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- PDB-5f5u: Crystal structure of the Snu23-Prp38-MFAP1(217-258) complex of Ch... -

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Basic information

Entry
Database: PDB / ID: 5f5u
TitleCrystal structure of the Snu23-Prp38-MFAP1(217-258) complex of Chaetomium thermophilum
Components
  • Prp38
  • Putative uncharacterized protein
  • Zinc finger domain-containing protein
KeywordsSPLICING / B-specific protein / heterotrimer / pre-mRNA splicing / SAH
Function / homology
Function and homology information


spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / zinc ion binding
Similarity search - Function
Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / PRP38 family / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger ...Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / PRP38 family / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Pre-mRNA-splicing factor 38 / Zinc finger domain-containing protein / Micro-fibrillar-associated protein 1 C-terminal domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.748 Å
AuthorsUlrich, A.K.C. / Seeger, M. / Bartlick, N. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationWA1126/7-1 Germany
CitationJournal: Structure / Year: 2016
Title: Scaffolding in the Spliceosome via Single alpha Helices.
Authors: Ulrich, A.K.C. / Seeger, M. / Schutze, T. / Bartlick, N. / Wahl, M.C.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prp38
B: Putative uncharacterized protein
C: Zinc finger domain-containing protein
D: Prp38
E: Putative uncharacterized protein
F: Zinc finger domain-containing protein
G: Prp38
H: Putative uncharacterized protein
I: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)119,8399
Polymers119,8399
Non-polymers00
Water1,820101
1
A: Prp38
B: Putative uncharacterized protein
C: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,9463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-15 kcal/mol
Surface area15150 Å2
MethodPISA
2
D: Prp38
E: Putative uncharacterized protein
F: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,9463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-17 kcal/mol
Surface area16180 Å2
MethodPISA
3
G: Prp38
H: Putative uncharacterized protein
I: Zinc finger domain-containing protein


Theoretical massNumber of molelcules
Total (without water)39,9463
Polymers39,9463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-15 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.960, 95.260, 133.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
31chain G
12chain B
22chain E
32chain H
13chain C
23chain F
33chain I

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUchain AAA22 - 20925 - 212
21LEULEUASNASNchain DDD15 - 21618 - 219
31GLYGLYLYSLYSchain GGG22 - 21525 - 218
12GLYGLYARGARGchain BBB213 - 2571 - 45
22VALVALARGARGchain EEE221 - 2589 - 46
32THRTHRARGARGchain HHH217 - 2585 - 46
13GLYGLYSERSERchain CCC131 - 1623 - 34
23GLUGLUVALVALchain FFF132 - 1604 - 32
33VALVALVALVALchain III133 - 1605 - 32

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Prp38


Mass: 25617.205 Da / Num. of mol.: 3 / Fragment: NTR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0013190 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0S1D3
#2: Protein Putative uncharacterized protein


Mass: 10139.329 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0069660 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0SHD7
#3: Protein/peptide Zinc finger domain-containing protein


Mass: 4189.787 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0035280 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0S6R0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 4.75 / Details: 0.1M citric acid, pH 4.75, and 15% (w/v) PEG 6,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.748→19.93 Å / Num. obs: 30180 / % possible obs: 99.5 % / Redundancy: 5 % / Rsym value: 0.15 / Net I/σ(I): 11.1
Reflection shellResolution: 2.748→2.82 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rz9

4rz9


Resolution: 2.748→19.927 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 1524 5.06 %Random selection
Rwork0.2294 28618 --
obs0.2317 30142 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 263.64 Å2 / Biso mean: 92.5637 Å2 / Biso min: 32.87 Å2
Refinement stepCycle: final / Resolution: 2.748→19.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6577 0 0 101 6678
Biso mean---64.1 -
Num. residues----798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046688
X-RAY DIFFRACTIONf_angle_d0.8368993
X-RAY DIFFRACTIONf_chiral_restr0.033974
X-RAY DIFFRACTIONf_plane_restr0.0041172
X-RAY DIFFRACTIONf_dihedral_angle_d14.362630
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2809X-RAY DIFFRACTION9.967TORSIONAL
12D2809X-RAY DIFFRACTION9.967TORSIONAL
13G2809X-RAY DIFFRACTION9.967TORSIONAL
21B612X-RAY DIFFRACTION9.967TORSIONAL
22E612X-RAY DIFFRACTION9.967TORSIONAL
23H612X-RAY DIFFRACTION9.967TORSIONAL
31C423X-RAY DIFFRACTION9.967TORSIONAL
32F423X-RAY DIFFRACTION9.967TORSIONAL
33I423X-RAY DIFFRACTION9.967TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7483-2.83670.4331520.38232528268099
2.8367-2.93780.42611250.356825582683100
2.9378-3.0550.33481260.334225972723100
3.055-3.19350.35691390.315725692708100
3.1935-3.36120.32271320.27525732705100
3.3612-3.57060.3241370.24425822719100
3.5706-3.84450.27721530.220225842737100
3.8445-4.2280.20511400.191226052745100
4.228-4.83220.22161240.179226322756100
4.8322-6.05960.26051420.208526522794100
6.0596-19.92780.24631540.19842738289299
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)
16.2235-6.1969-5.29486.14895.17245.8868-1.4736-1.55-2.22991.28240.50122.28651.4068-0.21541.0770.83-0.13650.00751.51090.23221.370327.404528.7551160.7698
22.0862-1.9929-3.70732.14233.73359.5504-0.4795-0.3748-1.96680.56830.63740.34861.6737-0.1802-0.48580.77850.0623-0.06570.74940.19761.2641.463124.0121154.4802
30.23670.98850.49894.8488-0.25588.60170.8167-0.9343-1.24870.9682-0.0692-0.43150.08291.1052-0.51690.35030.1077-0.47481.2630.59370.7650.604233.1222161.4001
45.91710.0893-0.55926.0693-1.12384.38290.1746-0.5581-0.51250.31720.10190.15540.19270.0196-0.26270.34690.0319-0.03030.52640.16560.458740.694640.2768155.5003
53.4314-0.79193.63012.0837-1.2079.25360.2983-0.36620.83-0.2489-0.4736-0.30550.4872-0.04980.22670.37980.00580.02650.6910.04760.609925.275543.172150.0569
69.68-1.07982.35018.1141-4.9273.3690.31062.5017-0.9146-1.6108-0.3171-0.51420.57860.08810.13660.59770.1180.01871.0809-0.0360.737443.046842.9993141.2201
78.98362.7482-0.3731.6507-0.18243.98620.0291.025-0.5444-0.39430.14180.21750.6054-0.5745-0.11790.46310.0345-0.11840.62250.02730.706928.51237.2376143.6194
80.5516-1.1447-0.04376.61321.51250.45640.25041.60342.3528-0.57251.39052.0617-0.8642-1.5775-1.53140.69430.0955-0.28041.22090.45731.279318.679650.7681139.1758
96.60535.3074-1.4297.13452.5465.12071.5915-1.25360.66640.6730.7290.8078-0.03691.6081-1.83660.6149-0.0636-0.03050.994-0.05350.909246.349154.1868143.0144
103.94065.53422.21098.26054.38092.3498-0.1191.5138-0.2862-0.364-0.11020.45530.149-0.28920.28740.62650.0328-0.21051.26440.08251.058123.087843.9054130.3005
116.7861.01686.36243.50971.4166.1126-0.9346-0.4372-2.80533.26710.3427-0.71360.1120.11390.41480.8688-0.0390.06721.52540.41431.082940.765638.0163173.6375
124.5223-0.9824.25723.1866-0.76954.05960.0711-0.98270.89550.4346-0.4207-1.0935-0.94511.51140.54240.6617-0.06950.08841.03990.01430.992748.746555.7628160.9174
139.45652.8073-4.48134.258-3.37596.1396-1.0967-1.0216-0.7782-0.2760.3101-1.27531.07270.47460.66040.53990.01070.02520.90540.02991.076236.0585-8.7223130.8748
147.3353-0.2850.76973.7884-1.03694.68990.0552-0.39280.630.20620.0507-0.3519-0.15910.3495-0.10310.3568-0.02720.07270.576-0.09020.655339.46768.0519128.5094
156.22522.71722.70053.6588-0.7782.52280.03220.57350.6176-0.2857-0.0016-0.2062-0.1155-0.0676-0.07750.4695-0.01080.06740.72890.01280.675330.08729.092116.5035
161.3799-2.5934-1.54644.94432.91591.76260.5371.7537-0.2597-1.33110.54341.0465-0.39-0.7543-0.65881.84630.6220.05332.83530.64321.917124.819526.5473103.2837
173.2434.96462.21677.95393.51945.0061-0.20541.40920.1219-0.61650.0028-0.6343-0.3236-0.00730.35330.72710.09220.08820.9960.28140.990723.08613.3947104.7197
181.5939-1.21220.2960.9294-0.09938.0315-0.7557-0.8757-1.44120.74151.7941-1.64861.1628-0.1197-1.25340.80950.03-0.07771.3415-0.0631.306240.16835.0989145.0514
191.6848-0.26880.86726.0625-1.90935.3310.3929-1.03361.90430.0536-0.0465-0.6409-1.99281.1228-0.26741.053-0.32020.14981.1943-0.35481.381947.080122.76135.5338
202.59651.61671.36771.4448-0.56387.30060.1872-1.47330.81770.68540.37350.4742-0.5214-1.6487-0.58780.9780.48680.22371.9588-0.07331.01957.8611-6.6664155.3376
215.9914-4.8291-1.51317.11393.27751.7332-1.1546-2.2935-1.11312.480.86851.0098-1.3042-0.1570.42681.17170.5176-0.00421.92240.01590.62722.8083-9.2755158.6931
226.45872.5403-3.67626.28750.52112.8099-0.1567-1.65720.35081.2678-0.32770.96691.6728-1.23740.31641.04980.20590.30652.46020.25671.061410.7614-20.5322156.9289
231.7614-0.1730.26591.5861-0.84640.56690.0575-1.5060.48270.9601-0.39820.1649-1.0085-0.7237-0.60730.94070.78040.3562.3945-0.07380.46313.717-6.8032153.0577
245.74025.8283-0.98358.97583.41266.7212-1.2105-2.7271.87440.36061.4361-1.9339-0.26590.0139-0.3410.95660.5026-0.17511.0886-0.24460.71827.047-6.6557146.0349
253.6755-0.0737-2.12881.97962.1225.9234-0.48-1.7503-0.54570.31090.59130.5594-0.2985-0.9422-0.2460.410.11450.03731.08020.17050.563818.7023-15.6079142.9229
264.0487-1.5680.64086.1279-1.56070.36580.2575-0.8267-0.7427-0.80910.40940.57570.5007-0.8215-0.47690.50870.0905-0.08621.2610.27120.824914.6899-16.2701133.6602
270.9865-1.36640.42921.9438-0.78890.598-0.6498-0.51161.1153-1.1624-0.3597-0.2129-0.0621-0.84150.56881.43890.2157-0.24651.6226-0.29241.203928.3358-34.585122.0406
285.5524-4.7191-7.32776.09855.47569.96932.0346-1.59940.90240.61911.5252-1.4926-0.8593-2.4088-2.57230.7508-0.0607-0.06332.05530.62181.69631.1635-29.1939148.1419
297.864-4.1215.28566.6619-5.29346.46090.3021-0.1299-1.0474-1.13380.13750.89210.3935-0.6524-0.30650.81130.1793-0.24170.9071-0.1640.774315.2454-24.6218125.0501
307.9485-0.9035-3.23993.14252.86293.4596-0.3065-1.6169-0.80850.48630.3449-0.1253-0.15510.2729-0.21471.29380.3575-0.26951.914-0.38970.594333.9211-10.1031157.7065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 30 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 45 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 57 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 127 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 142 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 155 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 190 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 191 through 206 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 213 through 222 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 223 through 257 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 131 through 137 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 138 through 162 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 16 through 45 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 46 through 142 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 143 through 199 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 200 through 216 )D0
17X-RAY DIFFRACTION17chain 'E' and (resid 221 through 258 )E0
18X-RAY DIFFRACTION18chain 'F' and (resid 132 through 137 )F0
19X-RAY DIFFRACTION19chain 'F' and (resid 138 through 159 )F0
20X-RAY DIFFRACTION20chain 'G' and (resid 22 through 57 )G0
21X-RAY DIFFRACTION21chain 'G' and (resid 58 through 68 )G0
22X-RAY DIFFRACTION22chain 'G' and (resid 69 through 83 )G0
23X-RAY DIFFRACTION23chain 'G' and (resid 84 through 98 )G0
24X-RAY DIFFRACTION24chain 'G' and (resid 99 through 112 )G0
25X-RAY DIFFRACTION25chain 'G' and (resid 113 through 155 )G0
26X-RAY DIFFRACTION26chain 'G' and (resid 156 through 202 )G0
27X-RAY DIFFRACTION27chain 'G' and (resid 203 through 215 )G0
28X-RAY DIFFRACTION28chain 'H' and (resid 217 through 222 )H0
29X-RAY DIFFRACTION29chain 'H' and (resid 223 through 258 )H0
30X-RAY DIFFRACTION30chain 'I' and (resid 135 through 160 )I0

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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

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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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