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- PDB-5ds6: Crystal structure the Escherichia coli Cas1-Cas2 complex bound to... -

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Basic information

Entry
Database: PDB / ID: 5ds6
TitleCrystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with splayed ends
Components
  • CRISPR-associated endonuclease Cas1
  • CRISPR-associated endoribonuclease Cas2
  • DNA (28-MER)
  • DNA (29-MER)
KeywordsHydrolase/DNA / Adaptive Immunity / CRISPR-Associated Proteins / CRISPR-Cas Systems / Clustered Regularly Interspaced Short Palindromic Repeats / Integrases / Endodeoxyribonucleases / Endonucleases / DNA binding protein / Hydrolase-DNA complex
Function / homology
Function and homology information


CRISPR-cas system / crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA repair / DNA damage response / protein homodimerization activity ...CRISPR-cas system / crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA repair / DNA damage response / protein homodimerization activity / DNA binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
CRISPR-associated protein Cas2 subtype / CRISPR-associated protein (Cas_Cas2CT1978) / CRISPR-associated protein Cas1, ECOLI subtype / CRISPR-associated protein Cas1, type I-E / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 ...CRISPR-associated protein Cas2 subtype / CRISPR-associated protein (Cas_Cas2CT1978) / CRISPR-associated protein Cas1, ECOLI subtype / CRISPR-associated protein Cas1, type I-E / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / CRISPR-associated endoribonuclease Cas2 / CRISPR-associated endonuclease Cas1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage M13 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.352 Å
AuthorsNunez, J.K. / Harrington, L.B. / Kranzusch, P.J. / Engelman, A.N. / Doudna, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2015
Title: Foreign DNA capture during CRISPR-Cas adaptive immunity.
Authors: Nunez, J.K. / Harrington, L.B. / Kranzusch, P.J. / Engelman, A.N. / Doudna, J.A.
History
DepositionSep 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Apr 6, 2016Group: Source and taxonomy
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 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: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2
F: CRISPR-associated endoribonuclease Cas2
G: DNA (29-MER)
H: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)176,9078
Polymers176,9078
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23460 Å2
ΔGint-156 kcal/mol
Surface area56670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.020, 123.006, 196.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CRISPR-associated endonuclease Cas1


Mass: 33322.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ygbT, cas1, b2755, JW2725 / Production host: Escherichia coli (E. coli)
References: UniProt: Q46896, Hydrolases; Acting on ester bonds
#2: Protein CRISPR-associated endoribonuclease Cas2


Mass: 11684.466 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ygbF, cas2, b2754, JW5438 / Production host: Escherichia coli (E. coli)
References: UniProt: P45956, Hydrolases; Acting on ester bonds
#3: DNA chain DNA (29-MER)


Mass: 10180.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage M13 (virus)
#4: DNA chain DNA (28-MER)


Mass: 10067.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage M13 (virus)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate tribasic pH 5.6, 200 mM sodium acetate and 8% PEG 8000 (w/v)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 3.35→49.003 Å / Num. obs: 31049 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.216 / Net I/σ(I): 5
Reflection shellResolution: 3.35→3.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 1.3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P6I
Resolution: 3.352→49.003 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 1729 5.58 %10
Rwork0.2309 ---
obs0.2333 30989 99.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.352→49.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9376 1165 0 0 10541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310851
X-RAY DIFFRACTIONf_angle_d0.74414957
X-RAY DIFFRACTIONf_dihedral_angle_d15.7554095
X-RAY DIFFRACTIONf_chiral_restr0.031737
X-RAY DIFFRACTIONf_plane_restr0.0031714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3523-3.45090.41431280.35092202X-RAY DIFFRACTION91
3.4509-3.56220.35061410.32032389X-RAY DIFFRACTION99
3.5622-3.68950.32641440.29982430X-RAY DIFFRACTION99
3.6895-3.83720.341450.29152431X-RAY DIFFRACTION100
3.8372-4.01170.31731420.27392411X-RAY DIFFRACTION100
4.0117-4.22310.33791440.23322440X-RAY DIFFRACTION100
4.2231-4.48760.26691440.20812425X-RAY DIFFRACTION100
4.4876-4.83380.20941450.19192449X-RAY DIFFRACTION100
4.8338-5.31970.27221460.20732464X-RAY DIFFRACTION100
5.3197-6.08820.26441470.22682481X-RAY DIFFRACTION100
6.0882-7.66580.27111490.22232515X-RAY DIFFRACTION100
7.6658-49.00820.2061540.17412623X-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)
15.4008-0.46990.73072.9184-2.31362.2263-0.4363-0.5082-0.06860.32690.46860.5899-0.44520.4791-0.49531.7964-0.1108-0.18510.85920.0870.547710.8992127.8282255.3102
23.6236-1.55411.86581.7276-0.33051.15950.4215-1.5786-0.5381-0.05480.00250.55371.11810.2512-0.21431.1113-0.09670.00290.91360.14310.58637.1235123.4886254.149
32.4031-2.6594-0.19873.39931.21670.27360.6362-1.05490.73210.5323-0.0945-0.0343-0.55910.0443-0.57810.9063-0.03170.24480.6283-0.04280.69780.5686142.963252.1456
45.1809-1.08740.03372.332-0.41342.2002-0.12780.06111.09970.3680.1667-0.2156-0.81040.11750.03121.0246-0.13060.17220.6811-0.05830.746311.4951159.4545256.7643
55.2470.70714.44353.6386-1.47094.9059-2.50620.40762.89931.31670.73761.74790.19570.55941.57781.2133-0.03110.19120.7573-0.15020.68298.546154.0571255.3346
65.11950.47241.01644.0751-1.72772.1427-0.54581.8379-1.45320.1639-0.1578-0.80140.0361-0.15940.52260.8468-0.1623-0.06681.0720.00640.949328.2036152.1367256.2597
73.4615-0.5985-0.84816.3003-2.04597.4906-0.1972-0.91580.19660.4176-0.197-1.19471.12321.70820.24110.5935-0.0528-0.11540.8143-0.02570.636923.2815142.3523255.439
82.8951-1.68750.39294.00490.2031.49490.6132-0.8451-0.3262-0.25260.05650.48530.1958-0.0557-0.59461.2935-0.29570.17320.9936-0.06340.63070.1688148.905263.9399
95.7025-0.39540.58313.4056-2.21335.1811-0.03840.26380.01640.3975-0.00950.2167-0.17050.03570.03760.45360.06590.02210.4665-0.01090.40094.2957130.2547235.6475
103.6957-0.5757-0.05031.31171.88291.51130.07130.01960.24350.0912-0.44120.7436-0.5651-0.80150.440.72290.10480.09660.95260.09070.8814-25.3192143.6361241.1883
114.79781.96551.09466.72013.19284.00550.1445-0.0211-0.075-0.07040.08230.4367-0.2414-0.6647-0.3180.48940.10470.03740.57090.22440.6177-15.8577133.2462234.8829
122.3936-2.1174-1.22583.9313-1.89964.59250.0002-0.03180.1841-1.5411-0.2062-1.38170.37780.0280.12510.90070.08890.02830.5832-0.03540.510125.3953130.8854168.6348
135.68520.148-0.3025.20730.89713.243-0.04730.20170.2539-1.33310.453-0.8694-1.38340.8034-0.23541.0872-0.06270.1790.77340.03240.493423.4211132.7963169.3317
147.095-0.54720.06640.5320.71020.63231.2010.5794-0.3876-0.7337-0.70770.5484-0.1464-0.3041-0.25141.00590.2525-0.13390.729-0.00770.69255.0849129.4895168.2163
153.17841.03041.49541.7745-0.87111.4956-0.16811.2552-0.50010.34720.63920.1829-0.2147-0.5765-0.33091.14380.3249-0.37061.5818-0.33261.3348-10.7335115.5584155.9843
161.05760.62941.02662.0981-1.1612.77280.38110.0274-0.50670.5817-0.06070.88780.7601-1.0443-0.12570.8002-0.0649-0.03150.8173-0.07361.0052-0.0969105.7572168.1319
171.2365-0.33610.71144.5972-1.29432.24660.2034-0.1476-0.551-0.8950.23910.85480.1117-0.5766-0.47150.67580.2166-0.30541.0583-0.22130.8994-1.6962118.1739166.8143
184.96180.32360.5733.05321.79011.4358-0.0222-0.2239-1.12990.44460.3183-0.40970.45740.0649-0.27410.82190.1354-0.14540.5954-0.10670.854414.2412104.7707170.6788
190.96180.72310.07632.169-1.10570.7967-0.02810.0283-0.2457-0.4849-0.34130.9959-0.9072-0.24690.1761.03150.0651-0.3071.0486-0.12990.67371.3789124.6003156.0562
204.4616-1.5775-0.76454.8254-0.35766.5066-0.0302-0.03830.095-0.25120.18990.1174-0.64550.2867-0.09840.71640.01820.00060.6391-0.05370.396214.0767135.118185.9324
211.8238-1.24121.13481.8168-1.63352.23960.068-0.10170.2722-0.295-0.25480.5203-1.1341-0.53580.29061.1450.231-0.04970.9375-0.05170.7975-6.1633152.4346174.8737
225.0085-0.80160.6344.51051.84453.16580.0253-0.22750.53410.0099-0.1441-0.5023-0.7312-0.11010.01951.45440.2119-0.03660.81390.02670.77031.1506150.2653183.5299
234.29750.91971.67314.6257-0.26612.11070.5967-0.06250.1251-0.4331-0.3251-0.5482-0.48140.0275-0.3270.57920.01360.13060.63950.13560.475215.8212135.0443220.753
241.35480.75181.5452.7544-3.21579.36380.5341-0.37480.18120.4185-0.18840.144-1.52890.4182-0.13960.7514-0.0550.06640.4285-0.02560.508811.6374138.2178220.0178
255.54990.02832.00632.71412.97575.22910.20880.69170.6712-0.2905-0.45160.0631-0.80710.70240.36810.8087-0.1570.1350.50010.15270.598414.4411141.17210.2289
263.5623-5.212.32998.9568-0.94324.37971.13080.3762-1.3031-0.4919-0.39371.0308-1.41541.0279-0.53510.8875-0.14010.24211.1337-0.09820.764822.0213139.5749201.2617
277.645-3.09982.06635.66091.09374.7080.97020.51160.4092-1.3746-0.5104-0.1244-0.21630.6767-0.56150.62330.08110.15110.48360.09490.49578.0483129.0436206.9125
283.8455-0.8801-1.91391.7096-1.09644.89840.24630.55010.0151-0.2406-0.5356-0.08580.70930.45830.34410.5230.10720.02130.64310.04010.424613.6174126.9418201.156
296.4061-1.40750.74724.5369-0.9533.97431.23330.6148-0.5688-0.2346-1.07140.54031.1917-2.1867-0.23880.8042-0.0734-0.07910.9957-0.00890.57853.3041121.9446200.553
304.5625-1.2544-0.4414.83752.18726.6285-0.01731.3721-0.36930.6522-0.56410.20970.8994-1.50680.23530.5314-0.159-0.01060.7009-0.00940.62314.3738123.9506211.4943
314.12760.39260.80093.49330.21766.00750.7360.282-0.04920.25-0.67870.60661.49920.5132-0.27821.00980.08830.00290.54260.07480.65148.0423118.9873221.992
324.44190.91711.88156.6879-2.25572.2041-0.5994-0.2831-1.3491-0.20530.7971-1.63421.94071.7687-0.05950.99080.2923-0.02350.8922-0.20940.9527.3607117.8974186.7069
33-0.02961.21261.28441.71571.71374.47180.23860.1247-0.20090.29390.9181-0.63270.4442.6883-1.18771.13540.188-0.0541.6840.03050.835731.3275120.9035220.6513
342.45110.1683-3.64286.4375.58166.04551.1315-1.07381.6448-2.1695-0.2675-1.7143-0.71430.5954-0.27250.8105-0.0826-0.00311.6946-0.04711.011422.3724142.7951244.004
351.1406-0.7352-0.75763.46072.83863.88910.4857-0.313-0.4509-0.6160.5063-0.80180.19842.1602-0.65010.89460.1737-0.14821.4605-0.0750.836128.6764123.8573230.6834
362.6002-1.938-0.29811.93921.25684.50880.7945-0.2482-0.3465-0.38580.2004-0.4541-0.03722.0509-1.05740.88860.11410.01991.3959-0.05980.848829.7012117.1628193.9045
372.49130.86253.61063.98780.81085.4729-0.2506-2.6473-2.2560.43490.65520.75150.3037-2.4663-0.08871.6032-0.010.06891.49440.33171.23685.7052112.2779180.6043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 71 )
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 213 )
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 223 )
6X-RAY DIFFRACTION6chain 'A' and (resid 224 through 242 )
7X-RAY DIFFRACTION7chain 'A' and (resid 243 through 259 )
8X-RAY DIFFRACTION8chain 'A' and (resid 260 through 281 )
9X-RAY DIFFRACTION9chain 'B' and (resid 4 through 95 )
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 156 )
11X-RAY DIFFRACTION11chain 'B' and (resid 157 through 279 )
12X-RAY DIFFRACTION12chain 'C' and (resid 16 through 35 )
13X-RAY DIFFRACTION13chain 'C' and (resid 36 through 71 )
14X-RAY DIFFRACTION14chain 'C' and (resid 72 through 107 )
15X-RAY DIFFRACTION15chain 'C' and (resid 108 through 133 )
16X-RAY DIFFRACTION16chain 'C' and (resid 134 through 198 )
17X-RAY DIFFRACTION17chain 'C' and (resid 199 through 227 )
18X-RAY DIFFRACTION18chain 'C' and (resid 228 through 259 )
19X-RAY DIFFRACTION19chain 'C' and (resid 260 through 280 )
20X-RAY DIFFRACTION20chain 'D' and (resid 4 through 95 )
21X-RAY DIFFRACTION21chain 'D' and (resid 96 through 198 )
22X-RAY DIFFRACTION22chain 'D' and (resid 199 through 272 )
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 21 )
24X-RAY DIFFRACTION24chain 'E' and (resid 22 through 50 )
25X-RAY DIFFRACTION25chain 'E' and (resid 51 through 73 )
26X-RAY DIFFRACTION26chain 'E' and (resid 74 through 93 )
27X-RAY DIFFRACTION27chain 'F' and (resid 1 through 9 )
28X-RAY DIFFRACTION28chain 'F' and (resid 10 through 36 )
29X-RAY DIFFRACTION29chain 'F' and (resid 37 through 50 )
30X-RAY DIFFRACTION30chain 'F' and (resid 51 through 73 )
31X-RAY DIFFRACTION31chain 'F' and (resid 74 through 94 )
32X-RAY DIFFRACTION32chain 'G' and (resid 1 through 8 )
33X-RAY DIFFRACTION33chain 'G' and (resid 9 through 21 )
34X-RAY DIFFRACTION34chain 'G' and (resid 22 through 29 )
35X-RAY DIFFRACTION35chain 'H' and (resid 2 through 13 )
36X-RAY DIFFRACTION36chain 'H' and (resid 14 through 24 )
37X-RAY DIFFRACTION37chain 'H' and (resid 25 through 29 )

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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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