[English] 日本語
Yorodumi
- PDB-9fbm: Structure of human protein kinase ck2 catalytic subunit (ck2alpha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fbm
TitleStructure of human protein kinase ck2 catalytic subunit (ck2alpha, csnk2a1 gene product) in complex with the cyclic peptidomimetic compound fmp37 discovered by high-throughput screening
Components
  • Casein kinase II subunit alpha
  • Cyclic peptidomimetic compound FMP37
KeywordsTRANSFERASE / human protein kinase ck2 catalytic subunit alpha / csnk2a1 gene product / inhibition of ck2alpha/ck2beta subunit interaction
Function / homology
Function and homology information


regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex ...regulation of chromosome separation / positive regulation of aggrephagy / Condensation of Prometaphase Chromosomes / WNT mediated activation of DVL / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Maturation of hRSV A proteins / Sin3-type complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of apoptotic signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signal transduction by L1 / Hsp90 protein binding / PML body / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / rhythmic process / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / double-strand break repair / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / DNA damage response / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
NICOTINIC ACID / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å
AuthorsWerner, C. / Niefind, K. / Pietsch, M. / Eimermacher, S. / Lindenblatt, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)NI 643/11-1 Germany
Citation
Journal: To Be Published
Title: Discovery and characterization of a novel class of cyclic peptidic compounds inhibiting the assembly of the protein kinase CK2alpha2/beta2 holoenzyme
Authors: Werner, C. / Eimermacher, S. / Lindenblatt, D. / Niefind, K. / Pietsch, M.
#1: Journal: Biol.Chem. / Year: 2025
Title: A CK2 alpha ' mutant indicating why CK2 alpha and CK2 alpha ', the isoforms of the catalytic subunit of human protein kinase CK2, deviate in affinity to CK2 beta.
Authors: Werner, C. / Eimermacher, S. / Harasimowicz, H. / Fischer, D. / Pietsch, M. / Niefind, K.
#2: Journal: ACS Chem Biol / Year: 2013
Title: First structure of protein kinase CK2 catalytic subunit with an effective CK2beta-competitive ligand.
Authors: Raaf, J. / Guerra, B. / Neundorf, I. / Bopp, B. / Issinger, O.G. / Jose, J. / Pietsch, M. / Niefind, K.
History
DepositionMay 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase II subunit alpha
B: Casein kinase II subunit alpha
C: Casein kinase II subunit alpha
F: Cyclic peptidomimetic compound FMP37
G: Cyclic peptidomimetic compound FMP37
H: Cyclic peptidomimetic compound FMP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,62621
Polymers127,2506
Non-polymers1,37615
Water13,781765
1
A: Casein kinase II subunit alpha
F: Cyclic peptidomimetic compound FMP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9478
Polymers42,4172
Non-polymers5306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Casein kinase II subunit alpha
G: Cyclic peptidomimetic compound FMP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8517
Polymers42,4172
Non-polymers4345
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Casein kinase II subunit alpha
H: Cyclic peptidomimetic compound FMP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8286
Polymers42,4172
Non-polymers4114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.016, 208.360, 76.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-405-

NA

21B-735-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 159 or resid 161...
d_2ens_1(chain "B" and (resid 2 through 159 or resid 161...
d_3ens_1(chain "C" and (resid 2 through 159 or resid 161...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERPROPROAA2 - 15916 - 173
d_12ASNASNGLYGLYAA161 - 235175 - 249
d_13ASPASPHISHISAA237 - 276251 - 290
d_14ARGARGHISHISAA278 - 286292 - 300
d_15GLUGLUGLNGLNAA288 - 310302 - 324
d_16ARGARGALAALAAA312 - 332326 - 346
d_17NIONIONIONIOAG401
d_21SERSERPROPROBB2 - 15916 - 173
d_22ASNASNGLYGLYBB161 - 235175 - 249
d_23ASPASPHISHISBB237 - 276251 - 290
d_24ARGARGHISHISBB278 - 286292 - 300
d_25GLUGLUGLNGLNBB288 - 310302 - 324
d_26ARGARGALAALABB312 - 332326 - 346
d_27NIONIONIONIOBM401
d_31SERSERPROPROCC2 - 15916 - 173
d_32ASNASNGLYGLYCC161 - 235175 - 249
d_33ASPASPHISHISCC237 - 276251 - 290
d_34ARGARGHISHISCC278 - 286292 - 300
d_35GLUGLUGLNGLNCC288 - 310302 - 324
d_36ARGARGALAALACC312 - 332326 - 346
d_37NIONIONIONIOCR401

NCS oper:
IDCodeMatrixVector
1given(-0.99898514473, 0.0447541554114, -0.00507406963997), (-0.0426281780958, -0.975830146354, -0.214332367827), (-0.0145436942188, -0.21389855315, 0.976747608095)0.683412947582, 136.558299047, 16.0161785921
2given(-0.999239864651, 0.0388331822228, -0.00341714069911), (0.0381878689396, 0.992701129823, 0.114394726777), (0.00783451070302, 0.11417727798, -0.993429499076)-38.3526302253, 35.1897828491, -0.479241582354

-
Components

-
Protein / Protein/peptide , 2 types, 6 molecules ABCFGH

#1: Protein Casein kinase II subunit alpha


Mass: 41685.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Protein/peptide Cyclic peptidomimetic compound FMP37


Mass: 731.301 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) synthetic construct (others)

-
Non-polymers , 4 types, 780 molecules

#3: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H5NO2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein solution: 97.5 mikroliter CK2alpha-1-335 solution (7 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter 20 millimolar FMP37 in DMSO and incubated for ...Details: protein solution: 97.5 mikroliter CK2alpha-1-335 solution (7 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 2.5 mikroliter 20 millimolar FMP37 in DMSO and incubated for 30 min. reservoir: 1.5 mol/l lithium sulphate, 100 mM sodium HEPES buffer, pH 7.5. crystallization drop: 4 microliter protein solution plus 2 microliter reservoir.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.054→76.718 Å / Num. obs: 68956 / % possible obs: 87.5 % / Redundancy: 35.3 % / Biso Wilson estimate: 21.56 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.562 / Rpim(I) all: 0.095 / Rrim(I) all: 0.57 / Rsym value: 0.562 / Net I/σ(I): 9.6
Reflection shellResolution: 2.054→2.182 Å / Redundancy: 37.4 % / Rmerge(I) obs: 6.641 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3448 / CC1/2: 0.563 / Rpim(I) all: 1.116 / Rrim(I) all: 6.738 / Rsym value: 6.641 / % possible all: 26.8

-
Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.21_5207refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.054→54.7 Å / SU ML: 0.2361 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2388 1023 1.48 %
Rwork0.1847 67912 -
obs0.1855 68935 87.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.82 Å2
Refinement stepCycle: LAST / Resolution: 2.054→54.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8387 0 226 765 9378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078892
X-RAY DIFFRACTIONf_angle_d0.899512046
X-RAY DIFFRACTIONf_chiral_restr0.05681234
X-RAY DIFFRACTIONf_plane_restr0.00771546
X-RAY DIFFRACTIONf_dihedral_angle_d12.91523340
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.790767879704
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.816510107953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.054-2.160.3998330.24192088X-RAY DIFFRACTION19.11
2.16-2.30.29581540.248710179X-RAY DIFFRACTION92.96
2.3-2.480.29061640.223710954X-RAY DIFFRACTION99.48
2.48-2.720.27041620.209110974X-RAY DIFFRACTION99.64
2.72-3.120.25931640.205111051X-RAY DIFFRACTION99.8
3.12-3.930.20721710.159111154X-RAY DIFFRACTION99.95
3.93-54.70.1991750.149511512X-RAY DIFFRACTION99.86
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)
10.7308307570120.07807039777540.03898616555460.604263448767-0.3496074170411.61244496304-0.0127336940006-0.122725117249-0.1328125790170.128640112806-0.0936835212836-0.1692830004890.09443842642590.1323615525210.07110074990120.2087717184920.0436218092166-0.007854519097710.163667164490.0504694484130.1379348524673.6545404529752.0123677229-18.0961639156
22.784505825260.1107904746820.6838542410481.93317391977-0.2634645943753.662275516120.03214741543170.09018929775210.04372967649620.178234913871-0.02898782224880.0563877380793-0.174036454589-0.7358217402590.04239068749160.1987011170550.01984080439360.04305853504820.1467698756980.05716049342950.102154830985-3.4829393429362.620606525-32.1892241117
31.10565233449-0.276841985559-0.2857198195192.34867013989-1.175908072351.230825264630.04773355346480.1681980743150.0284416980455-0.0192953251659-0.150176046224-0.2646312560360.1134898460710.1172261555970.08345390573470.1859807185840.005339812521710.003410387442810.1268945676790.006599116363660.07533701070982.9568089360856.5331445666-25.6088287938
45.51830753562.66853102418-0.1523253281622.617358742340.01709103547770.6504602399120.05588344559410.2596870279940.0450530465377-0.09388311174430.07900143860850.5673167380490.289251142959-0.632937246574-0.08232130770670.228185131285-0.0805405178426-0.05836531422130.4002498456560.05255836702610.240950217599-14.868301366653.8009519109-30.7987127232
50.498137317898-0.04708361988230.3095548904180.4826237444140.1089545857380.240032563165-0.06618146541780.403645212749-0.177310597602-0.297125948665-0.02360050839930.1539913648480.280195166476-0.263983232946-0.05637385423280.312267239847-0.107459518493-0.03666607104830.31190540816-0.05928925330080.146114364786-13.568253298345.8702928032-24.6060995204
61.81222783267-0.139345791756-1.069334614620.815114916412-0.3931042093081.546809640290.126100887303-0.05939253777980.1126736564550.25098692025-0.004904958550210.135490391015-0.0674237805206-0.253708727372-0.09739215054180.244401976051-0.04551160112750.02308517059640.2257472040490.0132990549810.101404357356-17.902423668853.992202875-5.99433739311
71.128145749650.478008591981.094722288861.153009712390.7850434646761.30449709396-0.01207863607920.126054304765-0.299589679202-0.148063209222-0.007655649215810.1477675454390.407894941963-0.635022421951-0.1053048778410.391991124873-0.2254154896160.0115828452460.396661606216-0.02170237092740.205980137827-24.276134799639.7252750182-15.2170418967
80.4090137384810.3744716447840.1041729657860.9201341663390.9943430692281.43491317352-0.183015378519-0.1175761198780.03884388765640.0173747965877-0.01467889021390.201167548225-0.238397416759-0.4136026342550.02438993302210.2397749042610.0781409893624-0.06921468018620.191076483939-0.02999739041980.177808014946-1.409041917791.1953583477-5.32614674949
91.086137124430.377417707985-0.239765749150.99587360941.021170562621.99678473946-0.2025844355050.0760494395656-0.0317126577879-0.2259715896750.0414545053294-0.0421800936049-0.2199676218110.1261852191210.1545499417870.297132315378-0.0441212769794-0.0355494187910.15452468903-0.0002455108143840.1439440906883.5942858674984.6281979622-26.4299817322
101.71145589110.8174981010110.3813675978751.154445168330.007755860393680.123096493321-0.1038679037390.230994187273-0.131403880225-0.10215154310.177558663925-0.572022011835-0.3425685623010.602828122548-0.113102239060.427666755135-0.2751970933220.03562185424070.485581368594-0.1028922632040.33354433076818.063317911191.0721752916-25.1805740812
110.529769272270.1955335124020.04393410281240.7678123156160.08513773047970.947734068845-0.3143419966220.07041430960390.0584171506709-0.07479779061240.0743171697168-0.366124979301-0.4890217680690.435790026257-0.2361701237240.265081580124-0.136900167649-0.1136144683660.0930812464970.03399109084690.33404907355121.384709757392.6558261881-6.20701700434
120.6146495993410.0763645134072-0.1948612281220.4933820346410.4925293427281.473663543465.27382620548E-5-0.3906133372010.07073772945030.08600483176460.1885015102730.251311242343-0.107342489373-0.269415549563-0.007879020901110.1669569307540.05014869376250.0241377143090.6557623890240.115194143360.391192153551-37.421769493888.333470223328.9128695332
131.233155363410.04449630789090.03693591673030.61514912555-0.2735817999540.8772862694670.0241692994153-0.201816302940.007273168513-0.02687531176110.1688224167160.2262105799560.0308555601123-0.228332196358-0.0308713397880.0836799926956-0.0183927561036-0.01969007310190.2150568335290.08238989394610.166150636972-19.753994647481.896781114920.1036336546
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 44 )AA2 - 441 - 43
22chain 'A' and (resid 45 through 74 )AA45 - 7444 - 73
33chain 'A' and (resid 75 through 108 )AA75 - 10874 - 107
44chain 'A' and (resid 109 through 129 )AA109 - 129108 - 128
55chain 'A' and (resid 130 through 173 )AA130 - 173129 - 172
66chain 'A' and (resid 174 through 280 )AA174 - 280173 - 279
77chain 'A' and (resid 281 through 332 )AA281 - 332280 - 331
88chain 'B' and (resid 1 through 35 )BE1 - 351 - 35
99chain 'B' and (resid 36 through 108 )BE36 - 10836 - 108
1010chain 'B' and (resid 109 through 129 )BE109 - 129109 - 129
1111chain 'B' and (resid 130 through 332 )BE130 - 332130 - 332
1212chain 'C' and (resid 2 through 87 )CG2 - 871 - 86
1313chain 'C' and (resid 88 through 332 )CG88 - 33287 - 331

+
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