[English] 日本語
Yorodumi
- PDB-3hhw: Complex of a vesicular stomatitis virus empty capsid with the nuc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hhw
TitleComplex of a vesicular stomatitis virus empty capsid with the nucleocapsid-binding domain of the phosphoprotein
Components
  • Nucleoprotein
  • Phosphoprotein
KeywordsVIRAL PROTEIN / protein complex / template / replication / negative strand RNA virus / Chaperone / Phosphoprotein / RNA replication / Virion / Ribonucleoprotein / RNA-binding / Viral nucleoprotein
Function / homology
Function and homology information


helical viral capsid / virion component / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA-directed RNA polymerase activity / RNA binding
Similarity search - Function
Vesicular stomatitis virus phosphoprotein C-terminal domain / Phosphoprotein, central domain / : / Vesiculovirus phosphoprotein / Phosphoprotein, C-terminal domain, viral / Rhabdovirus nucleoprotein-like / Nucleoprotein / Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / Rhabdovirus nucleocapsid ...Vesicular stomatitis virus phosphoprotein C-terminal domain / Phosphoprotein, central domain / : / Vesiculovirus phosphoprotein / Phosphoprotein, C-terminal domain, viral / 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 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Phosphoprotein / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGreen, T.J. / Luo, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of the vesicular stomatitis virus nucleocapsid in complex with the nucleocapsid-binding domain of the small polymerase cofactor, P.
Authors: Green, T.J. / Luo, M.
History
DepositionMay 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein
K: Nucleoprotein
L: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
O: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,49516
Polymers286,59510
Non-polymers9016
Water00
1
A: Phosphoprotein
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein
K: Nucleoprotein
L: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
O: Nucleoprotein
hetero molecules

A: Phosphoprotein
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein
K: Nucleoprotein
L: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
O: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)574,99032
Polymers573,18920
Non-polymers1,80112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area57100 Å2
ΔGint-278 kcal/mol
Surface area187910 Å2
Unit cell
Length a, b, c (Å)170.602, 234.520, 95.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Phosphoprotein / Protein P / Protein M1


Mass: 9887.040 Da / Num. of mol.: 5 / Fragment: UNP residues 183-265 / Mutation: S290W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Gene: nucleocapsid protein, P / Production host: Escherichia coli (E. coli) / References: UniProt: P04880
#2: Protein
Nucleoprotein / NP / Nucleocapsid protein / Protein N


Mass: 47431.883 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Gene: N, phosphoprotein / Production host: Escherichia coli (E. coli) / References: UniProt: Q77E03
#3: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O6
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.8 M K/Na tartrate, 0.2 M NaCl, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.94 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2008
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 77814 / Num. obs: 77814 / % possible obs: 73.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 20.79
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.419 / % possible all: 44.9

-
Processing

Software
NameVersionClassification
SERGUIdata collection
COMOphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QVJ

2qvj


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.862 / SU B: 32.446 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29573 3840 4.9 %RANDOM
Rwork0.26286 ---
all0.26447 73762 --
obs0.26447 73762 73.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.58 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å20 Å20 Å2
2---0.23 Å20 Å2
3----3.13 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19555 0 60 0 19615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02220049
X-RAY DIFFRACTIONr_angle_refined_deg0.9571.96927122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.38752460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8923.886875
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.028153515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.87515120
X-RAY DIFFRACTIONr_chiral_restr0.0670.22962
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0215098
X-RAY DIFFRACTIONr_nbd_refined0.180.28478
X-RAY DIFFRACTIONr_nbtor_refined0.2970.213784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2386
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.2171
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.213
X-RAY DIFFRACTIONr_mcbond_it0.3051.512592
X-RAY DIFFRACTIONr_mcangle_it0.554219800
X-RAY DIFFRACTIONr_scbond_it0.40938573
X-RAY DIFFRACTIONr_scangle_it0.6964.57322
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 173 -
Rwork0.389 3306 -
obs--45.62 %
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)
13.3884-0.79867.6383.8451-2.10224.9603-0.7217-0.13580.12960.30470.4377-1.153-0.30531.28590.2839-0.03410.270.2284-0.12210.13440.031-12.082538.351579.4777
26.796-1.4465-2.4918.0926-1.24447.1513-1.2098-1.0267-0.53190.97590.93550.04230.88470.66530.27420.03330.3146-0.0269-0.00250.03570.019-9.716435.817474.1791
38.0101-3.02961.951212.1346-17.696626.647-0.31550.566-0.61130.17291.4021-1.41921.25120.5411-1.08670.00290.22960.26090.0004-0.059-0.0156-7.054338.233471.9792
427.63885.969-19.84771.8238-8.330344.8357-0.6974-0.30341.05670.56170.45461.74260.00032.31190.2428-0.06430.1874-0.0484-0.0271-0.0109-0.0537-13.305544.277264.8154
57.03925.5867-1.392722.4538-14.381419.4778-0.3267-0.3228-0.68872.1893-0.0018-0.3015-1.330.45070.32850.00110.001-0.00020.00060.00030.000311.940236.133475.7533
6124.5119-35.313261.670558.216-49.6547107.41740.24725.402-7.4298-3.1530.46862.6741-1.37672.7894-0.71580.00480.00280.00060.0055-0.0032-0.003322.721833.241781.0185
733.780855.274220.253691.408828.71632.40741.57543.0733-2.4554.02512.3447-0.98752.2807-0.5171-3.9201-0.00230.0016-0.0020.0002-0.00050.002316.954934.592871.4481
843.5038-78.9615-37.4199143.591167.11634.55571.1631-4.35763.65544.55351.28481.35720.78711.3018-2.44790-0.00110.00170.0003-0.0020.000715.16242.216964.7592
97.7440.2285-4.20136.2161-8.218232.41011.2803-1.9674-1.2731-0.0543-1.00050.58590.3490.6911-0.2798-0.0298-0.1635-0.0191-0.0550.087-0.010532.664722.676880.4144
105.76545.18274.48695.75776.26499.56971.2364-0.8891-0.13340.2696-1.18050.02961.2958-0.7806-0.05590.0018-0.21680.0959-0.00510.0412-0.013732.399820.72273.8789
1110.5612.5682-6.152615.2284-5.166620.79930.5420.7659-2.6109-0.63481.1079-0.594-0.4702-0.9924-1.6499-0.009-0.0478-0.0749-0.0093-0.105-0.027435.727818.863573.3716
121.3345-1.81140.490435.915513.880428.6425-0.3609-0.1592-0.45751.8265-0.53470.12830.03760.69170.8956-0.04640.03470.1819-0.1510.0942-0.164737.405825.173164.6046
134.2839-3.4971-0.98633.09952.82616.92030.9121-1.7104-0.70740.9595-0.75750.6602-0.0342-0.0896-0.15470.0008-0.00140.00130.00090.0017-0.000339.0164-0.22975.8116
1442.813269.6938-37.3535137.2361-36.299657.84061.41193.2916-0.1895-0.31160.24440.74541.7947-2.0431-1.65630.00050.0024-0.00160.00270.00140.000140.4081-10.566679.9609
1513.2446-17.7438-16.721155.10268.42427.34563.10013.083-3.50730.2047-1.46985.2443-4.79442.537-1.63040.0012-0.0014-0.00110.0019-0.0004-0.000438.0936-5.123570.6554
161.2076-5.2443-1.763228.76320.292211.6341-1.1929-0.4187-0.5040.2417-0.1843-3.109-0.7013-0.88081.37720.0009-0.0040.0003-0.0013-0.00040.000546.1789-1.524264.7281
1710.9319-11.579316.868221.412-10.448934.4304-2.6084-2.6441.72282.74810.8672-2.9449-3.2378-2.42371.74120.00330.00530.00050.0052-0.00370.0015-34.150923.854678.6623
1829.6811-10.18277.43223.5082-2.97213.90871.1847-1.1985-0.15340.8971-0.7923-0.14921.39221.1078-0.39240.0021-0.0008-0.00070.00070.00220.0015-28.353822.768374.4261
1933.197-9.2736-13.4733.23914.655938.10750.1606-2.1570.330.03471.7306-2.36922.14010.3248-1.89120.0002-0.0011-0.0014-0.0005-0.00180.0004-28.971426.850672.669
202.95894.28310.646.3137-0.866928.4433-0.3835-2.3195-0.2723-0.0159-0.3163.1171-1.7983.29420.69950.00190.00050.0002-0.00120.0003-0.0001-37.620827.955265.1535
211.64-0.3930.63750.0942-0.15280.24780.00060.34720.3953-0.102-0.0496-0.2003-0.10280.35640.04890.29270.010.1617-0.06020.0936-0.0091-4.773558.644915.8893
222.9043-1.52470.53882.55651.28255.8484-0.04090.31830.3338-0.206-0.18870.2399-0.2642-0.56860.22970.14440.07350.0497-0.19120.1088-0.0786-28.374262.4378.1157
234.7419-0.7833-0.97237.36783.76457.61710.0320.65150.0895-0.2602-0.1044-0.3025-0.01320.56140.07240.04940.14190.0974-0.12970.1681-0.2984-21.713253.1755-1.1806
2433.8057-4.86861.382317.6984-1.55816.25010.28061.0957-2.99570.33230.31670.0536-1.33620.2583-0.59730.00020-0.0014-0.0002-0.00010.0006-22.757236.72322.4637
2540.0119-31.52748.304427.42712.466566.34472.1640.7545-3.1815-3.2479-0.7198-1.04260.8485-0.86-1.4442-0.0007-0.00170.00260.00190.00090.0014-10.822744.66252.5271
263.109-2.6753-2.36913.1787-0.38738.51980.1401-0.16460.1349-0.0468-0.36250.16930.1286-0.00930.22250.15290.0330.0662-0.13140.0827-0.1175-24.623256.276610.6668
270.8313-0.95961.07261.125-1.09842.52270.01640.0080.13380-0.02030.0001-0.09950.03310.00390.07720.02360.0824-0.08580.0344-0.0198-17.144151.101828.0685
281.7876-1.099-0.43730.67560.26880.107-0.2750.0666-0.0061-0.04550.15560.0457-0.0226-0.04230.11940.17430.01520.0516-0.02490.0207-0.0664-14.761937.973439.2397
2935.5337-2.964.85650.6118-2.341410.93430.4443-5.1786-0.87851.1392-0.39070.4176-0.7025-0.0943-0.05360.4519-0.21590.34860.0983-0.01760.0931-29.553834.606960.4465
302.9092-0.9677-1.26733.01681.46015.9794-0.0431-0.1085-0.42620.23960.1021-0.03670.35150.1273-0.0591-0.05760.01950.0052-0.14330.0209-0.0711-8.962933.164643.2791
312.9487-1.27660.53411.2997-0.25960.09780.4260.58570.4195-0.2597-0.1155-0.2760.02530.2403-0.31060.3002-0.06720.225-0.05420.1104-0.113632.782951.703418.0444
324.6786-2.3752-1.12675.2833-1.36475.71820.4241.13941.2083-1.0691-0.378-0.1182-1.166-0.4414-0.046-0.01260.14150.34940.00220.5041-0.254316.072266.21547.0877
337.0209-1.92762.46945.08872.239111.33260.01421.08930.0357-0.1297-0.24880.0137-0.7901-0.97170.2346-0.00040.0025-0.00220.00040.00050.000613.472653.102-2.6336
3417.4318-0.18360.657321.2950.181921.62120.00210.6053-0.55440.2741-0.60410.80450.23911.59720.6020.00030.00010-0.00020.00020.00013.43344.94072.1482
3537.080654.97815.9664115.257632.69421.72430.44650.5301-1.8597-1.803-1.14720.14780.7759-1.13730.70070.0007-0.001-0.00040.0011-0.00020.001919.085544.67342.6336
362.4014-0.4589-2.56097.35290.50162.73090.13030.560.0058-0.60950.09670.4568-0.1599-0.7773-0.2270.29320.08510.07750.0930.2441-0.16339.925359.330112.8987
371.18790.0665-0.5472.749-0.8311.43140.12780.08890.1815-0.06360.061-0.0741-0.1613-0.0015-0.18880.016-0.02210.0766-0.06750.0055-0.035618.275249.69232.0256
384.8177-1.5041-0.83020.5630.20270.1772-0.1511-0.20240.13560.14290.1736-0.1341-0.03650.0943-0.02260.0724-0.0250.0156-0.0590.0024-0.076910.625639.755939.9669
3939.9717-22.9057-2.587713.12611.464910.9262-1.7917-4.34760.99561.08251.99650.04080.47140.5423-0.20480.0579-0.2054-0.12760.1439-0.140.0497-1.773444.842461.1047
402.90540.2121-0.01333.77631.2024.354-0.0174-0.1844-0.35380.2050.02160.14390.1908-0.0465-0.0042-0.08110.02450.0238-0.11120.0166-0.070712.567731.887543.2452
410.2440.6479-0.47482.4423-1.35520.93630.01670.18180.0069-0.2301-0.3831-0.70450.09310.52680.36640.0384-0.02440.1557-0.0534-0.107-0.074355.620822.732716.7549
423.27991.08911.42984.3571-0.5352.9776-0.19340.27010.2358-0.35520.087-0.4545-0.2220.16240.1064-0.0314-0.15440.1491-0.08750.0599-0.131350.738245.36657.2584
435.124-1.58172.64180.7483-0.13563.1864-0.0820.6321-0.1329-0.9582-0.286-0.82940.49210.07650.3680.2358-0.25480.25950.039-0.1001-0.058542.738535.2057-2.6558
4421.99049.5505-10.084617.34136.230233.66390.9828-1.16790.5534-0.795-0.70491.89571.8761.8123-0.2779-0.0004-0.0010.0002-0.000200.000428.847432.10263.1874
4558.440538.37535.382650.0534.530815.607-0.35730.3376-0.2634-1.5880.44912.38520.187-2.17-0.0918-0.0219-0.0347-0.0097-0.0144-0.0086-0.001142.220824.99152.8803
460.56560.8862-1.32781.3891-2.03325.7889-0.0080.06810.00670.0110.2-0.0821-0.0406-0.2565-0.1921-0.0097-0.05960.0193-0.0528-0.0493-0.021941.636836.862923.6628
470.8626-0.47170.24090.6422-1.45734.6393-0.141-0.12690.01390.0372-0.1819-0.6115-0.10150.17980.323-0.0238-0.08310.0222-0.0525-0.03150.041151.217532.681125.3589
480.5116-0.5774-0.36172.06610.48160.2595-0.06740.0716-0.1048-0.0733-0.04240.0612-0.14540.04710.10980.0311-0.006-0.0103-0.0176-0.0189-0.040534.381624.143537.4217
4915.813-25.42487.744542.6043-8.990910.7366-1.7331-1.63640.7154.06911.2413-0.2418-0.5177-0.30570.49190.1079-0.17870.0920.2978-0.15330.066424.324639.59759.854
501.8790.65571.47133.70021.76766.43880.093-0.0731-0.25360.3791-0.08910.28830.1441-0.0992-0.00390.00020.00780.0321-0.1512-0.0325-0.059729.582618.557743.2387
514.74635.046-2.65459.6715-4.72282.6343-0.34320.0782-0.4371-0.54740.3649-1.2280.80860.0362-0.0217-0.01350.19140.0063-0.1338-0.1745-0.038555.2151-27.086434.9969
524.2370.47832.40573.20121.27045.2112-0.12810.6758-0.0557-1.38990.215-0.7431-0.19410.6074-0.08690.36860.00030.45880.1001-0.0553-0.269466.49483.84183.8091
534.5621-4.21063.90016.5125-0.24037.6314-0.0270.0639-0.4886-1.2528-0.10690.636-0.4978-0.03370.1339-0.00430.0031-0.0051-0.00080.00040.000457.20612.9698-1.549
5427.01862.7283-10.072614.192416.755226.4508-0.2437-0.65110.2438-0.5689-0.24981.62550.25860.60820.4935-0.0003-0.0003-0.00030.00090.00010.000543.23418.86212.3767
550.01330.2616-0.24368.28370.228812.5322-0.39350.74380.6299-1.60080.25881.5379-0.0197-0.26950.13480.11430.04650.23080.02440.03050.077458.07584.18228.3805
561.33890.8554-1.54412.906-2.01033.7813-0.02180.0992-0.0956-0.2310.0099-0.26-0.13260.02720.0119-0.01490.04870.0172-0.0876-0.043-0.004152.86153.426929.611
570.4644-0.0311-1.39471.0351-1.86887.9164-0.13330.0967-0.2436-0.14410.0288-0.73120.40990.1280.1044-0.0470.06620.15820.0197-0.1010.076162.3019-2.425525.9845
580.35860.87070.05343.24670.14640.00820.01380.0489-0.0305-0.0735-0.1550.05250.00970.06280.14120.07160.0374-0.0351-0.0345-0.0211-0.07343.9082-0.666236.1884
590.09210.83990.366111.6675-0.34184.83190.0867-0.30380.31042.6522-0.0442-0.2068-0.1369-0.5472-0.04250.20860.1223-0.11940.0634-0.09240.324543.543514.955759.257
604.6950.42313.74193.5350.3449.23970.0156-0.252-0.11490.24020.04530.43280.0173-0.3725-0.0609-0.05970.03660.0219-0.201-0.0246-0.067934.1839-2.701642.5099
615.03931.74582.88521.06611.02651.6535-0.50660.31850.8046-0.19650.36610.2815-1.0147-0.00550.14050.2510.16070.0127-0.02010.232-0.0252-37.029951.139425.8382
625.55582.2426-0.22643.89550.41416.1733-0.28521.52790.2494-1.0770.11170.64440.3277-0.86040.17360.30070.1665-0.27020.02760.3886-0.3915-57.021134.22413.2197
636.37441.4493.179416.0464-4.697114.38460.41841.10741.0152-0.3368-0.1332-0.32661.18730.014-0.2851-0.0001-0.0009-0.0009-0.0011-0.001-0.0004-46.579327.3554-2.0418
6427.7056-8.35964.489114.7939-4.167424.27380.5134-0.0079-1.6358-0.27630.5955-0.19551.1650.3679-1.10890.00020.00050.00020.0010.00070.0004-40.654518.33711.8791
653.10344.9779-1.22277.9886-2.14078.7255-0.36870.5229-1.1753-1.708-0.2109-0.91181.0397-0.45770.57960.15660.28070.05550.0710.2947-0.0221-52.740329.51599.631
661.4241-0.18661.12132.03440.48156.03840.2122-0.02390.1213-0.1715-0.0820.13250.0533-0.2841-0.1301-0.02520.13090.0687-0.03980.0779-0.0834-42.904829.444632.8288
672.6539-1.08440.77251.2506-0.82071.69340.22410.20280.2453-0.16550.02880.0236-0.0528-0.059-0.2530.0340.09770.0583-0.02040.1222-0.0437-43.140933.995528.1595
684.30882.6026-1.36882.2385-0.33170.80250.115-0.0945-0.06990.1869-0.1851-0.0247-0.1849-0.06320.0701-0.04150.10660.0333-0.06270.031-0.0667-35.562721.975640.0965
6918.242925.02782.630436.37658.659712.8831.4238-3.69820.88531.7236-2.55971.70950.0261-0.07981.13590.11030.23010.21430.07070.12450.0137-43.667512.383860.8284
703.28140.107-2.25163.2057-0.046.01920.003-0.1763-0.18330.3980.014-0.42870.17230.2178-0.0169-0.05320-0.0319-0.13930.0328-0.0906-27.138521.701843.2846
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A193 - 210
2X-RAY DIFFRACTION2A211 - 240
3X-RAY DIFFRACTION3A241 - 254
4X-RAY DIFFRACTION4A255 - 265
5X-RAY DIFFRACTION5B193 - 234
6X-RAY DIFFRACTION6B235 - 242
7X-RAY DIFFRACTION7B243 - 253
8X-RAY DIFFRACTION8B254 - 265
9X-RAY DIFFRACTION9C193 - 209
10X-RAY DIFFRACTION10C210 - 240
11X-RAY DIFFRACTION11C241 - 252
12X-RAY DIFFRACTION12C253 - 265
13X-RAY DIFFRACTION13D193 - 234
14X-RAY DIFFRACTION14D235 - 243
15X-RAY DIFFRACTION15D244 - 253
16X-RAY DIFFRACTION16D254 - 265
17X-RAY DIFFRACTION17E193 - 211
18X-RAY DIFFRACTION18E212 - 239
19X-RAY DIFFRACTION19E240 - 254
20X-RAY DIFFRACTION20E255 - 265
21X-RAY DIFFRACTION21K2 - 64
22X-RAY DIFFRACTION22K65 - 100
23X-RAY DIFFRACTION23K101 - 147
24X-RAY DIFFRACTION24K148 - 176
25X-RAY DIFFRACTION25K177 - 187
26X-RAY DIFFRACTION26K188 - 206
27X-RAY DIFFRACTION27K207 - 308
28X-RAY DIFFRACTION28K309 - 349
29X-RAY DIFFRACTION29K350 - 370
30X-RAY DIFFRACTION30K371 - 422
31X-RAY DIFFRACTION31L2 - 59
32X-RAY DIFFRACTION32L60 - 112
33X-RAY DIFFRACTION33L113 - 148
34X-RAY DIFFRACTION34L149 - 175
35X-RAY DIFFRACTION35L176 - 190
36X-RAY DIFFRACTION36L191 - 224
37X-RAY DIFFRACTION37L225 - 311
38X-RAY DIFFRACTION38L312 - 350
39X-RAY DIFFRACTION39L351 - 370
40X-RAY DIFFRACTION40L371 - 422
41X-RAY DIFFRACTION41M2 - 61
42X-RAY DIFFRACTION42M62 - 107
43X-RAY DIFFRACTION43M108 - 147
44X-RAY DIFFRACTION44M148 - 176
45X-RAY DIFFRACTION45M177 - 190
46X-RAY DIFFRACTION46M191 - 253
47X-RAY DIFFRACTION47M254 - 291
48X-RAY DIFFRACTION48M292 - 348
49X-RAY DIFFRACTION49M349 - 370
50X-RAY DIFFRACTION50M371 - 422
51X-RAY DIFFRACTION51N2 - 32
52X-RAY DIFFRACTION52N33 - 105
53X-RAY DIFFRACTION53N106 - 148
54X-RAY DIFFRACTION54N149 - 177
55X-RAY DIFFRACTION55N178 - 209
56X-RAY DIFFRACTION56N210 - 253
57X-RAY DIFFRACTION57N254 - 285
58X-RAY DIFFRACTION58N286 - 349
59X-RAY DIFFRACTION59N350 - 374
60X-RAY DIFFRACTION60N375 - 422
61X-RAY DIFFRACTION61O2 - 46
62X-RAY DIFFRACTION62O47 - 113
63X-RAY DIFFRACTION63O114 - 149
64X-RAY DIFFRACTION64O150 - 181
65X-RAY DIFFRACTION65O182 - 214
66X-RAY DIFFRACTION66O215 - 257
67X-RAY DIFFRACTION67O258 - 311
68X-RAY DIFFRACTION68O312 - 351
69X-RAY DIFFRACTION69O352 - 370
70X-RAY DIFFRACTION70O371 - 422

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more