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- PDB-2i9f: Structure of the equine arterivirus nucleocapsid protein -

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Basic information

Entry
Database: PDB / ID: 2i9f
TitleStructure of the equine arterivirus nucleocapsid protein
ComponentsNucleocapsid
KeywordsVIRAL PROTEIN / virus / capsid / assembly
Function / homology
Function and homology information


viral nucleocapsid / ribonucleoprotein complex / viral envelope / RNA binding
Similarity search - Function
Helix Hairpins - #90 / Arterivirus nucleocapsid / Arterivirus nucleocapsid protein / Nucleocapsid protein, C-terminal / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesEquine arteritis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDeshpande, A. / Wang, S. / Walsh, M. / Dokland, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of the equine arteritis virus nucleocapsid protein reveals a dimer-dimer arrangement.
Authors: Deshpande, A. / Wang, S. / Walsh, M.A. / Dokland, T.
History
DepositionSep 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid
B: Nucleocapsid
C: Nucleocapsid
D: Nucleocapsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,49710
Polymers31,0774
Non-polymers4206
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleocapsid
B: Nucleocapsid
C: Nucleocapsid
D: Nucleocapsid
hetero molecules

A: Nucleocapsid
B: Nucleocapsid
C: Nucleocapsid
D: Nucleocapsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,99520
Polymers62,1558
Non-polymers84012
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area20160 Å2
ΔGint-152 kcal/mol
Surface area20480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.230, 73.230, 138.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological unit is a tetramer in the asymmetric unit .

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Nucleocapsid


Mass: 7769.349 Da / Num. of mol.: 4 / Fragment: Capsid forming domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine arteritis virus / Genus: Arterivirus / Gene: ORF7 / Plasmid: pET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q66526, UniProt: P19810*PLUS

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Non-polymers , 5 types, 230 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 311 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M sodium phosphate, 25% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 311K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 1.95→49.94 Å / Num. all: 25482 / Num. obs: 25482 / % possible obs: 99.1 % / Redundancy: 19.5 % / Rmerge(I) obs: 0.079 / Rsym value: 0.095 / Net I/σ(I): 28.9
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 7 / Rsym value: 0.083 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2→49.94 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.326 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24753 1198 5.1 %RANDOM
Rwork0.21706 ---
obs0.21866 22474 99.04 %-
all-37807 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.866 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--1.36 Å20 Å2
3----0.56 Å2
Refine analyzeLuzzati sigma a obs: 0.287 Å
Refinement stepCycle: LAST / Resolution: 2→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 23 224 2069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211886
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9142545
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74923.22996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89815307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.3591516
X-RAY DIFFRACTIONr_chiral_restr0.1160.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021430
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2640.2964
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21269
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2173
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3230.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1851.51139
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0921828
X-RAY DIFFRACTIONr_scbond_it3.243771
X-RAY DIFFRACTIONr_scangle_it5.1614.5717
X-RAY DIFFRACTIONr_rigid_bond_restr5.55631930
X-RAY DIFFRACTIONr_sphericity_free5.576396
X-RAY DIFFRACTIONr_sphericity_bonded2.78431867
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 95 -
Rwork0.208 1605 -
obs--98.61 %
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)
166.6985-12.419-16.983820.68167.315.26120.45290.14120.111-0.5653-0.3719-1.023-0.77190.8635-0.08110.0998-0.052-0.04110.070.0437-0.003842.26442.2994.666
24.56990.68621.374613.5072-1.62650.66410.2587-0.53910.07870.3911-0.37280.22680.06080.15350.11410.0527-0.07140.01010.0066-0.00210.029735.07142.88812.917
37.5713-8.71812.452934.6456-3.38077.93490.3618-0.0006-0.01970.3241-0.3551-0.4462-0.33040.7676-0.00660.0002-0.1515-0.0090.06770.0342-0.045942.32639.03817.965
47.2414-0.63220.20371.01582.13794.84310.1583-0.0969-0.1258-0.161-0.1873-0.1506-0.30620.38650.0290.0528-0.0456-0.02980.06260.07410.019940.51234.37216.528
52.10871.6302-1.60113.48811.7375.18780.18350.02280.0070.1273-0.2726-0.20480.2460.25190.08910.04280.0321-0.03380.0280.00770.068536.99225.51913.355
60.58751.2649-1.16192.7237-2.50192.29820.05170.0694-0.01770.1604-0.23680.05720.26190.00380.18510.066-0.02930.01250.00250.00720.056431.87221.3111.534
70.5021-0.6584-0.65193.4273-1.01165.5113-0.04110.03360.3028-0.07410.07170.20880.061-0.6644-0.03060.0174-0.0520.00740.0455-0.01370.074924.54925.9115.095
81.44660.4414-3.95253.2928-1.601510.8491-0.02270.0710.0326-0.22820.09070.2658-0.0438-1.0607-0.0680.0766-0.0008-0.03420.0311-0.00730.038527.01628.8160.394
90.04440.18690.04682.10571.47761.29230.0976-0.289-0.07390.039-0.31260.01240.3443-0.41490.2150.0351-0.0416-0.02820.05730.00650.039628.37430.22415.702
101.43030.413-1.81624.6947-1.1932.40380.1299-0.6311-0.0728-0.075-0.29540.1018-0.50110.3660.16550.0644-0.08150.00090.08440.01650.027336.06233.3225.436
1124.678111.52519.991623.8533-6.287228.3564-0.41350.00680.70062.45460.29610.6139-1.896-1.00020.11740.1967-0.03040.0104-0.0856-0.01340.011933.91738.66325.823
125.6933-3.82719.327912.493-15.195823.31330.11680.4767-0.52450.0665-0.1613-0.12530.66390.22740.04450.1389-0.06640.0145-0.0956-0.03750.0925.71116.7158.731
1315.6865-2.5225-9.54656.11380.47786.0057-0.40830.4533-0.48720.0726-0.0164-0.03180.7067-0.50930.42470.1133-0.03070.0098-0.0674-0.00890.013129.54115.352.364
141.39160.52280.22654.24382.97592.1016-0.1235-0.2541-0.0289-0.27550.1021-0.0420.36960.45760.02140.11130.04780.0344-0.00140.01340.034835.8918.4351.735
151.16862.64813.281416.79146.71089.2629-0.1950.1118-0.0802-0.40480.2366-0.2463-0.08810.4827-0.04160.0030.01630.02010.0820.02320.038339.11127.8265.314
160.30561.7267-0.88679.7556-5.00992.5728-0.2868-0.23540.0361-0.2010.0621-0.0691-0.40560.11630.22470.0755-0.01520.00070.00750.01790.019838.81834.6516.543
177.0132-6.2957-6.25176.10433.471215.69550.37660.0738-0.22620.0119-0.20460.05-0.6189-0.6475-0.1720.0358-0.06-0.00330.00780.0010.029430.6237.92310.213
180.2321-1.11251.80385.3329-8.646114.0178-0.0820.14880.23470.40270.4914-0.0558-0.2975-0.5681-0.40930.0389-0.0399-0.02380.0494-0.00140.056927.934.75715.807
190.8626-0.27380.93620.0869-0.29721.01610.0177-0.13-0.0639-0.2635-0.12220.2723-0.07180.13460.10450.10.0198-0.00290.00170.00510.058330.77531.3040.767
204.1317-1.319-5.098911.981-3.19358.3034-0.13690.1230.0552-0.35210.025-0.55250.0912-0.73370.11190.14920.01820.0149-0.0252-0.0120.045634.40222.042-7.063
2112.136813.0162-4.023136.7388-21.147829.3734-0.2791.37040.21110.48650.10370.11290.5647-1.85880.17530.02160.01410.03920.049-0.0989-0.037229.00820.766-8.479
2219.8592-9.0514.12468.33353.92518.86370.5808-1.05920.0332-0.5895-0.48680.50080.0753-0.8959-0.094-0.001-0.1139-0.03620.21720.0011-0.01355.05921.35816.898
2311.9469-0.96314.49354.17686.180712.13370.0934-0.03-0.35580.0095-0.28170.05160.7919-0.48520.18830.0559-0.2033-0.03020.02850.04680.01837.93411.73414.663
248.46845.58981.1586.69931.32770.33730.3069-0.140.05660.0007-0.04350.0266-0.1139-0.2038-0.26340.0572-0.1462-0.03390.03470.05090.017312.64513.37216.987
2520.75087.17286.87383.74315.38439.4381-0.09560.0617-0.93060.0030.2857-0.27810.6941-0.0749-0.19010.0695-0.0967-0.0343-0.00210.07370.095721.04115.86821.899
265.97690.7688-1.33893.3375-1.29740.83910.3064-0.0645-0.04810.2261-0.2106-0.13870.2113-0.2089-0.09590.029-0.0731-0.01920.04610.0460.025225.75120.32823.833
276.515-2.4778-2.626516.33829.17298.95890.3323-0.29640.2643-0.2767-0.0464-0.1236-0.3799-0.1877-0.28590.0104-0.03960.00770.05110.010.003922.50830.04226.699
284.00310.97810.85832.0407-2.99455.88230.2246-0.45850.2870.3259-0.0733-0.1653-0.0344-0.9338-0.1514-0.0073-0.0520.02950.1843-0.0336-0.002517.4830.31830.189
290.70961.06062.21451.58523.30976.9105-0.1339-0.1651-0.1952-0.18940.19930.0501-0.21520.0451-0.06540.0666-0.07370.01960.04130.01880.03519.84923.88116.039
3017.5293-0.8955-8.05790.04950.170918.955-0.02790.1045-0.6786-0.29110.21340.01260.7704-0.019-0.18560.1579-0.2026-0.02020.03010.00050.031416.57714.5818.074
3132.6495.1501-7.370722.85149.074713.8060.06072.1281.0441-0.9468-0.2584-0.1073-0.1370.41940.19770.0929-0.2337-0.1350.10010.1638-0.048512.84218.2595.124
3231.79211.1206-1.29848.07447.9429.4747-0.4435-0.007-1.65480.02290.6014-0.28820.79210.623-0.15780.0427-0.0198-0.03190.01860.06520.092134.4321.88923.632
339.0177-4.21320.84632.21810.20521.52480.0218-0.22090.50190.1306-0.04720.05040.2588-0.41770.02550.0234-0.0466-0.00870.07740.0080.026428.7428.68329.994
344.99940.93314.937814.60072.41285.03110.3592-0.4681-0.15110.05860.0587-0.10890.5565-0.5089-0.41790.0757-0.0757-0.02520.04770.0373-0.01528.47221.49636.258
358.36991.56127.30184.03753.75197.89460.2123-0.3728-0.22860.0458-0.0736-0.030.2643-0.3224-0.13870.0349-0.1399-0.03190.09250.0867-0.017723.58719.7333.35
3620.7349-6.0705-5.10572.97274.990111.4770.4568-1.3263-0.4701-0.0232-0.4291-0.03170.1376-0.1565-0.02760.0519-0.2335-0.03470.20070.1049-0.007714.45317.90929.126
373.8499-0.55340.91510.1103-0.06580.35810.1258-0.6198-0.092-0.02540.02880.03990.3152-0.7588-0.1546-0.0069-0.09320.00980.16710.02360.0238.94619.52624.841
3810.6858-7.8298-6.65596.37119.092432.17391.06830.4930.884-0.374-0.0932-0.1075-1.76630.8118-0.9750.0025-0.0608-0.00840.207-0.0007-0.030813.3626.60912.748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 516 - 10
2X-RAY DIFFRACTION2AA52 - 5611 - 15
3X-RAY DIFFRACTION3AA57 - 6116 - 20
4X-RAY DIFFRACTION4AA62 - 6621 - 25
5X-RAY DIFFRACTION5AA67 - 7226 - 31
6X-RAY DIFFRACTION6AA73 - 7732 - 36
7X-RAY DIFFRACTION7AA78 - 8437 - 43
8X-RAY DIFFRACTION8AA85 - 9044 - 49
9X-RAY DIFFRACTION9AA91 - 9550 - 54
10X-RAY DIFFRACTION10AA96 - 10055 - 59
11X-RAY DIFFRACTION11AA101 - 10560 - 64
12X-RAY DIFFRACTION12BB7 - 547 - 13
13X-RAY DIFFRACTION13BB55 - 6014 - 19
14X-RAY DIFFRACTION14BB61 - 6620 - 25
15X-RAY DIFFRACTION15BB67 - 7226 - 31
16X-RAY DIFFRACTION16BB73 - 7732 - 36
17X-RAY DIFFRACTION17BB78 - 8437 - 43
18X-RAY DIFFRACTION18BB85 - 9044 - 49
19X-RAY DIFFRACTION19BB91 - 9550 - 54
20X-RAY DIFFRACTION20BB96 - 10055 - 59
21X-RAY DIFFRACTION21BB101 - 10560 - 64
22X-RAY DIFFRACTION22CC51 - 5610 - 15
23X-RAY DIFFRACTION23CC57 - 6116 - 20
24X-RAY DIFFRACTION24CC62 - 6621 - 25
25X-RAY DIFFRACTION25CC67 - 7226 - 31
26X-RAY DIFFRACTION26CC73 - 7732 - 36
27X-RAY DIFFRACTION27CC78 - 8437 - 43
28X-RAY DIFFRACTION28CC85 - 9044 - 49
29X-RAY DIFFRACTION29CC91 - 9550 - 54
30X-RAY DIFFRACTION30CC96 - 10055 - 59
31X-RAY DIFFRACTION31CC101 - 10560 - 64
32X-RAY DIFFRACTION32DD6 - 516 - 10
33X-RAY DIFFRACTION33DD52 - 5611 - 15
34X-RAY DIFFRACTION34DD57 - 6116 - 20
35X-RAY DIFFRACTION35DD62 - 6721 - 26
36X-RAY DIFFRACTION36DD68 - 7327 - 32
37X-RAY DIFFRACTION37DD74 - 7933 - 38
38X-RAY DIFFRACTION38DD80 - 8639 - 45

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  • 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

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