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- PDB-5dvw: Structure of minor nucleoprotein V30 from Zaire ebolavirus -

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Basic information

Entry
Database: PDB / ID: 5dvw
TitleStructure of minor nucleoprotein V30 from Zaire ebolavirus
ComponentsMinor nucleoprotein VP30
KeywordsVIRAL PROTEIN / SSGCID / Minor nucleoprotein VP30 / VP30 / Ebola / Zaire / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / positive regulation of viral transcription / viral nucleocapsid / host cell cytoplasm / single-stranded RNA binding / ribonucleoprotein complex / virus-mediated perturbation of host defense response / zinc ion binding / identical protein binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1160 / Transcriptional activator VP30, Filoviridae type / Ebola virus-specific transcription factor VP30 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator VP30
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of minor nucleoprotein V30 from Zaire ebolavirus
Authors: Clifton, M.C. / Lukacs, C.M. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Minor nucleoprotein VP30
B: Minor nucleoprotein VP30
C: Minor nucleoprotein VP30
D: Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6856
Polymers60,5614
Non-polymers1242
Water7,098394
1
A: Minor nucleoprotein VP30
B: Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3433
Polymers30,2812
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-31 kcal/mol
Surface area12930 Å2
MethodPISA
2
C: Minor nucleoprotein VP30
D: Minor nucleoprotein VP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3433
Polymers30,2812
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-29 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.090, 58.380, 66.600
Angle α, β, γ (deg.)96.330, 90.110, 106.980
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Minor nucleoprotein VP30 / Transcription activator VP30


Mass: 15140.336 Da / Num. of mol.: 4 / Fragment: UNP residues 142-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: VP30 / Plasmid: EbzaA.17250.a.EW11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05323
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions Morpheus screen e12: 40mM each Di-Ethyleneglycol, Tri-Ethyleneglycol, TetraEthyleneglycol, Penta-Ethyleneglycol; 12.% each MPD, PEG 1000; PEG 3350; 100mM Tris(base) ...Details: Molecular Dimensions Morpheus screen e12: 40mM each Di-Ethyleneglycol, Tri-Ethyleneglycol, TetraEthyleneglycol, Penta-Ethyleneglycol; 12.% each MPD, PEG 1000; PEG 3350; 100mM Tris(base)/Bicine pH 8.5; EbzaA.17250.a.EW11.PD00370 at 22 mg/ml, tray 262514e12, puck otj5-3; cryo: direct

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 9, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 47118 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 16.99 Å2 / Rmerge F obs: 0.994 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.095 / Χ2: 0.993 / Net I/σ(I): 8.9 / Num. measured all: 114699
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.75-1.82.40.6720.4571.968645371735530.59895.6
1.8-1.840.7690.3732.428210350633600.48695.8
1.84-1.90.8240.3032.998195350233630.39596
1.9-1.960.8760.2463.697768331131800.32196
1.96-2.020.920.1914.627707328731690.24996.4
2.02-2.090.9470.155.887293310129800.19596.1
2.09-2.170.9620.1256.87105304429170.16395.8
2.17-2.260.970.1068.136871293628290.13896.4
2.26-2.360.9750.0939.086476276126610.12296.4
2.36-2.470.9790.0869.966305268825830.11296.1
2.47-2.610.9850.07411.25993256424580.09795.9
2.61-2.770.9850.0712.295626239223030.09196.3
2.77-2.960.9880.06113.365177222921300.0895.6
2.96-3.20.9890.05415.144921213720300.07195
3.2-3.50.9920.04716.924405192218190.06194.6
3.5-3.910.9920.04318.584050176816630.05694.1
3.91-4.520.9930.04219.323479152114360.05594.4
4.52-5.530.9930.04219.842986131212370.05494.3
5.53-7.830.9930.04319.0522869979430.05694.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i8b
Resolution: 1.75→24.579 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 2363 5.02 %Random selection
Rwork0.1665 44746 --
obs0.1686 47109 95.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.47 Å2 / Biso mean: 21.9758 Å2 / Biso min: 5.87 Å2
Refinement stepCycle: final / Resolution: 1.75→24.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 8 394 4341
Biso mean--47.17 31.7 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014172
X-RAY DIFFRACTIONf_angle_d1.0955698
X-RAY DIFFRACTIONf_chiral_restr0.063700
X-RAY DIFFRACTIONf_plane_restr0.006709
X-RAY DIFFRACTIONf_dihedral_angle_d16.4482586
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7501-1.78580.28041490.23742686283596
1.7858-1.82460.27151300.22312634276496
1.8246-1.8670.29081230.21612631275496
1.867-1.91370.27381180.20632650276896
1.9137-1.96540.28181290.19152669279896
1.9654-2.02320.21691660.17742650281696
2.0232-2.08850.20331560.17152603275996
2.0885-2.16310.19361520.16822650280296
2.1631-2.24970.20651310.16132606273796
2.2497-2.3520.22591330.15552653278696
2.352-2.47590.22461220.16282669279196
2.4759-2.63080.22771620.16142637279996
2.6308-2.83370.17661300.16512632276296
2.8337-3.11830.19531500.16812642279296
3.1183-3.56840.20371460.15282547269394
3.5684-4.49130.1691340.14042595272994
4.4913-24.58180.19471320.16182592272494
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.4506-2.9362-1.4127.44543.32693.36410.0503-0.08440.13320.02940.1169-0.5178-0.2560.269-0.20860.1083-0.0259-0.00540.13820.0430.132227.526-7.54773.6402
22.1001-0.7136-0.86594.55840.1811.8363-0.0265-0.073-0.1473-0.04140.0648-0.09080.16680.0735-0.00380.0654-0.0074-0.01420.0888-0.01140.067120.986-17.02153.2138
31.9928-0.44081.17713.92850.27321.0933-0.02180.31-0.0777-1.21580.25740.17990.0468-0.00110.00250.3272-0.0351-0.03360.1462-0.00010.145316.6174-10.5118-12.1953
43.7172-0.8473-1.572.52280.50764.7207-0.10110.8408-0.5611-0.5291-0.26460.68210.6663-0.89290.29570.3164-0.044-0.10330.2697-0.06740.228911.0877-16.464-9.8743
53.29133.1761-3.32672.0009-7.08015.67920.1780.40930.39170.40330.2940.4003-0.5529-0.3007-0.36790.12650.0024-0.01610.18120.03740.24236.3379-9.50214.1357
63.8992-3.916-0.82386.09512.28634.2745-0.25890.3161-0.45640.0210.06710.66210.3747-0.29520.14570.1092-0.045-0.0120.1587-0.00570.17499.7481-21.48842.7762
76.73852.9876-1.12516.6847-3.89925.97060.14990.0699-0.1736-0.1456-0.25980.01040.08070.29780.10660.11530.01560.00740.1215-0.01970.070220.7588-19.9027-3.938
87.5634-5.423-2.02454.55231.23434.79960.06520.0494-0.1948-0.66040.01820.2734-0.12840.114-0.07420.1704-0.0348-0.01010.11580.03680.15620.743-2.8386-9.5617
96.25834.07234.61533.5882.33214.0065-0.00890.16980.0859-0.45120.06450.0728-0.0080.1382-0.06370.22820.04410.01550.16630.00270.128420.24068.5585-13.3212
105.441-0.5014-4.23294.28823.77916.0699-0.01150.5442-0.1846-0.2779-0.2824-1.01280.89191.04110.07140.33950.06440.10280.39070.09840.396136.03225.4457-11.2037
112.7251.3850.63873.70523.99014.7196-0.07570.0318-0.18270.03430.2087-0.34920.23140.329-0.18690.12540.01510.01690.13660.05020.146228.11035.9661-4.0643
121.95670.53620.94233.76340.46422.0076-0.03140.09520.0930.01950.0171-0.1564-0.17150.06490.04840.06930.01480.01750.0784-0.0090.075420.982414.6914-3.6986
131.2318-0.53620.58534.30790.45034.7326-0.0867-0.25040.02690.87210.13640.2906-0.1594-0.1148-0.03120.23050.02830.06410.1611-0.00090.133116.33448.650311.3024
143.00750.58111.26882.41190.82433.27370.0297-0.8620.43650.5074-0.21050.5658-0.4527-1.16280.16540.28810.05790.12290.2927-0.05630.215510.29313.76119.1883
152.9323-2.61311.60238.9576-5.56074.45770.3484-0.4735-0.0406-0.54230.16720.47540.4685-0.4284-0.45360.1142-0.0124-0.00310.18220.02660.22126.28027.1959-4.6172
163.02432.05610.1334.62130.56184.1679-0.2877-0.19610.38050.03160.26760.5246-0.345-0.26980.05980.12140.0450.0220.1422-0.01060.21649.752619.1788-3.2688
174.6217-0.76070.20022.1186-3.0824.90390.0287-0.21810.20070.2272-0.0808-0.0386-0.16410.25230.06230.1334-0.019-0.01120.1459-0.01150.121520.810617.74773.6019
185.23542.0946-2.33512.1428-3.75157.11110.0655-0.02070.31030.2867-0.05870.0318-0.20530.2640.10050.20640.02430.01740.16510.02280.154921.48731.09439.1531
198.5317-6.5679-5.30896.71073.70494.13170.0911-0.2057-0.08030.45030.0401-0.057-0.0880.0429-0.17860.2117-0.0335-0.01890.18270.01650.141720.1894-10.905212.8468
202.96862.88950.98523.98112.53876.28040.2244-0.1798-0.12520.2456-0.0282-1.8491-0.92790.9668-0.360.2331-0.0394-0.04230.28640.03120.516233.947-8.95719.3417
211.45260.5187-0.51077.81593.77854.7931-0.11750.15210.0409-0.18630.4735-0.60630.1380.5103-0.19130.1361-0.02560.0690.19160.00110.210419.537910.4986-35.3301
222.84151.1880.33395.7533-0.1442.583-0.04320.11890.1842-0.01190.1046-0.2304-0.16150.1166-0.06150.1325-0.00780.01160.1361-0.00510.079712.989619.1556-32.6891
232.37650.2540.60542.80140.39034.2090.0198-0.1329-0.17420.05130.13320.00680.1521-0.1679-0.0990.1080.0067-0.0070.13480.02140.12688.62069.2691-19.1943
244.69232.21762.81275.09482.29366.9967-0.0519-0.42690.35820.2258-0.09980.375-0.2836-0.81910.15570.10130.03580.03020.18460.00210.15932.8216.0536-20.2644
253.4831-1.18620.48032.7505-1.78273.76950.0745-0.12320.35410.05550.04230.1071-0.4468-0.0911-0.08690.1457-0.00680.03040.1061-0.01760.146.85820.9612-28.4641
261.9946-0.4947-0.57015.715-0.84831.17990.2057-0.0155-0.18180.5830.08790.20360.4020.0073-0.27830.35520.0478-0.09280.2612-0.03420.138313.4251-4.57-23.9693
273.6716-1.3744-1.46276.62885.10137.2946-0.1087-0.0724-0.02180.01130.2478-0.3046-0.25230.3961-0.14340.16030.0344-0.0520.2087-0.00310.193519.5096-5.1518-30.9672
283.0519-1.8089-0.28256.3757-0.30252.3029-0.0484-0.1113-0.20260.05080.1136-0.21660.18580.1307-0.07690.11890.0187-0.00980.1455-0.01160.092212.9936-13.7888-33.9499
293.1053-0.5597-2.76083.94253.33458.1326-0.09040.10640.05970.05620.2167-0.1280.0558-0.0009-0.04080.0982-0.0126-0.00240.0990.0170.10059.2891-4.6349-47.7769
303.9301-1.7341-2.3514.04310.94245.0425-0.06120.6377-0.3012-0.3399-0.07710.42010.2158-1.00430.16590.1201-0.037-0.02890.2563-0.00960.17932.2362-10.4421-46.4598
313.08320.88111.69416.9227-1.1913.54010.01050.0058-0.27660.23370.27420.41290.2098-0.3197-0.23860.1225-0.04230.00150.14520.04790.18340.9432-15.6157-34.6869
324.49252.26050.05862.2299-1.74052.80660.06740.1917-0.5301-0.2679-0.0807-0.43910.53690.31670.05570.1930.0688-0.00390.1607-0.03120.147112.8559-15.1991-41.5068
331.95550.4927-0.37154.6686-0.43132.03940.30760.08330.1964-0.57680.0629-0.0394-0.5344-0.0631-0.31380.3619-0.03650.08720.2746-0.03210.138413.382610.0958-42.7481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 140 through 156 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 157 through 180 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 196 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 215 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 216 through 220 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 231 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 232 through 246 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 247 through 253 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 254 through 264 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 265 through 271 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 140 through 156 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 157 through 180 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 181 through 197 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 198 through 215 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 216 through 220 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 221 through 231 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 232 through 246 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 247 through 253 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 254 through 264 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 265 through 269 )B0
21X-RAY DIFFRACTION21chain 'C' and (resid 140 through 156 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 157 through 180 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 181 through 196 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 197 through 215 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 216 through 245 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 246 through 266 )C0
27X-RAY DIFFRACTION27chain 'D' and (resid 140 through 156 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 157 through 180 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 181 through 197 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 198 through 215 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 216 through 231 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 232 through 245 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 246 through 266 )D0

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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

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