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- PDB-8bs7: Multimerisation domain of Borna disease virus 1 -

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Basic information

Entry
Database: PDB / ID: 8bs7
TitleMultimerisation domain of Borna disease virus 1
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / phosphoprotein / bornavirus
Function / homologyexit of virus from host cell nucleus through nuclear pore / Borna disease virus P24 / Borna disease virus P24 protein / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / host cell nucleus / Phosphoprotein
Function and homology information
Biological speciesBorna disease virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWhitehead, J.D. / Grimes, J.M. / Keown, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Structural and biophysical characterization of the Borna disease virus 1 phosphoprotein.
Authors: Whitehead, J.D. / Grimes, J.M. / Keown, J.R.
History
DepositionNov 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein
F: Phosphoprotein
G: Phosphoprotein
H: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)196,8318
Polymers196,8318
Non-polymers00
Water00
1
A: Phosphoprotein
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)98,4164
Polymers98,4164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Phosphoprotein
F: Phosphoprotein
G: Phosphoprotein
H: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)98,4164
Polymers98,4164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.873, 35.154, 153.125
Angle α, β, γ (deg.)89.970, 90.010, 90.540
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 85 through 93 or (resid 94...
d_2ens_1(chain "B" and resid 85 through 152)
d_3ens_1(chain "D" and resid 85 through 152)
d_4ens_1(chain "E" and (resid 85 through 93 or (resid 94...
d_5ens_1(chain "F" and (resid 85 through 93 or (resid 94...
d_6ens_1chain "G"
d_7ens_1(chain "H" and (resid 85 through 93 or (resid 94...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNMETA1 - 68
d_21ens_1ASNMETB3 - 70
d_31ens_1ASNMETD3 - 70
d_41ens_1ASNMETE4 - 71
d_51ens_1ASNMETF4 - 71
d_61ens_1ASNMETG1 - 68
d_71ens_1ASNMETH1 - 68

NCS oper:
IDCodeMatrixVector
1given(0.00136601902539, -0.999996756202, -0.00214978565884), (0.999996363656, 0.00136101343316, 0.00232815757469), (-0.00232522413545, -0.00215295814902, 0.999994979039)69.502736089, -2.8350934233, 0.141176911832
2given(0.0180804451254, 0.999836370442, 0.000574322445635), (-0.999825912409, 0.0180776021564, 0.00462008395063), (0.00460894559565, -0.000657755637568, 0.99998916243)1.88605342626, 67.7747990604, -0.262481455558
3given(0.00114077568051, 0.999987453235, -0.00487770473417), (0.999985675536, -0.0011152386688, 0.00523497520716), (0.00522946972022, -0.00488360679606, -0.999974401188)-14.1993962028, -20.7274833577, 294.518238409
4given(0.999994359384, 0.000627752897313, 0.00329956463492), (0.000628595113291, -0.99999977012, -0.000254219788046), (0.00329940428921, 0.000256292444295, -0.999994524108)-17.5189313642, 49.1254405551, 294.424285138
5given(0.0310488085397, -0.99951676132, 0.0014883980448), (-0.999500877462, -0.0310569292695, -0.00578472971803), (0.00582815938568, -0.00130804618632, -0.999982160628)50.6072418725, 53.5707095862, 294.325799719
6given(-0.999966968871, -0.0078621919723, -0.00206085017079), (-0.00786140575358, 0.999969022883, -0.000389325623685), (0.00206384728438, -0.00037311158443, -0.999997800659)54.9449791972, -17.3216234939, 294.373481343

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Components

#1: Protein
Phosphoprotein / P protein / p23 / p24


Mass: 24603.912 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borna disease virus 1 / Gene: P/X / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0C799

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M (NH4)2-tartarate and 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.2→51.04 Å / Num. obs: 11877 / % possible obs: 93.22 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.32 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.9
Reflection shellResolution: 3.2→3.314 Å / Num. unique obs: 905 / CC1/2: 0.895

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→51.04 Å / SU ML: 0.499 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 43.6487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.387 589 5.27 %
Rwork0.3352 10589 -
obs0.3382 11178 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.79 Å2
Refinement stepCycle: LAST / Resolution: 3.2→51.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4525 0 0 0 4525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254533
X-RAY DIFFRACTIONf_angle_d0.45536052
X-RAY DIFFRACTIONf_chiral_restr0.0307731
X-RAY DIFFRACTIONf_plane_restr0.0023780
X-RAY DIFFRACTIONf_dihedral_angle_d3.0701618
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.95374861074
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.19965532808
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.15203766323
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.14617668982
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.969841529932
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS1.14815522404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.520.4491380.35512302X-RAY DIFFRACTION80.55
3.52-4.030.3811120.3392728X-RAY DIFFRACTION96.73
4.03-5.080.35381610.30592829X-RAY DIFFRACTION98.61
5.08-51.040.39451780.35272730X-RAY DIFFRACTION97.45
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)
12.58577545023-0.232367098152-0.3307980052312.412984675661.384865502862.01737200492-0.452681647028-0.5513294858620.2172712054940.514138689721-0.00788748397905-0.160880818030.3976922572010.4729211796440.1771965943390.2127547920430.01627000751750.09877086318270.2890338886890.01328236864320.22092461102522.702901342321.5579278809181.213339395
20.3086848391230.3395388911990.1086120353310.387752427473-0.1717436829230.643333084185-0.323893474344-0.2242167490570.1233872548430.2054110709490.03773662192160.2170992059240.01337272208840.1565667912640.04487153069170.349510534241-0.00272461512931-0.04095354417070.401374007912-0.054907097387-0.29526336745341.757809696837.042044171168.988216306
30.770326128487-0.332032951630.1698251763260.8722433143620.3849363897881.09673230088-0.218937860969-0.2875409881830.2697229587630.3234518220880.2207832266310.0697927012795-0.164581148205-0.1017242093820.1640598910780.2757231322220.2778613417820.110778330168-0.187537094539-0.01404561473310.16998664483732.056329085539.40029981115.592363225
40.5839867541140.1853403031220.0181411611520.5990968957140.2970415970070.244869517906-0.0935872995366-0.218598641840.2343627473180.273276332466-0.1469007911740.170401207364-0.13098965520.0910555963182-0.3061934114690.1919868370420.094778641796-0.5465456604840.337182344510.335173095714-0.61700610816132.206483407639.4207938844170.097185327
51.089457124550.2307812100380.8039419839031.63061353780.2962781978631.72829862309-0.0822263417422-0.0676979474224-0.0192654075039-0.0314051067483-0.37863618660.1341606418020.1855721547060.2094014449920.1742576715030.4261131847270.184269248212-0.07948088110610.1062760864590.154717476179-0.069073512126230.329497994928.8478193583110.815775841
60.5585300091340.05562728277040.6238511912250.4602686828710.4219388961711.224305098020.240363442263-0.367772146015-0.4869788100230.294556636846-0.1769837203290.235910956330.312669594215-0.5696949684670.1123621090740.178896054785-0.295529652112-0.3086065754850.179906461272-0.204089226671-0.012384343083729.818097643429.7958171261171.142825913
71.577328995180.8219909470820.3621594188861.024026178880.6173561980472.99498398662-0.3523046292070.286785599712-0.349064194487-0.1586434550580.200559914742-0.196688620325-0.2754202540440.5419303542250.1274469996890.3866149730650.015789522372-0.1224605321850.08571164946320.1425929371970.1038714849940.727774009428.2505813477108.275871701
80.994833911679-0.0966769830155-0.4314859236180.868024470914-0.09100112231342.91795567123-0.0209953794559-0.412620451314-0.1519230177930.229505447743-0.450259035591-0.409165905480.335828774151-0.2472347236330.1372954341320.292521567143-0.156532850402-0.1120206247310.292131415674-0.0355632244209-0.017194923222839.650799889327.3501600892169.914313537
90.4437978416020.1851955732870.1642108345990.4188266499190.3017018330981.12016197782-0.1731685180960.1551794475050.138760075029-0.541015758573-0.07639522270430.00687063731469-0.286195972238-0.0418114324134-0.2539527823250.6498384641650.3340843723470.1502664102120.210733453897-0.293333096573-0.15550318471940.958804967337.94915052108.067092213
100.826518321048-0.3952504740340.5380460001370.674652501817-0.3091566301450.745358044988-0.03904135439040.1980377994090.144416411853-0.254270473659-0.20339425848-0.0717118424164-0.216713880842-0.476483513065-0.4421038784430.470599737649-0.195474379559-0.04933986959570.403507765937-0.197542310017-0.73182150702521.927248733321.9697696353123.328260239
110.70128165251-0.02378310483210.8405215345860.3331806414050.08673404453361.654192608590.24765193543-0.0993995809613-0.08257269463830.362306742416-0.0678432590793-0.02042461974640.3558112237870.0473008359375-0.1021996985340.375824390431-0.362561523838-0.1051618369090.467197824222-0.1970883693470.1838738378224.693948558311.8693083886179.013551861
120.8817939844450.3811937967640.18281541020.6312578068410.03085371253011.53488301994-0.5565928604240.3191017726890.159691492357-0.3050144158970.194423384546-0.116178113676-0.347915234240.166555144205-0.3073635220790.5490083585340.0417139190207-0.1977663002250.470504728848-0.170037967164-0.067192262207424.891475342212.1211066862123.406920125
131.25835448594-0.03373569328330.03820388571850.368529299648-0.06187724378260.675434670288-0.153743629611-0.104563315191-0.4051466088730.1889589522130.166595557614-0.1487505281660.0737620137282-0.152777658952-0.156187707366-0.10156580816-0.209738016572-0.4128812987010.4147951738190.1646435351250.50199999514114.607540755110.02152698181.289333408
140.258981361477-0.29185612047-0.4956148905650.590804552143-0.1671911722872.23567889622-0.197229269756-0.0382713442808-0.0476009063861-0.374466158685-0.466479711074-0.05502356156180.006373634876890.262354602924-0.06273986985160.340729211107-0.08665414420310.05901017012350.296103285209-0.157765719574-0.19394212058315.17271365019.72506545073125.801764603
150.483895136498-0.0908892581620.05497625706691.25490246633-0.5492275699661.28406380195-0.0698843078127-0.08011457138370.2927768235970.3538777282170.0754227478518-0.197368909219-0.240322886157-0.04362222567470.04209792148890.0563812940535-0.249925776225-0.1038059841560.2828049585410.0652930914652-0.0042082590583512.398621324119.6643061021179.037929591
160.7033364400180.281115838990.110734857770.513794565347-0.02596339703322.84825041758-0.3978671962790.44391857103-0.0891518989668-0.20726391511-0.0383982341632-0.189344667977-0.0526047518747-0.295332549420.08523931973950.1633083282140.0816848676035-0.03178164729990.562140452384-0.04920097786670.11979202571512.616898046619.3201422442125.448884354
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 126 through 155 )HH126 - 15542 - 71
22chain 'A' and (resid 85 through 125 )AA85 - 1251 - 41
33chain 'A' and (resid 126 through 152 )AA126 - 15242 - 68
44chain 'B' and (resid 83 through 125 )BB83 - 1251 - 43
55chain 'B' and (resid 126 through 158 )BB126 - 15844 - 76
66chain 'C' and (resid 82 through 125 )CC82 - 1251 - 44
77chain 'C' and (resid 126 through 162 )CC126 - 16245 - 81
88chain 'D' and (resid 83 through 125 )DD83 - 1251 - 43
99chain 'D' and (resid 126 through 162 )DD126 - 16244 - 80
1010chain 'E' and (resid 82 through 125 )EE82 - 1251 - 44
1111chain 'E' and (resid 126 through 152 )EE126 - 15245 - 71
1212chain 'F' and (resid 82 through 125 )FF82 - 1251 - 44
1313chain 'F' and (resid 126 through 155 )FF126 - 15545 - 74
1414chain 'G' and (resid 85 through 125 )GG85 - 1251 - 41
1515chain 'G' and (resid 126 through 152 )GG126 - 15242 - 68
1616chain 'H' and (resid 85 through 125 )HH85 - 1251 - 41

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