPASPAA118 - 14686 - 114
29GLNGLNASPASPBB118 - 14686 - 114
39GLNGLNASPASPCC118 - 14686 - 114
49GLNGLNASPASPDD118 - 14686 - 114
59GLNGLNASPASPEE118 - 14686 - 114
110VALVALTHRTHRAA190 - 192158 - 160
210VALVALTHRTHRBB190 - 192158 - 160
310VALVALTHRTHRCC190 - 192158 - 160
410VALVALTHRTHRDD190 - 192158 - 160
510VALVALTHRTHREE190 - 192158 - 160
111LYSLYSLYSLYSAA194162
211LYSLYSLYSLYSBB194162
311LYSLYSLYSLYSCC194162
411LYSLYSLYSLYSDD194162
511LYSLYSLYSLYSEE194162
112ILEILETHRTHRAA196 - 197164 - 165
212ILEILETHRTHRBB196 - 197164 - 165
312ILEILETHRTHRCC196 - 197164 - 165
412ILEILETHRTHRDD196 - 197164 - 165
512ILEILETHRTHREE196 - 197164 - 165
113LYSLYSLYSLYSAA199167
213LYSLYSLYSLYSBB199167
313LYSLYSLYSLYSCC199167
413LYSLYSLYSLYSDD199167
513LYSLYSLYSLYSEE199167
114ASNASNASNASNAA203171
214ASNASNASNASNBB203171
314ASNASNASNASNCC203171
414ASNASNASNASNDD203171
514ASNASNASNASNEE203171
115ASPASPGLNGLNAA205 - 206173 - 174
215ASPASPGLNGLNBB205 - 206173 - 174
315ASPASPGLNGLNCC205 - 206173 - 174
415ASPASPGLNGLNDD205 - 206173 - 174
515ASPASPGLNGLNEE205 - 206173 - 174
116ASNASNPROPROAA209 - 210177 - 178
216ASNASNPROPROBB209 - 210177 - 178
316ASNASNPROPROCC209 - 210177 - 178
416ASNASNPROPRODD209 - 210177 - 178
516ASNASNPROPROEE209 - 210177 - 178
117SERSERALAALAAA212 - 214180 - 182
217SERSERALAALABB212 - 214180 - 182
317SERSERALAALACC212 - 214180 - 182
417SERSERALAALADD212 - 214180 - 182
517SERSERALAALAEE212 - 214180 - 182
118LEULEUASPASPAA216 - 217184 - 185
218LEULEUASPASPBB216 - 217184 - 185
318LEULEUASPASPCC216 - 217184 - 185
418LEULEUASPASPDD216 - 217184 - 185
518LEULEUASPASPEE216 - 217184 - 185
119ASPASPGLYGLYAA219 - 220187 - 188
219ASPASPGLYGLYBB219 - 220187 - 188
319ASPASPGLYGLYCC219 - 220187 - 188
419ASPASPGLYGLYDD219 - 220187 - 188
519ASPASPGLYGLYEE219 - 220187 - 188
120TYRTYRTHRTHRAA222 - 237190 - 205
220TYRTYRTHRTHRBB222 - 237190 - 205
320TYRTYRTHRTHRCC222 - 237190 - 205
420TYRTYRTHRTHRDD222 - 237190 - 205
520TYRTYRTHRTHREE222 - 237190 - 205
121TYRTYRGLYGLYAA239 - 246207 - 214
221TYRTYRGLYGLYBB239 - 246207 - 214
321TYRTYRGLYGLYCC239 - 246207 - 214
421TYRTYRGLYGLYDD239 - 246207 - 214
521TYRTYRGLYGLYEE239 - 246207 - 214
122THRTHRPROPROAA248 - 251216 - 219
222THRTHRPROPROBB248 - 251216 - 219
322THRTHRPROPROCC248 - 251216 - 219
422THRTHRPROPRODD248 - 251216 - 219
522THRTHRPROPROEE248 - 251216 - 219
123LEULEULEULEUAA253221
223LEULEULEULEUBB253221
323LEULEULEULEUCC253221
423LEULEULEULEUDD253221
523LEULEULEULEUEE253221
124PHEPHETHRTHRAA255 - 258223 - 226
224PHEPHETHRTHRBB255 - 258223 - 226
324PHEPHETHRTHRCC255 - 258223 - 226
424PHEPHETHRTHRDD255 - 258223 - 226
524PHEPHETHRTHREE255 - 258223 - 226
125THRTHRTRPTRPAA260 - 288228 - 256
225THRTHRTRPTRPBB260 - 288228 - 256
325THRTHRTRPTRPCC260 - 288228 - 256
425THRTHRTRPTRPDD260 - 288228 - 256
525THRTHRTRPTRPEE260 - 288228 - 256
126THRTHRARGARGAA291 - 292259 - 260
226THRTHRARGARGBB291 - 292259 - 260
326THRTHRARGARGCC291 - 292259 - 260
426THRTHRARGARGDD291 - 292259 - 260
526THRTHRARGARGEE291 - 292259 - 260
127ASPASPASPASPAA295263
227ASPASPASPASPBB295263
327ASPASPASPASPCC295263
427ASPASPASPASPDD295263
527ASPASPASPASPEE295263
128HISHISLYSLYSAA297 - 312265 - 280
228HISHISLYSLYSBB297 - 312265 - 280
328HISHISLYSLYSCC297 - 312265 - 280
428HISHISLYSLYSDD297 - 312265 - 280
528HISHISLYSLYSEE297 - 312265 - 280

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.306393, 0.460119, 0.833315), (-0.456332, 0.839267, -0.295622), (-0.835395, -0.289692, 0.467112)35.023609, 51.123241, 93.308273
3given(-0.811984, 0.286517, 0.508517), (-0.274595, 0.581274, -0.765975), (-0.515053, -0.761596, -0.393309)146.948837, 50.285789, 92.887497
4given(-0.809727, -0.275897, -0.517902), (0.291208, 0.577302, -0.762837), (0.50945, -0.768507, -0.387114)180.975845, -1.09966, 0.21322
5given(0.310322, -0.456099, -0.834071), (0.45966, 0.839992, -0.288318), (0.832114, -0.293917, 0.470318)90.059593, -32.071159, -57.71809

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Components

#1: Protein
VP1


Mass: 31630.723 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine polyomavirus / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76TX8, UniProt: P49302*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1812 / 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: 4.4 Å3/Da / Density % sol: 72.07 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5 1 M sodium phosphate monobasic 0.8 M potassium phosphate dibasic

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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: Mar 15, 2012
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 334981 / % possible obs: 99.9 % / Redundancy: 5 % / Rsym value: 0.105 / Net I/σ(I): 10.5
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.687 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VPN

1vpn


Resolution: 1.64→48.15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.995 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.173 10169 3 %RANDOM
Rwork0.1585 ---
obs0.1589 324802 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.84 Å2 / Biso mean: 20.739 Å2 / Biso min: 8.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å20 Å2
2--0.08 Å20 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.64→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10863 0 28 1812 12703
Biso mean--41.05 29.4 -
Num. residues----1396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211448
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.96815661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83551469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37224.699481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.776151915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1981555
X-RAY DIFFRACTIONr_chiral_restr0.0770.21773
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218688
Refine LS restraints NCS

Ens-ID: 1 / Number: 1322 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.175
2BLOOSE POSITIONAL0.125
3CLOOSE POSITIONAL0.115
4DLOOSE POSITIONAL0.175
5ELOOSE POSITIONAL0.115
1ALOOSE THERMAL1.6810
2BLOOSE THERMAL1.2210
3CLOOSE THERMAL1.3210
4DLOOSE THERMAL1.5410
5ELOOSE THERMAL1.6510
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 726 -
Rwork0.231 23907 -
all-24633 -
obs--99.93 %
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)
11.0762-1.92731.37528.2836-3.57032.01820.001-0.0286-0.03630.25820.03330.0717-0.0824-0.0314-0.03420.2135-0.00570.04210.09830.00460.093197.48923.91352.602
21.0391-0.0316-0.10290.6359-0.04860.54560.0131-0.06330.02470.0824-0.01070.0235-0.05960.0032-0.00230.062-0.01560.0010.0084-0.00170.0021102.83945.94732.612
30.9511-0.52240.46013.229-2.22282.58810.0285-0.0482-0.08370.0748-0.0390.00820.03680.02470.01050.0245-0.01660.01270.0168-0.00840.022898.48337.1537.808
40.4226-0.2380.47153.1841-1.91241.92990.0396-0.1845-0.13980.08190.17120.34240.1462-0.2395-0.21080.1110.00010.04380.1720.02730.172663.85430.00434.887
50.56740.0840.19540.59230.0680.94170.0286-0.06920.02120.06230.00480.1015-0.011-0.1024-0.03340.03350.01520.0340.0511-0.00180.082273.80841.89930.117
60.56160.0349-0.29210.4481-0.08040.7505-0.00560.0155-0.0386-0.050.01460.14580.0799-0.1361-0.00910.0527-0.0041-0.02930.05580.00260.094868.18928.4194.806
71.05430.9423-0.56923.919-1.45851.3464-0.0156-0.0402-0.0637-0.00810.03110.12460.1078-0.0853-0.01550.02720.0062-0.01870.0433-0.01760.049171.10320.9016.803
80.78630.0553-0.03771.1097-0.41610.7506-0.00120.0555-0.1224-0.1795-0.0525-0.11720.12160.04920.05370.10580.01020.00140.0287-0.01760.045498.80718.663-10.101
90.46830.18560.05540.93710.04490.30960.01310.0052-0.0352-0.0321-0.01420.02140.0426-0.02820.0010.05540.0053-0.00040.0097-0.0070.012193.26319.845-4.187
100.24080.5283-0.12864.178-0.74390.92020.0373-0.0606-0.1490.2848-0.1161-0.4220.06670.13660.07880.0670.004-0.0380.0640.01950.1046121.95727.76122.042
110.42-0.0955-0.01061.01630.17090.79070.00540.0136-0.04760.0099-0.0219-0.07670.06390.07110.01640.0148-0.0013-0.00540.01380.00750.0236114.16930.4510.761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 52
2X-RAY DIFFRACTION2A53 - 258
3X-RAY DIFFRACTION3A259 - 316
4X-RAY DIFFRACTION4B35 - 65
5X-RAY DIFFRACTION5B66 - 316
6X-RAY DIFFRACTION6C35 - 258
7X-RAY DIFFRACTION7C259 - 316
8X-RAY DIFFRACTION8D34 - 108
9X-RAY DIFFRACTION9D109 - 316
10X-RAY DIFFRACTION10E35 - 71
11X-RAY DIFFRACTION11E72 - 316

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