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- PDB-9yit: Crystal structure of glutamate dehydrogenase from Babesia microti... -

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Basic information

Entry
Database: PDB / ID: 9yit
TitleCrystal structure of glutamate dehydrogenase from Babesia microti in complex with NADP
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / glutamate dehydrogenase / Babesia microti
Function / homology
Function and homology information


glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / nucleotide binding / cytosol
Similarity search - Function
: / Glutamate dehydrogenase / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal ...: / Glutamate dehydrogenase / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glutamate dehydrogenase
Similarity search - Component
Biological speciesBabesia microti strain RI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of glutamate dehydrogenase from Babesia microti in complex with NADP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionOct 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate dehydrogenase
B: Glutamate dehydrogenase
C: Glutamate dehydrogenase
D: Glutamate dehydrogenase
E: Glutamate dehydrogenase
F: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,43418
Polymers319,8086
Non-polymers5,62612
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34040 Å2
ΔGint14 kcal/mol
Surface area91060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.667, 125.313, 123.706
Angle α, β, γ (deg.)90.00, 100.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutamate dehydrogenase


Mass: 53301.367 Da / Num. of mol.: 6 / Fragment: 2-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Babesia microti strain RI (eukaryote) / Gene: BMR1_03g03380 / Plasmid: BamiA.17991.a.A21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K3AUK4
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% 3350, 0.1M Bis-Tris 6.5, 0.2M MgCl2. BamiA.17991.a.A21.PW39288 at 16.7 mg/mL. 2mM NADP added to the protein prior to crystallization. plate 19938 F4 drop1, Puck: PSL-0509, Cryo: 12.5% ...Details: 25% 3350, 0.1M Bis-Tris 6.5, 0.2M MgCl2. BamiA.17991.a.A21.PW39288 at 16.7 mg/mL. 2mM NADP added to the protein prior to crystallization. plate 19938 F4 drop1, Puck: PSL-0509, Cryo: 12.5% P200 + 87.5% crystallant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 25, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.28→48.86 Å / Num. obs: 144200 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.073 / Rrim(I) all: 0.191 / Χ2: 1.05 / Net I/σ(I): 9.4 / Num. measured all: 994280
Reflection shellResolution: 2.28→2.34 Å / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.332 / Num. measured all: 72665 / Num. unique obs: 10631 / CC1/2: 0.493 / Rpim(I) all: 0.548 / Rrim(I) all: 1.442 / Χ2: 0.98 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(dev_5438: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→48.02 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 7171 4.97 %
Rwork0.1902 --
obs0.1919 144167 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21277 0 366 253 21896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422098
X-RAY DIFFRACTIONf_angle_d0.70129880
X-RAY DIFFRACTIONf_dihedral_angle_d15.2448352
X-RAY DIFFRACTIONf_chiral_restr0.0453258
X-RAY DIFFRACTIONf_plane_restr0.0063867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.310.31412070.27694587X-RAY DIFFRACTION100
2.31-2.330.30822400.2654539X-RAY DIFFRACTION100
2.33-2.360.31581920.25584575X-RAY DIFFRACTION100
2.36-2.390.27032400.25184535X-RAY DIFFRACTION100
2.39-2.420.28462450.24844552X-RAY DIFFRACTION100
2.42-2.460.26622650.23184557X-RAY DIFFRACTION100
2.46-2.490.3052310.24094509X-RAY DIFFRACTION100
2.49-2.530.28542560.23144566X-RAY DIFFRACTION100
2.53-2.570.25762290.23534538X-RAY DIFFRACTION100
2.57-2.610.28512400.23054545X-RAY DIFFRACTION100
2.61-2.650.2822270.2224569X-RAY DIFFRACTION100
2.65-2.70.26432420.21554521X-RAY DIFFRACTION100
2.7-2.760.27272580.21224526X-RAY DIFFRACTION100
2.76-2.810.26292510.20474598X-RAY DIFFRACTION100
2.81-2.870.24982590.21244480X-RAY DIFFRACTION100
2.87-2.940.28082350.22224598X-RAY DIFFRACTION100
2.94-3.010.25282420.22584556X-RAY DIFFRACTION100
3.01-3.090.26432480.21454566X-RAY DIFFRACTION100
3.09-3.190.26282240.21844573X-RAY DIFFRACTION100
3.19-3.290.23462330.20194582X-RAY DIFFRACTION100
3.29-3.410.22632320.20554586X-RAY DIFFRACTION100
3.41-3.540.21952320.19684556X-RAY DIFFRACTION100
3.54-3.70.1961940.18184619X-RAY DIFFRACTION100
3.7-3.90.2262440.16944595X-RAY DIFFRACTION100
3.9-4.140.18282590.15384524X-RAY DIFFRACTION100
4.14-4.460.172370.1454593X-RAY DIFFRACTION100
4.46-4.910.15992370.14164587X-RAY DIFFRACTION100
4.91-5.620.18042640.15924572X-RAY DIFFRACTION100
5.62-7.080.22242450.17994630X-RAY DIFFRACTION100
7.08-48.020.17622630.16054662X-RAY DIFFRACTION100
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)
10.476-0.27670.06220.1102-0.03010.14460.1239-0.022-0.1377-0.2581-0.0763-0.04270.2316-0.010300.44060.01860.00710.3781-0.01860.469544.077-36.5589-24.3977
20.1852-0.1546-0.19050.6324-0.30660.6489-0.01750.0632-0.1486-0.09270.02140.01540.13550.0529-00.3844-0.0056-0.0120.3486-0.04660.29740.8578-21.9202-36.5482
3-0.0059-0.137-0.06550.29290.20010.1090.09110.0893-0.2391-0.005-0.0211-0.06240.25370.0490.00060.436-0.02230.04340.4138-0.04160.307845.2454-17.7348-39.874
40.28170.3436-0.1060.3410.1820.36620.0596-0.03980.0434-0.0591-0.0203-0.067-0.15040.129800.4209-0.03590.01980.3713-0.00740.337437.8484-4.5319-43.1997
50.066-0.4628-0.13621.04430.05480.80780.1380.15510.2174-0.3391-0.1724-0.347-0.0270.2996-0.02520.41250.0390.11020.50660.03780.358167.2849-11.1681-46.8407
60.52780.2305-0.46390.4205-0.15250.2453-0.1310.0826-0.2092-0.18280.02280.09060.5563-0.036800.61540.10370.12710.5788-0.0020.447770.7956-25.6071-50.1618
70.2275-0.2731-0.12070.1919-0.01650.3292-0.06040.0061-0.1095-0.0702-0.00080.10360.1410.1122-00.38670.03530.06540.31960.00020.341660.1987-15.0709-35.2642
80.1673-0.1660.04850.2140.1380.4827-0.0568-0.09880.09510.0121-0.0882-0.6611-0.09670.11-00.4154-0.01170.06270.4585-0.00370.447564.633-13.6991-28.027
90.1409-0.11160.17890.0555-0.13030.1989-0.0356-0.0468-0.1530.0737-0.0084-0.03950.17220.007700.33480.01540.06190.3560.01320.354554.4021-24.8323-23.1231
100.438-0.0520.33630.41320.09890.2952-0.0029-0.06050.34210.3519-0.02340.3526-0.079-0.138100.4420.00680.05110.356-0.04680.421934.861620.48988.7432
110.45850.32010.07711.34960.28610.5648-0.02440.0133-0.02110.08720.0537-0.0093-0.0280.0193-00.2410.03110.01390.25050.0150.254437.7088-2.5254-2.4793
120.09190.21640.0090.08920.02750.5174-0.10460.1315-0.1517-0.09590.1406-0.1628-0.05750.1474-00.3470.00360.00720.349-0.02350.392256.8544-2.4642-7.9313
130.8592-0.0448-0.15440.9524-0.39921.25830.0244-0.0259-0.18430.06750.0097-0.12050.12680.142400.31410.0239-0.02810.32090.02570.355666.8625-7.168710.7119
14-0.07870.06680.25660.0284-0.27220.7109-0.05180.04380.0267-0.03880.01080.0017-0.01930.0892-00.31450.015-0.00070.3328-0.01510.338954.82529.4023-2.4715
150.63490.4988-0.25010.5124-0.2840.09330.16160.2198-0.1698-0.4009-0.06480.3871-0.2243-0.0483-0.01080.6201-0.0065-0.01130.58570.04410.316537.685320.2982-58.087
160.6883-0.2073-0.67560.7070.06080.84050.01450.05970.0614-0.13880.0020.0703-0.15040.018600.3659-0.0354-0.01360.33130.02390.326535.470122.3687-32.6522
170.1803-0.11390.02890.7138-0.13170.45120.0355-0.00160.11260.1197-0.02-0.15-0.10670.175700.3779-0.03280.03770.39950.01540.38359.400829.6168-28.7797
180.50190.2643-0.15771.09820.67680.4827-0.1093-0.00460.1919-0.30010.0058-0.0957-0.31260.030800.5194-0.04780.03840.38810.01830.459959.272743.5391-30.9476
190.4983-0.0610.29920.14220.05030.1614-0.21710.2146-0.1481-0.14640.1253-0.30240.0148-0.0457-0.00010.3858-0.0460.04610.34680.00980.309254.601823.3689-35.1353
200.1265-0.06810.00640.25070.04440.1268-0.26040.0938-0.37760.0196-0.1163-0.18340.00770.3152-0.00140.4043-0.01340.0720.4251-0.02290.388461.124117.7302-36.7518
210.22120.0350.12620.1248-0.12270.1276-0.1330.4447-0.2467-0.70360.1401-0.28790.11530.1418-0.00070.3993-0.06230.06540.4260.02170.281550.099616.314-49.8531
220.6433-0.1683-0.51320.4361-0.24730.3941-0.01680.0930.0605-0.13260.07310.1866-0.0455-0.03890.00090.3610.0017-0.07420.38520.03990.366911.466617.2159-38.3721
230.65670.365-0.09142.152-0.58070.7517-0.10640.15880.3378-0.62860.32620.7285-0.004-0.19980.91920.4751-0.016-0.27450.47170.20730.5988-9.797818.0271-43.9484
240.142-0.02430.06070.51910.42210.34740.15870.56010.025-0.6006-0.14230.0243-0.07670.5152-00.5836-0.0297-0.08740.6816-0.0420.351419.912-21.4526-58.4149
250.2494-0.11390.12190.05980.10650.2731-0.01510.2736-0.0573-0.1772-0.0210.02170.02610.220100.39120.0056-0.06120.411-0.04280.332919.1188-22.5945-46.6796
260.2372-0.20750.14370.5768-0.14370.55760.01890.0337-0.1341-0.16570.0550.08830.1296-0.053500.3303-0.0238-0.0180.34840.00690.389820.0975-22.8508-27.3929
270.0321-0.1667-0.2390.74140.33050.9308-0.049-0.0743-0.0680.0942-0.00430.28330.1435-0.281400.3276-0.0655-0.0890.43030.02290.5102-5.3036-33.2975-27.7257
280.35080.13580.01670.31710.13940.555-0.20760.1734-0.0602-0.66090.09180.31490.4346-0.3326-0.00980.6539-0.1453-0.16660.558-0.06550.6489-4.2775-44.3543-38.0457
290.4020.011-0.24530.1374-0.07780.2459-0.24430.2321-0.0447-0.60510.29190.1023-0.16080.2705-00.509-0.0513-0.09690.4419-0.01810.40390.9491-23.9091-36.4129
300.2383-0.191-0.09360.20840.26620.30690.02140.1744-0.087-0.12390.07510.241-0.0784-0.1334-00.4785-0.0086-0.10340.5361-0.00930.52760.9032-17.6744-45.2401
310.61690.2782-0.05841.7469-0.21440.26270.0283-0.06490.02320.1622-0.01510.1902-0.04150.0126-00.29130.03450.03670.3227-0.00410.344615.7056-1.3619-1.2871
320.1610.1994-0.4160.46350.34790.576-0.28630.2040.0579-0.14550.1410.09570.1868-0.189400.313-0.0196-0.04670.36220.01190.4862-3.25782.752-9.8397
330.9452-0.8601-0.63950.74540.38651.9347-0.103-0.04850.10790.08320.02130.1175-0.02380.0518-00.31320.0016-00.3495-0.04450.4527-13.50187.65778.6382
340.2797-0.26090.07590.7160.12810.0893-0.1281-0.07160.00980.0820.07360.14760.09530.120800.28740.02960.00360.34120.06110.4593-2.8802-3.3022-3.6006
350.3418-0.4682-0.16970.5636-0.28950.9457-0.05990.2094-0.2342-0.07340.03430.2110.1436-0.1259-00.3316-0.03530.00390.3674-0.00740.4989-0.9855-13.6986-4.5696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 153 )
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 201 )
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 314 )
6X-RAY DIFFRACTION6chain 'A' and (resid 315 through 371 )
7X-RAY DIFFRACTION7chain 'A' and (resid 372 through 413 )
8X-RAY DIFFRACTION8chain 'A' and (resid 414 through 439 )
9X-RAY DIFFRACTION9chain 'A' and (resid 440 through 467 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 37 )
11X-RAY DIFFRACTION11chain 'B' and (resid 38 through 201 )
12X-RAY DIFFRACTION12chain 'B' and (resid 202 through 240 )
13X-RAY DIFFRACTION13chain 'B' and (resid 241 through 371 )
14X-RAY DIFFRACTION14chain 'B' and (resid 372 through 467 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 37 )
16X-RAY DIFFRACTION16chain 'C' and (resid 38 through 201 )
17X-RAY DIFFRACTION17chain 'C' and (resid 202 through 285 )
18X-RAY DIFFRACTION18chain 'C' and (resid 286 through 371 )
19X-RAY DIFFRACTION19chain 'C' and (resid 372 through 413 )
20X-RAY DIFFRACTION20chain 'C' and (resid 414 through 438 )
21X-RAY DIFFRACTION21chain 'C' and (resid 439 through 467 )
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 240 )
23X-RAY DIFFRACTION23chain 'D' and (resid 241 through 467 )
24X-RAY DIFFRACTION24chain 'E' and (resid 2 through 37 )
25X-RAY DIFFRACTION25chain 'E' and (resid 38 through 82 )
26X-RAY DIFFRACTION26chain 'E' and (resid 83 through 201 )
27X-RAY DIFFRACTION27chain 'E' and (resid 202 through 314 )
28X-RAY DIFFRACTION28chain 'E' and (resid 315 through 371 )
29X-RAY DIFFRACTION29chain 'E' and (resid 372 through 413 )
30X-RAY DIFFRACTION30chain 'E' and (resid 414 through 467 )
31X-RAY DIFFRACTION31chain 'F' and (resid 2 through 201 )
32X-RAY DIFFRACTION32chain 'F' and (resid 202 through 240 )
33X-RAY DIFFRACTION33chain 'F' and (resid 241 through 371 )
34X-RAY DIFFRACTION34chain 'F' and (resid 372 through 413 )
35X-RAY DIFFRACTION35chain 'F' and (resid 414 through 467 )

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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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