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- PDB-7up7: Crystal structure of C-terminal Domain of MSK1 in complex with co... -

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Basic information

Entry
Database: PDB / ID: 7up7
TitleCrystal structure of C-terminal Domain of MSK1 in complex with covalently bound with literature RSK2 inhibitor indazole cyanoacrylamide compound 26 (soak)
ComponentsRibosomal protein S6 kinase alpha-5
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN KINASE / TRANSFERASE / PHOSPHORYLATION / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of CREB transcription factor activity / CREB phosphorylation / TORC1 signaling / regulation of postsynapse organization / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / ERK/MAPK targets / Recycling pathway of L1 / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling ...positive regulation of CREB transcription factor activity / CREB phosphorylation / TORC1 signaling / regulation of postsynapse organization / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / ERK/MAPK targets / Recycling pathway of L1 / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / post-translational protein modification / axon guidance / positive regulation of NF-kappaB transcription factor activity / protein tyrosine kinase activity / 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 / intracellular signal transduction / protein phosphorylation / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
Chem-1LE / Ribosomal protein S6 kinase alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYano, J.K. / Abendroth, J. / Hall, A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Discovery and Characterization of a Novel Series of Chloropyrimidines as Covalent Inhibitors of the Kinase MSK1.
Authors: Hall, A. / Abendroth, J. / Bolejack, M.J. / Ceska, T. / Dell'Aiera, S. / Ellis, V. / Fox 3rd, D. / Francois, C. / Muruthi, M.M. / Prevel, C. / Poullennec, K. / Romanov, S. / Valade, A. / ...Authors: Hall, A. / Abendroth, J. / Bolejack, M.J. / Ceska, T. / Dell'Aiera, S. / Ellis, V. / Fox 3rd, D. / Francois, C. / Muruthi, M.M. / Prevel, C. / Poullennec, K. / Romanov, S. / Valade, A. / Vanbellinghen, A. / Yano, J. / Geraerts, M.
History
DepositionApr 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase alpha-5
B: Ribosomal protein S6 kinase alpha-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2434
Polymers69,3382
Non-polymers9052
Water41423
1
A: Ribosomal protein S6 kinase alpha-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1212
Polymers34,6691
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal protein S6 kinase alpha-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1212
Polymers34,6691
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.930, 90.520, 135.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEU(chain 'A' and (resid 416 through 484 or resid 486...AA416 - 4844 - 72
12GLUGLUSERSER(chain 'A' and (resid 416 through 484 or resid 486...AA486 - 52274 - 110
13ILEILEMETMET(chain 'A' and (resid 416 through 484 or resid 486...AA524 - 525112 - 113
14LYSLYSASPASP(chain 'A' and (resid 416 through 484 or resid 486...AA527 - 554115 - 142
15LEULEUPROPRO(chain 'A' and (resid 416 through 484 or resid 486...AA559 - 573147 - 161
16ASPASPGLNGLN(chain 'A' and (resid 416 through 484 or resid 486...AA599 - 622168 - 191
17LEULEULYSLYS(chain 'A' and (resid 416 through 484 or resid 486...AA628 - 723197 - 292
181LE1LE1LE1LE(chain 'A' and (resid 416 through 484 or resid 486...AC900
29ASPASPLEULEU(chain 'B' and (resid 416 through 441 or (resid 442...BB416 - 4844 - 72
210GLUGLUSERSER(chain 'B' and (resid 416 through 441 or (resid 442...BB486 - 52274 - 110
211ILEILEMETMET(chain 'B' and (resid 416 through 441 or (resid 442...BB524 - 525112 - 113
212LYSLYSASPASP(chain 'B' and (resid 416 through 441 or (resid 442...BB527 - 554115 - 142
213LEULEUPROPRO(chain 'B' and (resid 416 through 441 or (resid 442...BB559 - 573147 - 161
214ASPASPGLNGLN(chain 'B' and (resid 416 through 441 or (resid 442...BB599 - 622168 - 191
215LEULEULYSLYS(chain 'B' and (resid 416 through 441 or (resid 442...BB628 - 723197 - 292
2161LE1LE1LE1LE(chain 'B' and (resid 416 through 441 or (resid 442...BD900

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Components

#1: Protein Ribosomal protein S6 kinase alpha-5 / S6K-alpha-5 / 90 kDa ribosomal protein S6 kinase 5 / Nuclear mitogen- and stress-activated protein ...S6K-alpha-5 / 90 kDa ribosomal protein S6 kinase 5 / Nuclear mitogen- and stress-activated protein kinase 1 / RSK-like protein kinase / RSKL


Mass: 34668.809 Da / Num. of mol.: 2 / Fragment: Msk1 C-terminal domain, residues 414-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA5, MSK1 / Production host: Escherichia coli (E. coli)
References: UniProt: O75582, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-1LE / (2S)-2-cyano-N-(1-hydroxy-2-methylpropan-2-yl)-3-[3-(3,4,5-trimethoxyphenyl)-1H-indazol-5-yl]propanamide


Mass: 452.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H28N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystals were produced by sitting drop vapor diffusion with an equal volume of the protein, Msk1-C terminal domain (PID7059-1, CID101276) at 5 mg/ml with 1.5mM UCB1590591/BSI106893 in 25mM ...Details: Crystals were produced by sitting drop vapor diffusion with an equal volume of the protein, Msk1-C terminal domain (PID7059-1, CID101276) at 5 mg/ml with 1.5mM UCB1590591/BSI106893 in 25mM HEPES pH 7.5, 150mM NaCl, 5% Glycerol, 5mM BME and a crystallization buffer containing 100mM sodium malonate pH 8.0, 100mM Tris pH 8.0, 30% w/v PEG 1000 (tray ID 305760, well F2, CID101276_fine1 screen). Crystals were soaked for 4 days in 2.5ul of reservoir with 1mM UCB1590956/BSI100006.Crystals were cryo protected with 20% EG + compound and vitrified in in liquid N2. Puck ID WJP9-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 13, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16052 / % possible obs: 99.8 % / Redundancy: 5.267 % / Biso Wilson estimate: 51.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.095 / Χ2: 1.027 / Net I/σ(I): 16.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.875.3770.576311700.8530.637100
2.87-2.955.3740.4513.811340.8940.49999.9
2.95-3.045.3920.4294.0111020.9140.474100
3.04-3.135.3480.3394.9810700.9410.375100
3.13-3.235.3390.2666.5410570.9560.295100
3.23-3.355.3590.2028.5310050.9750.22399.8
3.35-3.475.3220.15810.539820.9890.175100
3.47-3.615.3270.12113.159410.9920.13399.7
3.61-3.785.3130.08917.248990.9950.099100
3.78-3.965.310.07120.448680.9970.07899.9
3.96-4.175.250.05625.38280.9980.062100
4.17-4.435.2710.04729.367750.9980.052100
4.43-4.735.2720.04331.417560.9990.04799.9
4.73-5.115.2310.04530.026930.9990.0599.7
5.11-5.65.1980.04927.346370.9980.05499.7
5.6-6.265.1020.04827.915890.9980.05399.8
6.26-7.235.0510.04131.765320.9990.04699.8
7.23-8.854.9590.02740.544010.0399.5
8.85-12.524.7960.02146.9736710.02399.5
12.52-504.1110.02242.942070.9990.02694.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 2.8→47.68 Å / SU ML: 0.369 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1603 9.99 %0
Rwork0.1813 14444 --
obs0.1877 16047 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.16 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4282 0 0 23 4305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324395
X-RAY DIFFRACTIONf_angle_d0.59145966
X-RAY DIFFRACTIONf_chiral_restr0.0431675
X-RAY DIFFRACTIONf_plane_restr0.0034760
X-RAY DIFFRACTIONf_dihedral_angle_d19.03731528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.890.34171270.2271302X-RAY DIFFRACTION99.86
2.89-2.990.29441560.22451283X-RAY DIFFRACTION100
2.99-3.110.33181530.2291260X-RAY DIFFRACTION100
3.11-3.260.29391530.21631297X-RAY DIFFRACTION99.93
3.26-3.430.28081370.19521305X-RAY DIFFRACTION99.93
3.43-3.640.29471530.19181299X-RAY DIFFRACTION99.79
3.64-3.920.23921500.17731297X-RAY DIFFRACTION99.93
3.92-4.320.19591430.14431304X-RAY DIFFRACTION100
4.32-4.940.21251350.13671337X-RAY DIFFRACTION99.86
4.94-6.220.23321360.1911351X-RAY DIFFRACTION99.66
6.22-47.680.20531600.18681409X-RAY DIFFRACTION98.87
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)
16.00804986526-0.790842328609-1.053703519043.426805007891.585839896993.80132410325-0.01330051313610.1452465119380.695071635711-0.1071734349830.2836138308340.3769294220550.0828216780579-0.599514382669-0.1696816967230.3326766144450.0759344700457-0.1322470832670.548418564185-0.01395938079720.44854934477410.747450405342.949767369285.6024055206
25.81933771079-0.519529936787-1.528412946382.71221933819-0.9206119842823.735976219120.01015921920910.249819190656-0.197144186629-0.25005055161-0.06265797403980.0022084272510.178173796801-0.1897189527290.1209456160020.205876134620.00920223008867-0.00296114947410.3464458776190.007333408700780.28988437430519.192501066135.882643377786.6779342719
38.823061160440.878997676663-3.301951475811.88625915530.01888024819613.1520445210.103890182202-0.3427058619430.104132957799-0.0234834607022-0.1431857276780.2279256924470.136579146626-0.1046476370270.04475072195720.242277019750.0129995783477-0.04449529217120.318200384158-0.03607805660770.24983485650121.916733378437.443825186690.9085081044
48.408433558070.0885647860313-4.99336154451.72710333131-0.1913019235136.30860684540.2965267783930.3929382331650.535902420609-0.2124667466490.17878460226-0.0962654519448-0.682788875185-0.340309526761-0.4278715818080.3882332620050.0189969778786-0.01917372925410.3328486987610.06411291223970.40888297664135.704249988946.945530502773.5101258796
55.687406626610.911260528247-2.176323332913.96838189662-2.176732748725.926980477290.0115206658714-0.5547661757420.208364067380.107026761152-0.0086976982926-0.0604702143592-0.03703531466890.428046729416-0.03966493044860.283220332118-0.006638253350390.01330396757690.252078072241-0.07217965565620.24535091245339.03326148438.357634804882.9746524548
66.295219116651.26806191571-3.597677562532.96643050173-0.8819043101955.4521513309-0.419929763135-0.288085899025-0.7224365464-0.4133353997720.05756467895450.08329095277290.977474623815-0.0004869015205780.2753915652250.3199741410650.0214525669768-0.01926832783260.337961804690.04129341783550.39565164880538.733581569629.842189250479.9298460521
74.393577476961.93751220717-1.84315063526.831496957740.2299993857184.50296597062-0.5118676015170.601033901624-0.334108078874-1.057090110360.135045542601-0.4183946392110.8316816104480.5569684851740.2354841369950.6152707870640.07522262570270.06564017699080.4744712228450.01201192726030.57176197674847.114958471729.484328542366.5488558361
86.26974495326-1.105371670963.293825279135.019062618760.1906106985862.731110938680.118231651081-0.0863486125137-0.2844167230470.1474788220060.0438889530344-0.2088899487460.4050253069140.6114841417060.1941692666040.4569633839260.0594409818443-0.05382762454360.498125637954-0.007685706355930.47228646366152.5076866635.805969600979.6581352656
93.53314066679-0.1312564699561.589766238571.586735442521.872698302574.59735647858-0.3475035279760.626106735355-0.669673265517-0.7780050539030.1826034016670.9882320027060.89707727499-1.045372368360.08913366030450.562291130223-0.1047822674770.03393098300110.658579274815-0.1722183999040.67087432284636.255131453333.35235309766.4582783516
106.393412181830.638131020006-0.7381559293173.76004449115-1.23565791743.639437422790.00436266387195-0.277277835566-0.01139532664170.293517517252-0.0972962475280.22879668864-0.142902163976-0.1696801096170.03938607314320.2572041432750.0257856086836-0.02287082429110.339179282875-0.07712621692520.2350771162410.54666952922755.882649551141.324296627
116.05413031410.5786004850792.179098292660.5923107225690.6557939139882.088329804590.04486282530910.110057757558-0.3310996116730.05573643475230.0807036621126-0.05773399580250.09600240762650.14141189201-0.1327410907410.2970289544210.05129429725350.01217946520960.2800488155720.01000308040780.3245972188618.61259467957.647401122844.648330244
124.37568671197-2.25651624060.4888116162556.092207070620.4006249264282.14739480527-0.0567524962577-0.1477088672740.384043112410.07782542403610.259123497489-0.371271165267-0.3243920084560.20993875141-0.1366358120030.365317223560.0216905695198-0.02316039003240.381204461985-0.01605971992050.43055993382632.905644645469.113680599852.3703018304
135.95422351756-0.376929669971-2.476833693894.64996097611-0.6495269522556.60082668131-0.411921206447-0.6108079951180.1425566538420.6654009317520.3576222717970.6171676265-0.448915080808-0.1430591113930.1261688682270.341717306726-0.0365891662238-0.1243412813380.419539591152-0.1156744549430.48646475917825.428803711163.912781763555.9750403356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 415 through 432 )
2X-RAY DIFFRACTION2chain 'A' and (resid 433 through 474 )
3X-RAY DIFFRACTION3chain 'A' and (resid 475 through 498 )
4X-RAY DIFFRACTION4chain 'A' and (resid 499 through 517 )
5X-RAY DIFFRACTION5chain 'A' and (resid 518 through 563 )
6X-RAY DIFFRACTION6chain 'A' and (resid 564 through 616 )
7X-RAY DIFFRACTION7chain 'A' and (resid 617 through 667 )
8X-RAY DIFFRACTION8chain 'A' and (resid 668 through 698 )
9X-RAY DIFFRACTION9chain 'A' and (resid 699 through 724)
10X-RAY DIFFRACTION10chain 'B' and (resid 416 through 474 )
11X-RAY DIFFRACTION11chain 'B' and (resid 475 through 616 )
12X-RAY DIFFRACTION12chain 'B' and (resid 617 through 686 )
13X-RAY DIFFRACTION13chain 'B' and (resid 687 through 727 )

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  • 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

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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

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