[English] 日本語
Yorodumi
- PDB-4e4s: Crystal structure of Pika GITRL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e4s
TitleCrystal structure of Pika GITRL
ComponentsTumor necrosis factor ligand superfamily member 18
KeywordsIMMUNE SYSTEM / GITRL / GLUCOCORTICOID-INDUCED TNF RECEPTOR LIGAND / TNFRSF18 / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / IFN / Atoms-to-Animals: The Immune Function Network
Function / homologyJelly Rolls - #40 / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesOchotona princeps (American pika)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKumar, P.R. / Bhosle, R. / Bonanno, J. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hillerich, B. / Hammonds, J. / Seidel, R. / Toro, R. ...Kumar, P.R. / Bhosle, R. / Bonanno, J. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hillerich, B. / Hammonds, J. / Seidel, R. / Toro, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: to be published
Title: Crystal structure of GITRL from Ochotona princeps
Authors: Kumar, P.R. / Bhosle, R. / Bonanno, J. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hillerich, B. / Hammonds, J. / Seidel, R. / Toro, R. / Nathenson, S.G. / Almo, S.C.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 18
B: Tumor necrosis factor ligand superfamily member 18
C: Tumor necrosis factor ligand superfamily member 18
D: Tumor necrosis factor ligand superfamily member 18
E: Tumor necrosis factor ligand superfamily member 18
F: Tumor necrosis factor ligand superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,64015
Polymers83,8796
Non-polymers7619
Water4,342241
1
A: Tumor necrosis factor ligand superfamily member 18
B: Tumor necrosis factor ligand superfamily member 18
F: Tumor necrosis factor ligand superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2407
Polymers41,9393
Non-polymers3014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tumor necrosis factor ligand superfamily member 18
D: Tumor necrosis factor ligand superfamily member 18
E: Tumor necrosis factor ligand superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4008
Polymers41,9393
Non-polymers4605
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.371, 164.588, 54.103
Angle α, β, γ (deg.)90.000, 117.160, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a trimer. Two such trimers are present in the asymmetric unit (Chains A-C and chains D-F)

-
Components

#1: Protein
Tumor necrosis factor ligand superfamily member 18


Mass: 13979.791 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: synthesized gene / Source: (gene. exp.) Ochotona princeps (American pika) / Strain: synthetic gene / Gene: GITRL / Plasmid: modified pET28b with N-terminal Smt3 tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2 M Calcium Chloride, 0.1 M HEPES:NaOH pH 7.5, 30% (w/v) PEG 4000); Cryoprotection (30% glycerol), Sitting Drop Vapor ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2 M Calcium Chloride, 0.1 M HEPES:NaOH pH 7.5, 30% (w/v) PEG 4000); Cryoprotection (30% glycerol), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.441
ReflectionResolution: 1.95→50 Å / Num. obs: 55662 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.094 / Χ2: 0.962 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.987.40.75527450.8871100
1.98-2.027.50.62927710.9021100
2.02-2.067.50.55128280.941100
2.06-2.17.50.46527480.9591100
2.1-2.157.60.39228020.9551100
2.15-2.27.60.35827460.9631100
2.2-2.257.60.29428300.9561100
2.25-2.317.60.27827100.9871100
2.31-2.387.60.2427940.9971100
2.38-2.467.60.21628490.9871100
2.46-2.547.60.18127190.9691100
2.54-2.657.60.16427520.9931100
2.65-2.777.60.13627880.9981100
2.77-2.917.60.1127860.991100
2.91-3.17.60.09527791.0551100
3.1-3.337.50.07728031.0971100
3.33-3.677.40.06227881.0531100
3.67-4.27.30.05327970.9491100
4.2-5.297.20.04727910.831100
5.29-507.40.04628360.757199.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.203 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.7765 / σ(F): 1.36 / Phase error: 29.85 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1777 2616 5.14 %RANDOM
Rwork0.1467 ---
obs0.1483 50869 91.35 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.01 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 119.17 Å2 / Biso mean: 26.2909 Å2 / Biso min: 6.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.2223 Å20 Å20.1262 Å2
2--0.8726 Å2-0 Å2
3---1.3496 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 49 241 5732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065625
X-RAY DIFFRACTIONf_angle_d1.0947597
X-RAY DIFFRACTIONf_chiral_restr0.072827
X-RAY DIFFRACTIONf_plane_restr0.004975
X-RAY DIFFRACTIONf_dihedral_angle_d13.9362077
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9505-1.9880.2431730.18441570164351
1.988-2.02860.2289940.1761836193060
2.0286-2.07270.21761050.1782080218567
2.0727-2.12090.16771370.18042265240274
2.1209-2.17390.2131170.16172554267182
2.1739-2.23270.22071460.16812740288689
2.2327-2.29840.21891340.17292895302994
2.2984-2.37260.1971640.16032969313395
2.3726-2.45740.1951550.16542989314495
2.4574-2.55580.21251340.1642903303796
2.5558-2.67210.17821480.16142922307095
2.6721-2.81290.19921590.16942940309995
2.8129-2.98910.17251730.15092928310194
2.9891-3.21990.19861660.15152928309495
3.2199-3.54380.16221700.12782928309895
3.5438-4.05620.1471670.11562943311095
4.0562-5.10920.14051660.10422929309595
5.1092-43.93980.18011790.16332961314094
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)
10.44940.2347-0.13850.4198-0.26251.6257-0.08490.0175-0.02420.21970.1210.1835-0.009-0.1289-0.23670.27210.02960.18310.0770.10930.0714-25.0904-22.362866.0495
21.31820.6635-0.65921.61-1.13491.4646-0.15190.0592-0.12870.10080.09010.13190.2148-0.1231-0.00010.20390.00420.1370.05240.00750.1047-20.6357-32.060563.888
31.8357-0.31922.65032.44520.25636.7227-0.0957-0.02110.10350.1890.0642-0.207-0.42280.49430.03310.1594-0.0685-0.04140.14670.00920.0253-3.9074-16.713853.2278
43.60090.2624-2.41590.0191-0.17591.6209-0.0064-0.55750.06960.53240.00860.1309-0.41170.3710.01470.3284-0.00080.03960.1550.0290.0864-9.7442-27.046767.5762
51.04740.403-0.43281.0324-0.68412.4104-0.0537-0.0747-0.0340.2101-0.09150.0004-0.10310.1778-0.01680.27510.01480.08240.09020.02360.0406-13.3551-29.301963.8766
60.1446-0.28530.28660.7908-0.85191.1816-0.04260.03290.06950.24260.10830.1728-0.1818-0.1218-0.13110.2408-0.01820.07670.09010.03750.045-17.4465-24.183760.4066
71.62520.2780.88163.52411.65443.38290.1212-0.3291-0.21970.2771-0.06790.14930.193-0.1695-0.02540.12820.00040.0290.10070.03490.0816-20.6902-52.363274.7374
84.48980.881.78732.35760.72183.45050.11170.2219-0.2207-0.0193-0.0049-0.6579-0.04480.7812-0.04120.1867-0.02040.08940.25070.07220.2344-6.5101-47.990868.5415
90.11350.07690.21640.20.28960.551-0.02710.12680.1395-0.1707-0.0921-0.5192-0.19780.5672-0.110.2296-0.05240.09850.35820.16430.4258-3.0895-40.289367.589
102.48592.62771.15043.9559-0.20473.0432-0.03890.3036-0.1546-0.2470.1512-0.0520.26610.3142-0.06140.16550.04380.08790.11880.01850.0895-16.0822-52.59563.6095
115.54141.58653.02041.72411.11985.00830.317-0.296-0.36220.0785-0.1462-0.3703-0.00590.2074-0.11510.1683-0.01740.04210.13090.08830.1572-11.793-47.061272.3125
121.26310.4533-0.28391.3102-1.12380.99530.106-0.37010.23260.2959-0.1756-0.0073-0.23720.26290.04280.21840.0047-0.0730.1809-0.0670.1251-29.8994-70.860377.8941
131.26480.12120.10312.1883-0.43921.4234-0.0055-0.1191-0.04720.08260.05250.5790.029-0.5619-0.0190.118-0.0003-0.03180.2495-0.0640.191-43.7585-77.619874.2871
142.84383.5902-0.9964.5472-1.0343.661-0.11130.15990.3876-0.24390.10110.5484-0.1908-0.48570.0650.19410.0311-0.1360.1744-0.04640.2015-41.6075-70.481466.36
154.01350.55041.19653.58130.11733.6727-0.16630.2865-0.6413-0.1792-0.02470.96420.747-0.89670.18830.3555-0.1098-0.05430.2925-0.05760.3703-46.2154-83.223970.6955
163.33972.3293-1.47713.8526-0.79743.58290.17860.08280.2087-0.1953-0.2310.0439-0.3531-0.12710.01290.15850.0332-0.08480.0657-0.00860.073-33.2945-70.616966.5198
173.14510.8866-2.61711.4193-1.4014.27190.0539-0.193-0.054-0.0763-0.08880.3367-0.0559-0.08350.090.14590.0164-0.02980.0674-0.07880.2025-36.6042-75.839774.5677
185.3839-2.17340.56275.7721-0.08683.37690.07440.34280.1891-0.1-0.149-0.6596-0.1620.61740.06770.1903-0.0218-0.02120.19980.00970.1332-21.8096-77.422747.0864
192.2852-0.10691.53390.1155-0.03661.80950.01320.0783-0.0277-0.0235-0.05290.01420.0489-0.0542-0.01880.24960.0171-0.11210.1016-0.02660.0757-36.2769-81.528748.0289
206.59052.58057.14883.54222.11568.8139-0.1607-0.98240.12030.4565-0.12310.3676-0.1119-1.04230.23750.17690.0261-0.02970.2951-0.00230.1826-42.5188-77.822553.5639
212.6444-1.6367-1.00914.4390.0892.95290.08820.0409-0.1395-0.25590.0439-0.27670.33570.272-0.0740.21080.0284-0.04190.0431-0.04070.127-27.0949-87.263750.6751
220.6528-0.10310.45651.6377-0.3241.4013-0.14810.19530.15630.1174-0.0711-0.1096-0.03930.0696-0.05270.23770.0089-0.10110.1333-0.05340.0996-31.2732-77.284949.3776
230.11040.1057-0.42580.275-0.30921.7008-0.0243-0.0980.04290.29420.0819-0.2915-0.02980.2275-0.17590.33560.0596-0.18210.0878-0.10510.1704-22.4507-99.495469.2678
241.52230.63222.26641.27081.75974.6467-0.0451-0.11540.11270.28910.0724-0.21480.04320.0395-0.12390.21750.0255-0.11880.056-0.02890.1031-26.9276-89.640869.9834
250.2691-0.19140.8173.58682.91836.03290.03350.11-0.12140.217-0.04090.08950.4157-0.4535-0.03020.1596-0.01520.01050.1188-0.04180.0067-43.6646-105.070656.2957
262.0104-0.3831.75750.6718-0.29821.5387-0.0076-0.5365-0.02830.5656-0.0090.00820.0684-0.67440.03390.3259-0.00940.04250.1744-0.00170.0529-39.6513-96.286871.2807
270.51790.2937-0.1740.81740.47511.0303-0.09020.00040.05980.1569-0.0002-0.0403-0.0241-0.1447-0.0490.29430.0566-0.07330.1164-0.02920.0554-36.4507-91.922265.0346
283.025-1.12772.66892.34692.47068.58910.1727-0.38-0.06650.5003-0.34210.24460.76-0.58050.15090.3556-0.0444-0.02780.1332-0.01620.1019-34.3722-99.710472.3232
290.1944-0.08330.08530.38580.53441.2119-0.04760.00270.00360.1860.1317-0.13510.03870.09530.03590.24170.0409-0.07470.0529-0.08720.0665-31.3466-98.225164.3081
302.6972-1.3326-0.23724.3273-0.37142.9658-0.01310.2478-0.5368-0.2704-0.07950.57660.2211-0.53320.06830.2231-0.07680.00240.2124-0.03110.1865-27.6116-45.772244.0767
311.9580.0962-1.42640.03450.03821.46990.0383-0.00960.1107-0.0964-0.077-0.1114-0.09610.1007-0.040.23070.01850.06830.09610.05630.063-13.1644-41.721644.9794
325.28140.3348-0.14952.52-0.55540.1524-0.2999-0.1827-0.16320.09880.1278-0.2033-0.03980.31750.16230.3048-0.01220.04170.25350.0150.1104-6.8981-45.528150.3956
334.2795-2.16682.56044.829-0.0282.1098-0.07950.02130.1348-0.1643-0.00950.0921-0.5724-0.26670.01390.23720.03550.03820.12510.05790.0921-22.3641-36.03247.6577
342.5992-1.9912-1.1984.00341.33060.7256-0.19550.2315-0.34620.0436-0.05180.18440.2285-0.22620.24890.16480.02710.01360.15570.03520.0827-19.8534-43.948947.6531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:39)A4 - 39
2X-RAY DIFFRACTION2chain 'A' and (resseq 40:49)A40 - 49
3X-RAY DIFFRACTION3chain 'A' and (resseq 50:61)A50 - 61
4X-RAY DIFFRACTION4chain 'A' and (resseq 62:74)A62 - 74
5X-RAY DIFFRACTION5chain 'A' and (resseq 75:99)A75 - 99
6X-RAY DIFFRACTION6chain 'A' and (resseq 100:121)A100 - 121
7X-RAY DIFFRACTION7chain 'B' and (resseq 4:39)B4 - 39
8X-RAY DIFFRACTION8chain 'B' and (resseq 40:74)B40 - 74
9X-RAY DIFFRACTION9chain 'B' and (resseq 75:84)B75 - 84
10X-RAY DIFFRACTION10chain 'B' and (resseq 85:99)B85 - 99
11X-RAY DIFFRACTION11chain 'B' and (resseq 100:121)B100 - 121
12X-RAY DIFFRACTION12chain 'C' and (resseq 4:39)C4 - 39
13X-RAY DIFFRACTION13chain 'C' and (resseq 40:61)C40 - 61
14X-RAY DIFFRACTION14chain 'C' and (resseq 62:74)C62 - 74
15X-RAY DIFFRACTION15chain 'C' and (resseq 75:84)C75 - 84
16X-RAY DIFFRACTION16chain 'C' and (resseq 85:99)C85 - 99
17X-RAY DIFFRACTION17chain 'C' and (resseq 100:123)C100 - 123
18X-RAY DIFFRACTION18chain 'D' and (resseq 3:39)D3 - 39
19X-RAY DIFFRACTION19chain 'D' and (resseq 40:74)D40 - 74
20X-RAY DIFFRACTION20chain 'D' and (resseq 75:84)D75 - 84
21X-RAY DIFFRACTION21chain 'D' and (resseq 85:99)D85 - 99
22X-RAY DIFFRACTION22chain 'D' and (resseq 100:123)D100 - 123
23X-RAY DIFFRACTION23chain 'E' and (resseq 3:39)E3 - 39
24X-RAY DIFFRACTION24chain 'E' and (resseq 40:47)E40 - 47
25X-RAY DIFFRACTION25chain 'E' and (resseq 48:61)E48 - 61
26X-RAY DIFFRACTION26chain 'E' and (resseq 62:74)E62 - 74
27X-RAY DIFFRACTION27chain 'E' and (resseq 75:93)E75 - 93
28X-RAY DIFFRACTION28chain 'E' and (resseq 94:99)E94 - 99
29X-RAY DIFFRACTION29chain 'E' and (resseq 100:123)E100 - 123
30X-RAY DIFFRACTION30chain 'F' and (resseq 3:39)F3 - 39
31X-RAY DIFFRACTION31chain 'F' and (resseq 40:74)F40 - 74
32X-RAY DIFFRACTION32chain 'F' and (resseq 75:84)F75 - 84
33X-RAY DIFFRACTION33chain 'F' and (resseq 85:99)F85 - 99
34X-RAY DIFFRACTION34chain 'F' and (resseq 100:124)F100 - 124

+
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