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- PDB-5ugh: Crystal structure of Mat2a bound to the allosteric inhibitor PF-0... -

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Basic information

Entry
Database: PDB / ID: 5ugh
TitleCrystal structure of Mat2a bound to the allosteric inhibitor PF-02929366
ComponentsS-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE / Mat2A / SAM / methionine adenosyltransferase
Function / homology
Function and homology information


methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #10 / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain ...GMP Synthetase; Chain A, domain 3 - #10 / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2. / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8AJ / S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.062 Å
AuthorsKaiser, S.E. / Feng, J. / Stewart, A.E.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A.
Authors: Quinlan, C.L. / Kaiser, S.E. / Bolanos, B. / Nowlin, D. / Grantner, R. / Karlicek-Bryant, S. / Feng, J.L. / Jenkinson, S. / Freeman-Cook, K. / Dann, S.G. / Wang, X. / Wells, P.A. / Fantin, V. ...Authors: Quinlan, C.L. / Kaiser, S.E. / Bolanos, B. / Nowlin, D. / Grantner, R. / Karlicek-Bryant, S. / Feng, J.L. / Jenkinson, S. / Freeman-Cook, K. / Dann, S.G. / Wang, X. / Wells, P.A. / Fantin, V.R. / Stewart, A.E. / Grant, S.K.
History
DepositionJan 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 12, 2017Group: Non-polymer description / Structure summary / Category: entity
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description
Revision 2.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine synthase isoform type-2
B: S-adenosylmethionine synthase isoform type-2
C: S-adenosylmethionine synthase isoform type-2
D: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,8628
Polymers175,4594
Non-polymers1,4034
Water6,936385
1
A: S-adenosylmethionine synthase isoform type-2
C: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4314
Polymers87,7302
Non-polymers7022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-23 kcal/mol
Surface area25350 Å2
MethodPISA
2
B: S-adenosylmethionine synthase isoform type-2
D: S-adenosylmethionine synthase isoform type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4314
Polymers87,7302
Non-polymers7022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-22 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.731, 109.100, 149.012
Angle α, β, γ (deg.)90.00, 100.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II


Mass: 43864.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P31153, methionine adenosyltransferase
#2: Chemical
ChemComp-8AJ / 2-(7-chloro-5-phenyl[1,2,4]triazolo[4,3-a]quinolin-1-yl)-N,N-dimethylethan-1-amine / PF-02929366


Mass: 350.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H19ClN4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.062→38.14 Å / Num. obs: 96483 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03252 / Net I/σ(I): 13.92
Reflection shellResolution: 2.062→2.135 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3049 / Mean I/σ(I) obs: 2.22 / CC1/2: 0.903 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P02
Resolution: 2.062→38.136 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.27
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 4639 4.81 %1
Rwork0.1761 ---
obs0.1774 96357 99.59 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Refinement stepCycle: LAST / Resolution: 2.062→38.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11147 0 100 385 11632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311502
X-RAY DIFFRACTIONf_angle_d0.79815613
X-RAY DIFFRACTIONf_dihedral_angle_d12.2864141
X-RAY DIFFRACTIONf_chiral_restr0.0341760
X-RAY DIFFRACTIONf_plane_restr0.0031994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0616-2.0850.33411500.29113039X-RAY DIFFRACTION100
2.085-2.10960.31161280.28093093X-RAY DIFFRACTION100
2.1096-2.13530.30521810.25732983X-RAY DIFFRACTION100
2.1353-2.16230.27891570.26033071X-RAY DIFFRACTION100
2.1623-2.19080.26351630.23773050X-RAY DIFFRACTION100
2.1908-2.22080.24781690.23633044X-RAY DIFFRACTION100
2.2208-2.25250.2581540.21533060X-RAY DIFFRACTION100
2.2525-2.28610.2321450.21023014X-RAY DIFFRACTION100
2.2861-2.32180.2271340.20343113X-RAY DIFFRACTION100
2.3218-2.35990.23281810.20122972X-RAY DIFFRACTION99
2.3599-2.40060.23731440.19253087X-RAY DIFFRACTION100
2.4006-2.44420.23781580.19813050X-RAY DIFFRACTION100
2.4442-2.49120.27451480.19573071X-RAY DIFFRACTION100
2.4912-2.54210.25141520.19993050X-RAY DIFFRACTION100
2.5421-2.59730.22451600.19113046X-RAY DIFFRACTION100
2.5973-2.65770.21441490.19363067X-RAY DIFFRACTION100
2.6577-2.72420.22191490.1833065X-RAY DIFFRACTION100
2.7242-2.79780.2111590.18543043X-RAY DIFFRACTION100
2.7978-2.88010.24331570.17813057X-RAY DIFFRACTION100
2.8801-2.9730.18211510.183063X-RAY DIFFRACTION100
2.973-3.07920.21381540.18923080X-RAY DIFFRACTION100
3.0792-3.20250.20361600.18313066X-RAY DIFFRACTION100
3.2025-3.34810.18291380.16873081X-RAY DIFFRACTION100
3.3481-3.52450.19421620.16073052X-RAY DIFFRACTION100
3.5245-3.74520.21181620.16253023X-RAY DIFFRACTION99
3.7452-4.03410.1771530.15243057X-RAY DIFFRACTION99
4.0341-4.43950.16131500.14483067X-RAY DIFFRACTION99
4.4395-5.08060.17231510.13933061X-RAY DIFFRACTION99
5.0806-6.39610.20181520.16933092X-RAY DIFFRACTION99
6.3961-38.14230.14881680.15653101X-RAY DIFFRACTION98
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)
12.530.97623.05732.54752.73948.65640.1359-0.2845-0.06260.1503-0.1039-0.06030.2621-0.0579-0.03510.2048-0.0319-0.03060.21460.06270.252423.3915-2.626735.1808
24.1186-0.57920.64988.39318.21992.06170.1196-0.7646-0.31730.71840.2971-0.060.50750.2056-0.36550.5583-0.0799-0.07980.53830.15520.276928.5907-5.196747.3169
35.1451-1.45312.48564.6263-0.30023.162-0.3143-0.66410.40841.07270.1908-0.76540.01470.10560.07190.5202-0.0241-0.08620.6060.01060.294830.5368-1.895140.7849
45.8219-4.96282.76814.4261-1.92923.58540.3827-0.3818-0.6862-0.17620.00150.43970.552-0.3532-0.39360.3184-0.1126-0.06340.29880.03320.29512.7963-12.244326.2261
54.4333-1.54921.98034.6281-0.9423.60620.58190.4123-0.8196-0.2052-0.0793-0.09410.98780.4118-0.50360.54320.0341-0.11760.302-0.03760.337821.3827-20.611720.2261
67.2006-1.40050.33394.8737-1.03625.54130.46860.0978-0.4922-0.34440.0388-0.16241.05560.4906-0.49670.57430.089-0.11210.2973-0.03940.381622.471-21.765819.0078
75.72540.3422.10852.2443-0.12264.4776-0.1021-0.57090.41790.0325-0.12710.3832-0.3156-0.76340.23420.2620.0077-0.06050.3479-0.01830.29827.72262.430527.4017
82.47441.14411.20191.30061.45727.66-0.106-1.13730.70550.0394-0.27130.6603-0.9074-1.56250.45730.43280.1325-0.03670.8849-0.16870.6474-2.30176.636632.9339
99.17260.99411.15282.71990.35433.48870.2741-1.1662-0.33490.463-0.34350.42930.3485-0.98020.00490.3615-0.1476-0.00210.58940.02520.30877.9371-5.553736.9734
102.851-0.28413.551.2564-1.23457.88730.00440.1867-0.0836-0.0428-0.02890.1187-0.0599-0.1020.00210.2610.0447-0.01430.2276-0.0890.34661.43853.413543.1292
115.8231.60643.54441.95060.8254.9454-0.05640.42160.0259-0.39420.00980.36150.0905-0.32590.04490.2970.03240.00990.4193-0.05730.283557.14571.516436.8303
123.30322.83372.95994.49481.38873.33430.07170.4283-0.45770.03230.1637-0.2490.4270.3343-0.24060.29150.0673-0.00520.2539-0.04430.387474.5665-7.21550.3303
132.1021.25891.18564.48291.16533.0740.5421-0.1334-0.91960.4002-0.1483-0.28551.0305-0.1491-0.41130.47880.0142-0.01970.23620.03320.452369.2972-14.043656.3461
144.43380.09021.01386.3543-0.99764.55710.398-0.1744-0.94230.3797-0.0554-0.09761.0666-0.2015-0.34060.601-0.0317-0.05910.24470.00680.499768.8213-15.634557.5038
154.57561.21460.95281.44050.27672.9273-0.0710.19730.4102-0.1003-0.12970.0589-0.3472-0.00450.2130.22170.0463-0.02120.1639-0.01130.250874.770712.787451.5097
166.41442.04456.92376.79922.31337.4972-0.75880.5460.5847-0.74390.0905-0.183-1.30640.5470.68930.3448-0.0153-0.03110.42090.07010.402582.723520.314546.0952
174.42333.5504-1.15814.7978-0.98912.8347-0.01280.5931-0.561-0.31460.0105-0.66290.1340.31150.00580.26650.08290.03550.3941-0.03440.318876.91545.817541.2711
189.4146-1.42052.38331.7083-0.03912.6178-0.08250.24070.3071-0.0008-0.0227-0.2833-0.10850.49880.09490.3089-0.0576-0.03130.27340.04920.254433.47889.164121.5672
196.5243-6.1566-0.58996.67611.15934.8919-0.4175-0.66810.99960.28190.4917-0.8339-0.75160.8001-0.08640.4346-0.1695-0.0960.4911-0.04620.474139.820420.816228.8662
202.87510.4731.22433.28350.9122.7410.21120.5044-0.2226-0.0653-0.1188-0.42370.23770.9343-0.05020.30920.00310.00320.52510.01430.223128.72582.137714.2868
213.91011.25221.95732.99261.31373.047-0.4825-0.38251.2112-0.1625-0.17990.5332-0.8742-0.25790.66240.49670.0605-0.14710.3182-0.06190.551514.688425.620420.8484
223.5652-0.22851.23753.2680.51953.80130.02060.2204-0.1113-0.18370.0501-0.04130.12530.2959-0.0940.2142-0.0159-0.02640.21510.02520.179821.14792.440411.6838
236.66351.35027.10572.17150.71317.89960.15931.2598-0.7231-0.6060.1776-0.11380.30530.9494-0.33260.55930.1099-0.06660.5266-0.09030.341423.0029-4.5231-0.9836
243.34940.70672.38353.88282.53412.0673-0.25290.85860.3137-0.65040.1504-0.285-0.44680.7890.15110.396-0.0702-0.00890.49340.07170.289728.80869.73376.179
259.75013.84881.8983.50870.4711.61340.0533-0.38890.1548-0.0885-0.15350.2904-0.0185-0.3180.08970.27410.0544-0.01410.2826-0.08250.244449.4911.054556.9448
265.20883.71070.06565.62880.17271.8984-0.2041-0.11260.6513-0.43190.15771.0473-0.1887-0.62450.04150.29830.0726-0.1240.5416-0.09640.489937.762915.506851.2855
274.1267-0.66591.46533.931-1.00093.3419-0.2453-0.53470.37830.1650.05080.0482-0.2471-0.42640.21960.22170.00970.00410.2902-0.07970.253358.65319.848563.8917
281.10241.0855-0.44374.5069-0.01581.7318-0.68850.12071.23910.0050.05010.1179-1.0417-0.14720.62770.44250.0364-0.12670.3095-0.06690.639961.186133.49957.4673
293.3878-0.29450.7996.04970.34891.9766-0.18640.08720.8787-0.2392-0.0803-0.0876-0.575-0.05620.28090.35010.0281-0.0230.3182-0.03510.397861.22725.916758.3885
306.9736-0.28942.10133.2366-0.27024.00090.2146-0.7383-0.45150.2117-0.15110.08410.3749-0.6258-0.05960.2565-0.048-0.00160.34440.02230.201763.09883.649971.4461
312.01731.78796.07983.75690.03487.87920.3526-1.3085-1.08750.39270.0385-0.0750.5035-0.9387-0.3860.4833-0.092-0.03870.60820.0650.345361.9814-1.377478.6617
322.2713-0.62622.27393.3143-3.67612.0577-0.2673-1.02950.14090.66750.23140.1894-0.3376-0.85180.02670.40910.06320.04220.7503-0.13330.313652.265111.104472.5604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 15:72)
2X-RAY DIFFRACTION2chain 'A' and (resseq 73:90)
3X-RAY DIFFRACTION3chain 'A' and (resseq 91:135)
4X-RAY DIFFRACTION4chain 'A' and (resseq 136:169)
5X-RAY DIFFRACTION5chain 'A' and (resseq 170:224)
6X-RAY DIFFRACTION6chain 'A' and (resseq 225:259)
7X-RAY DIFFRACTION7chain 'A' and (resseq 260:341)
8X-RAY DIFFRACTION8chain 'A' and (resseq 342:364)
9X-RAY DIFFRACTION9chain 'A' and (resseq 365:395)
10X-RAY DIFFRACTION10chain 'B' and (resseq 15:72)
11X-RAY DIFFRACTION11chain 'B' and (resseq 73:143)
12X-RAY DIFFRACTION12chain 'B' and (resseq 144:169)
13X-RAY DIFFRACTION13chain 'B' and (resseq 170:224)
14X-RAY DIFFRACTION14chain 'B' and (resseq 225:259)
15X-RAY DIFFRACTION15chain 'B' and (resseq 260:341)
16X-RAY DIFFRACTION16chain 'B' and (resseq 342:364)
17X-RAY DIFFRACTION17chain 'B' and (resseq 365:395)
18X-RAY DIFFRACTION18chain 'C' and (resseq 15:78)
19X-RAY DIFFRACTION19chain 'C' and (resseq 79:104)
20X-RAY DIFFRACTION20chain 'C' and (resseq 105:151)
21X-RAY DIFFRACTION21chain 'C' and (resseq 152:249)
22X-RAY DIFFRACTION22chain 'C' and (resseq 250:341)
23X-RAY DIFFRACTION23chain 'C' and (resseq 342:363)
24X-RAY DIFFRACTION24chain 'C' and (resseq 364:395)
25X-RAY DIFFRACTION25chain 'D' and (resseq 15:72)
26X-RAY DIFFRACTION26chain 'D' and (resseq 73:110)
27X-RAY DIFFRACTION27chain 'D' and (resseq 111:191)
28X-RAY DIFFRACTION28chain 'D' and (resseq 192:222)
29X-RAY DIFFRACTION29chain 'D' and (resseq 223:279)
30X-RAY DIFFRACTION30chain 'D' and (resseq 280:341)
31X-RAY DIFFRACTION31chain 'D' and (resseq 342:364)
32X-RAY DIFFRACTION32chain 'D' and (resseq 365:395)

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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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