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- PDB-2gic: Crystal Structure of a vesicular stomatitis virus nucleocapsid-RN... -

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Basic information

Entry
Database: PDB / ID: 2gic
TitleCrystal Structure of a vesicular stomatitis virus nucleocapsid-RNA complex
Components
  • 45-MER
  • Nucleocapsid protein
KeywordsVIRUS/VIRAL PROTEIN/RNA / nucleocapsid / protein-rna complex / negative strand virus / VIRUS-VIRAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


RNA replication / helical viral capsid / viral transcription / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Rhabdovirus nucleoprotein-like / Nucleoprotein / Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
URANYL (VI) ION / RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.92 Å
AuthorsGreen, T.J. / Zhang, X. / Wertz, G.W. / Luo, M.
CitationJournal: Science / Year: 2006
Title: Structure of the vesicular stomatitis virus nucleoprotein-RNA complex unveils how the RNA is sequestered
Authors: Green, T.J. / Zhang, X. / Wertz, G.W. / Luo, M.
History
DepositionMar 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 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_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
R: 45-MER
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
E: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,10321
Polymers251,0526
Non-polymers4,05015
Water00
1
R: 45-MER
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
E: Nucleocapsid protein
hetero molecules

R: 45-MER
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
E: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)510,20542
Polymers502,10412
Non-polymers8,10130
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)166.160, 236.316, 75.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61A
71B
81C
91D
101E
111A
121B
131C
141D
151E
161A
171B
181C
191D
201E
12A
22B
32C
42D
52E
62A
72B
82C
92D
102E
112A
122B
132C
142D
152E
13A
23B
33C
43D
53E

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLUGLUAB2 - 222 - 22
211SERSERGLUGLUBC2 - 222 - 22
311SERSERGLUGLUCD2 - 222 - 22
411SERSERGLUGLUDE2 - 222 - 22
511SERSERGLUGLUEF2 - 222 - 22
621ASPASPLYSLYSAB224 - 270224 - 270
721ASPASPLYSLYSBC224 - 270224 - 270
821ASPASPLYSLYSCD224 - 270224 - 270
921ASPASPLYSLYSDE224 - 270224 - 270
1021ASPASPLYSLYSEF224 - 270224 - 270
1131SERSERSERSERAB287 - 340287 - 340
1231SERSERSERSERBC287 - 340287 - 340
1331SERSERSERSERCD287 - 340287 - 340
1431SERSERSERSERDE287 - 340287 - 340
1531SERSERSERSEREF287 - 340287 - 340
1641ALAALALYSLYSAB368 - 422368 - 422
1741ALAALALYSLYSBC368 - 422368 - 422
1841ALAALALYSLYSCD368 - 422368 - 422
1941ALAALALYSLYSDE368 - 422368 - 422
2041ALAALALYSLYSEF368 - 422368 - 422
112ASPASPLEULEUAB23 - 16023 - 160
212ASPASPLEULEUBC23 - 16023 - 160
312ASPASPLEULEUCD23 - 16023 - 160
412ASPASPLEULEUDE23 - 16023 - 160
512ASPASPLEULEUEF23 - 16023 - 160
622ASNASNLYSLYSAB187 - 223187 - 223
722ASNASNLYSLYSBC187 - 223187 - 223
822ASNASNLYSLYSCD187 - 223187 - 223
922ASNASNLYSLYSDE187 - 223187 - 223
1022ASNASNLYSLYSEF187 - 223187 - 223
1132ALAALALYSLYSAB271 - 286271 - 286
1232ALAALALYSLYSBC271 - 286271 - 286
1332ALAALALYSLYSCD271 - 286271 - 286
1432ALAALALYSLYSDE271 - 286271 - 286
1532ALAALALYSLYSEF271 - 286271 - 286
113SERSERLYSLYSAB341 - 354341 - 354
213SERSERLYSLYSBC341 - 354341 - 354
313SERSERLYSLYSCD341 - 354341 - 354
413SERSERLYSLYSDE341 - 354341 - 354
513SERSERLYSLYSEF341 - 354341 - 354

NCS ensembles :
ID
1
2
3
DetailsThe biological assembly contains a ten-mer of the nucleocapsid protein and a 90-mer of RNA. One-half of the assembly is the contents of the asymmetric unit. The second half is generated by the two fold axis along z.

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Components

#1: RNA chain 45-MER


Mass: 13732.498 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein
Nucleocapsid protein / Nucleoprotein


Mass: 47463.949 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Genus: Vesiculovirus / Gene: N / Production host: Escherichia coli (E. coli) / References: UniProt: P03521
#3: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: O2U

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 7 % PEG 3350, 250 mM sodium chloride, 100mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2sodium chloride11
3sodium acetate11
4H2O11
5PEG 335012
6sodium chloride12
7sodium acetate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.92→44.86 Å / Num. all: 64651 / Num. obs: 59391 / % possible obs: 96.96 %
Reflection shellResolution: 2.92→3.02 Å / % possible all: 91.86

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.92→44.86 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.883 / SU B: 53.428 / SU ML: 0.49 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.306 3007 5.1 %RANDOM
Rwork0.255 ---
all0.258 59391 --
obs0.258 59391 91.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.477 Å2
Baniso -1Baniso -2Baniso -3
1-8.07 Å20 Å20 Å2
2---0.09 Å20 Å2
3----7.97 Å2
Refinement stepCycle: LAST / Resolution: 2.92→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16517 900 15 0 17432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02217880
X-RAY DIFFRACTIONr_angle_refined_deg1.1532.02924398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16552078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.85424.048756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.856152930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.07815100
X-RAY DIFFRACTIONr_chiral_restr0.0820.22715
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213196
X-RAY DIFFRACTIONr_nbd_refined0.210.28646
X-RAY DIFFRACTIONr_nbtor_refined0.3040.212259
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2453
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.2168
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.29
X-RAY DIFFRACTIONr_mcbond_it0.2071.510558
X-RAY DIFFRACTIONr_mcangle_it0.386216753
X-RAY DIFFRACTIONr_scbond_it0.54738393
X-RAY DIFFRACTIONr_scangle_it0.9584.57645
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A708MEDIUM POSITIONAL0.240.5
12B708MEDIUM POSITIONAL0.220.5
13C708MEDIUM POSITIONAL0.240.5
14D708MEDIUM POSITIONAL0.240.5
15E708MEDIUM POSITIONAL0.250.5
11A687LOOSE POSITIONAL0.655
12B687LOOSE POSITIONAL0.635
13C687LOOSE POSITIONAL0.655
14D687LOOSE POSITIONAL0.675
15E687LOOSE POSITIONAL0.725
11A708MEDIUM THERMAL0.222
12B708MEDIUM THERMAL0.232
13C708MEDIUM THERMAL0.212
14D708MEDIUM THERMAL0.272
15E708MEDIUM THERMAL0.242
11A687LOOSE THERMAL0.8610
12B687LOOSE THERMAL0.8410
13C687LOOSE THERMAL0.7710
14D687LOOSE THERMAL0.8210
15E687LOOSE THERMAL0.8210
21A764MEDIUM POSITIONAL0.380.5
22B764MEDIUM POSITIONAL0.360.5
23C764MEDIUM POSITIONAL0.420.5
24D764MEDIUM POSITIONAL0.420.5
25E764MEDIUM POSITIONAL0.340.5
21A758LOOSE POSITIONAL0.975
22B758LOOSE POSITIONAL0.955
23C758LOOSE POSITIONAL1.025
24D758LOOSE POSITIONAL1.055
25E758LOOSE POSITIONAL0.885
21A764MEDIUM THERMAL0.162
22B764MEDIUM THERMAL0.162
23C764MEDIUM THERMAL0.142
24D764MEDIUM THERMAL0.152
25E764MEDIUM THERMAL0.142
21A758LOOSE THERMAL0.4610
22B758LOOSE THERMAL0.610
23C758LOOSE THERMAL0.4910
24D758LOOSE THERMAL0.610
25E758LOOSE THERMAL0.4510
31A56MEDIUM POSITIONAL0.150.5
32B56MEDIUM POSITIONAL0.160.5
33C56MEDIUM POSITIONAL0.230.5
34D56MEDIUM POSITIONAL0.140.5
35E56MEDIUM POSITIONAL0.250.5
31A47LOOSE POSITIONAL0.325
32B47LOOSE POSITIONAL0.315
33C47LOOSE POSITIONAL0.245
34D47LOOSE POSITIONAL0.35
35E47LOOSE POSITIONAL0.495
31A56MEDIUM THERMAL0.252
32B56MEDIUM THERMAL0.192
33C56MEDIUM THERMAL0.332
34D56MEDIUM THERMAL0.282
35E56MEDIUM THERMAL0.642
31A47LOOSE THERMAL0.710
32B47LOOSE THERMAL0.8410
33C47LOOSE THERMAL0.8410
34D47LOOSE THERMAL0.6810
35E47LOOSE THERMAL1.7310
LS refinement shellResolution: 2.92→2.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 151 -
Rwork0.353 3083 -
obs-3083 80.23 %
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)
14.29862.9749-0.17823.7114-0.70031.26460.1315-0.2281-0.12820.1706-0.029-0.0948-0.2145-0.068-0.1025-0.74310.21370.1478-0.78650.0386-0.8913-32.70729.956976.5917
25.70891.09510.52561.5310.04310.69580.1244-0.3397-0.21070.3313-0.0754-0.0286-0.30530.0398-0.0489-0.54530.02450.1034-0.8222-0.0131-0.829-8.524842.969576.6379
34.4043-1.49880.132.07870.18630.92330.1122-0.1648-0.09660.2930.0570.0737-0.04750.1386-0.1691-0.5401-0.0757-0.0423-0.8528-0.012-0.897218.697339.740376.5981
43.366-2.33750.11526.22360.15840.4311-0.0646-0.0822-0.25640.38410.21630.0496-0.01010.1758-0.1517-0.7311-0.0608-0.0752-0.7307-0.0434-0.90339.033121.313376.5817
51.58820.3358-0.20358.49220.65441.26060.058-0.0649-0.01150.17050.07020.05820.0837-0.2354-0.1282-0.88260.03540.1-0.69560.0869-0.8875-44.50355.375576.6213
63.4441-0.47130.91035.24190.667614.87950.10140.9016-0.3603-1.00890.04550.30930.5989-0.975-0.1469-0.49020.0447-0.0238-0.39780.1008-0.5149-52.360332.17544.6397
74.88240.63512.67454.89021.348213.3257-0.2581.45070.0806-0.85510.21170.1309-0.44220.14050.0462-0.58390.03560.0942-0.46180.1251-0.5712-22.556455.738944.581
85.4575-0.517-0.51393.9002-0.743314.06050.19750.95950.2349-0.68350.21020.1297-0.2239-1.8269-0.4077-0.438-0.08570.1565-0.31840.1623-0.636514.694859.198644.8746
94.5025-0.19431.16616.175-2.38419.11130.36141.46970.0754-1.2906-0.392-0.28810.42830.4510.0306-0.43890.03190.1476-0.245-0.0044-0.556645.900738.904844.4457
102.9207-0.96021.42696.35131.689513.76050.21610.85230.0109-1.5131-0.17860.53080.862-0.5511-0.0374-0.13250.0095-0.2002-0.1490.0802-0.3397-61.9842-4.406444.8043
1112.4745-4.00168.13431.761-0.526814.38890.9653-0.1093-0.67931.70840.47750.8450.3795-1.196-1.4428-0.32730.00840.2217-0.5405-0.1168-0.6716-52.26385.516288.0322
1214.6737-16.98459.557321.2344-5.974122.66080.5814-0.3093-0.85420.14680.43581.0098-1.0267-0.3345-1.0171-0.3223-0.140.0977-0.6932-0.0641-0.7707-38.789634.753688.039
132.4531-4.15695.521723.0988-4.713913.77150.5953-2.06950.0814-0.03670.42731.2646-0.4649-0.2977-1.0226-0.2850.03580.0969-0.4308-0.0142-0.5171-10.568850.51187.994
148.82829.36711.9389.9412.216712.8262-0.3607-0.11550.8360.40221.1809-1.1372-0.94240.6399-0.8202-0.4799-0.0428-0.1557-0.29650.0339-0.867921.344146.853788.1003
1513.41717.085112.320619.66999.446911.85670.9849-1.99031.11615.29640.80553.29431.1004-1.6724-1.79040.1286-0.0040.4365-0.69370.3508-0.8955-45.5461-25.822187.7897
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AB2 - 222 - 22
21AB224 - 270224 - 270
31AB287 - 340287 - 340
41AB368 - 422368 - 422
52BC2 - 222 - 22
62BC224 - 270224 - 270
72BC287 - 340287 - 340
82BC368 - 422368 - 422
93CD2 - 222 - 22
103CD224 - 270224 - 270
113CD287 - 340287 - 340
123CD368 - 422368 - 422
134DE2 - 222 - 22
144DE224 - 270224 - 270
154DE287 - 340287 - 340
164DE368 - 422368 - 422
175EF2 - 222 - 22
185EF224 - 270224 - 270
195EF287 - 340287 - 340
205EF368 - 422368 - 422
216AB23 - 16023 - 160
226AB187 - 223187 - 223
236AB271 - 286271 - 286
247BC23 - 16023 - 160
257BC187 - 223187 - 223
267BC271 - 286271 - 286
278CD23 - 16023 - 160
288CD187 - 223187 - 223
298CD271 - 286271 - 286
309DE23 - 16023 - 160
319DE187 - 223187 - 223
329DE271 - 286271 - 286
3310EF23 - 16023 - 160
3410EF187 - 223187 - 223
3510EF271 - 286271 - 286
3611AB341 - 354341 - 354
3712BC341 - 354341 - 354
3813CD341 - 354341 - 354
3914DE341 - 354341 - 354
4015EF341 - 354341 - 354

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