[English] 日本語
Yorodumi
- PDB-3beh: Structure of a Bacterial Cyclic Nucleotide Regulated Ion Channel -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3beh
TitleStructure of a Bacterial Cyclic Nucleotide Regulated Ion Channel
ComponentsMll3241 protein
KeywordsMEMBRANE PROTEIN / transmembrane protein
Function / homology
Function and homology information


intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / potassium channel activity / cGMP binding / cAMP binding / protein-containing complex binding / identical protein binding / plasma membrane
Similarity search - Function
Voltage-gated potassium channels / Cyclic nucleotide-regulated ion channel, N-terminal / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Helix Hairpins - #70 / Cyclic nucleotide-binding, conserved site / Ion channel / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...Voltage-gated potassium channels / Cyclic nucleotide-regulated ion channel, N-terminal / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Helix Hairpins - #70 / Cyclic nucleotide-binding, conserved site / Ion channel / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Cyclic nucleotide-gated potassium channel mll3241
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsClayton, G.M. / Morais-Cabral, J.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel.
Authors: Clayton, G.M. / Altieri, S. / Heginbotham, L. / Unger, V.M. / Morais-Cabral, J.H.
History
DepositionNov 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mll3241 protein
B: Mll3241 protein
C: Mll3241 protein
D: Mll3241 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,17813
Polymers151,0654
Non-polymers1,1139
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)282.730, 282.730, 105.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
Mll3241 protein


Mass: 37766.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Plasmid: PASK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (RP) / References: UniProt: Q98GN8
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.37 Å3/Da / Density % sol: 77.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG2000, pH 6.0, temperature 298K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorDetector: CCD / Date: Sep 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.1→48.45 Å / Num. obs: 56604
Reflection shellResolution: 3.1→3.18 Å

-
Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.2.0019 24/04/2001refinement
XSCALEdata scaling
RefinementResolution: 3.1→48.45 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.234 / SU B: 50.192 / SU ML: 0.389 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1970 3.5 %RANDOM
Rwork0.276 ---
obs0.276 56604 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.192 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6581 0 69 23 6673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226787
X-RAY DIFFRACTIONr_angle_refined_deg0.8981.989282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8815891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.98521.564211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60615983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.551549
X-RAY DIFFRACTIONr_chiral_restr0.0510.21127
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024973
X-RAY DIFFRACTIONr_nbd_refined0.180.23548
X-RAY DIFFRACTIONr_nbtor_refined0.2910.24886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2163
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.220
X-RAY DIFFRACTIONr_mcbond_it0.0691.54440
X-RAY DIFFRACTIONr_mcangle_it0.1327047
X-RAY DIFFRACTIONr_scbond_it0.17632367
X-RAY DIFFRACTIONr_scangle_it0.3274.52235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.180.5691430.5853743417693.056
3.18-3.2670.5251590.5253913410599.196
3.267-3.3610.471180.463857398399.799
3.361-3.4640.4711450.4113744389299.923
3.464-3.5770.3561320.3823600373899.839
3.577-3.7020.3451260.3193502363199.917
3.702-3.8410.2991290.2823346347699.971
3.841-3.9970.2551110.253285339999.912
3.997-4.1730.265960.2483122322499.814
4.173-4.3750.2461090.2332989309999.968
4.375-4.610.2531130.2462827294299.932
4.61-4.8870.2931040.25126722776100
4.887-5.220.278930.2542551264699.924
5.22-5.6330.283760.2762327240499.958
5.633-6.1630.333730.2922042277100
6.163-6.8760.319610.2421952201899.752
6.876-7.9130.193580.1871726178899.776
7.913-9.6280.165610.1711459152499.738
9.628-13.3550.131410.15511571198100
13.355-48.450.322220.34465869997.282
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)
18.91235.3922-4.27683.2625-2.58762.05240.4415-4.33380.4005-0.592-0.4552-1.42071.2459-0.49390.01381.4554-0.112-0.02661.2572-0.05521.522665.2984-21.109428.5029
23.3167-0.0292-4.20741.54780.10875.3405-0.13640.0472-0.67170.06220.08350.1222-0.3014-0.56540.05290.68470.00920.0221-0.2157-0.2331.275461.2375-10.104815.3835
32.0893-1.1522-1.19450.63540.65880.683-0.1072-1.7832-0.65071.32960.1448-0.41610.36160.9824-0.03761.35620.0539-0.15241.0618-0.03991.46581.271-13.399834.4096
48.35011.7609-2.35850.9927-1.35671.8548-0.0646-0.0739-0.38520.85830.3140.3598-0.99970.0268-0.24940.7918-0.11210.0048-0.0946-0.29240.931572.4568-5.430514.2579
50.4306-1.2493-1.38753.62484.02594.4713-0.9675-1.1613-0.15590.70150.511-1.1372-1.3784-0.98670.45650.7242-0.17270.00670.2001-0.23131.196369.8808-13.018713.9428
61.28760.99231.89381.5365-0.64788.5393-0.4666-2.0414-0.56520.6450.92890.2330.03521.3188-0.46220.657-0.32010.04550.4118-0.15651.19282.2278-30.0421.042
74.457-0.6563-2.36435.3428-2.92333.29410.29420.4026-0.1827-0.47180.08-0.2209-0.7382-0.321-0.37420.0613-0.19250.19480.0957-0.14881.079584.4927-35.2862-10.9382
815.99568.075-3.597711.8492-1.30990.8422-0.80360.45980.82460.44481.158-0.458-0.0025-0.1286-0.35440.3009-0.11380.18510.2513-0.11110.720377.5118-33.5582-9.0331
94.5488-0.54332.67142.427-2.27696.2716-0.14790.0083-0.41320.00350.1292-0.1498-0.1158-0.1170.01870.1644-0.250.21620.054-0.16060.972679.3641-42.3589-3.7972
107.71270.47659.93460.02940.613812.79660.2492-2.3145-0.13091.41830.77780.02481.48951.0802-1.02691.1851-0.05550.03781.1545-0.0531.307885.4962-40.375529.6957
112.6611-11.898-5.831553.19726.072912.7789-3.1754-0.04474.35766.97555.02060.73493.1169-5.4861-1.84520.84690.0485-0.66451.62460.25681.319657.4146-64.118716.3181
129.49090.7041-6.2640.65020.10044.66850.0209-0.653-0.70240.61771.31610.1834-0.3494-1.3575-1.3370.2322-0.41890.17150.3422-0.04341.247345.4626-53.0027.0464
136.8271-2.6307-0.89556.9737-1.18780.5117-0.38590.5225-0.1298-0.7139-0.27181.4708-0.687-0.87260.65770.2414-0.43560.17670.69520.06671.259637.141-54.46695.6393
140.2609-0.72460.51092.012-1.41871.00030.3409-1.2211-0.32031.75960.5239-0.53780.27540.613-0.86471.0584-0.16190.141.36630.1231.51546.23-57.582432.866
150.9750.5365-1.38946.5683.20954.4976-0.11440.0329-0.96580.57540.550.5514-0.9176-0.344-0.43560.2154-0.28820.3480.74910.17591.197938.4472-46.808418.0463
162.37450.2113-2.25373.8652-0.43742.15370.2874-0.6236-0.85611.1760.14220.14490.4354-0.3429-0.42960.3157-0.20230.31990.35790.15630.975355.1457-48.022119.6912
177.30340.3719-1.30812.80441.28670.89180.04840.06960.2704-0.1888-0.09910.2636-0.4417-0.10760.05070.4495-0.20990.2371-0.1512-0.31230.877967.9314-22.13294.717
182.8484.1075-2.55138.005-0.08678.489-0.55550.76331.2299-0.13910.6008-0.097-0.4171-0.1011-0.04530.132-0.0890.17980.0294-0.07560.793366.7731-28.7274-2.0623
193.22791.733-0.89837.1039-1.14380.32080.3738-0.3481-0.09730.4486-0.34090.5956-0.32321.395-0.0330.3432-0.18040.09520.3006-0.23150.957876.1052-34.63937.9983
209.54623.19768.687913.6187-2.264310.04060.6249-2.1113-0.74620.0025-0.0395-0.86231.31510.2751-0.58541.30160.17850.14421.33290.20451.247877.8286-53.14833.2153
2178.707528.74980.769931.70968.09392.88560.1598-3.4571-3.3364-5.4174-2.5668-4.3575-0.67380.33552.4071.6070.0146-0.26581.25390.04581.262591.1175-65.4997-2.5688
225.3908-2.0828-5.44149.91566.12137.2653-0.34920.5348-0.8821-0.08630.6495-0.83981.46141.2588-0.30030.643-0.30940.10780.14-0.30841.255578.0753-63.8315-14.9563
234.1155-3.7376-3.11038.18385.74974.1371.08271.3293-0.9076-0.6897-0.0410.7108-0.44820.5525-1.04170.6026-0.13320.0220.4142-0.48591.298277.0391-67.6272-22.8034
242.9788-2.98444.2513.0169-4.39996.80680.0652-1.0367-0.50671.0766-0.13221.0494-0.19122.56680.0671.2457-0.0595-0.02690.9521-0.19331.664984.0018-82.07961.8566
254.23883.3941-0.82367.57534.09854.82050.53120.4299-2.00080.62680.39490.60391.13870.5722-0.92610.8277-0.14150.1231-0.0213-0.2971.255370.8017-75.4583-11.6732
263.396-0.74782.76162.7581-0.41242.26050.0332-0.7635-1.13950.28420.4120.10290.86720.8293-0.44520.4411-0.20170.13880.0366-0.07440.995872.0757-61.45314.7158
273.43682.43720.31196.03436.21638.37520.07981.04940.1513-0.45280.04271.2724-0.4919-0.6622-0.12250.3715-0.04140.28240.32460.00521.060348.0543-38.77870.8694
280.4582-2.02470.579115.20053.96567.5387-0.39640.3122-0.03670.8470.8569-0.02710.2636-0.3937-0.46050.29070.02280.14140.2078-0.09830.805859.2858-42.0795-0.8115
298.6625-2.90641.28855.4770.05571.4164-0.1357-0.6653-0.20430.5060.5063-0.1641-0.2934-0.3062-0.37050.2511-0.1370.25230.0603-0.14020.860464.947-40.24768.1293
3011.7781-10.71726.51069.7519-5.92423.59890.346-0.0511-1.32271.0865-0.13951.19051.0292.3881-0.20651.30730.0411-0.20041.34060.17141.377987.8304-61.950523.7658
3115.8248-26.2083-16.958643.404928.086118.17370.0805-1.7180.9264-2.00980.44020.664-0.4131-0.6934-0.52061.3657-0.1857-0.16321.74090.0311.630499.5486-23.48337.0486
324.27381.4302-1.78624.98242.78233.2832-0.18940.3996-0.09280.09640.13190.0441-0.70510.08050.05750.2217-0.30060.36130.38580.12421.160492.7581-23.6385-13.7374
3310.3846-3.02724.855611.4886-0.41059.3291-0.1255-0.81730.56680.17210.0109-0.46080.2052-0.05150.11450.0747-0.40990.33280.39650.09870.9419104.2563-25.1136-11.9153
340.6354-0.83590.24551.0998-0.3230.09490.0254-0.38950.43022.07010.2594-0.00170.47480.4556-0.28481.3906-0.18330.1551.49140.11081.5843116.593-39.14113.7076
354.7109-0.8358-1.42794.841-1.08412.06180.26340.0687-0.77780.06450.0233-0.0823-0.10560.5186-0.28670.284-0.25680.36370.42810.09821.2984103.9601-34.9804-15.1164
360.78580.6342-1.05833.60051.40283.07450.2819-0.20610.09640.58740.0967-0.57730.22180.9426-0.37860.0897-0.27230.2210.4440.08111.192496.5886-39.3955-1.3534
373.1056-0.0912-2.52833.13020.56632.1358-0.4060.5191-0.0451-0.32110.10660.05580.00770.1270.29940.435-0.15250.0853-0.019-0.20851.08469.7978-55.8158-9.546
3823.55326.6311-9.6611.8669-2.723.96280.4681-0.5928-0.0926-0.6469-0.99450.19190.18451.00640.52640.3337-0.14220.04320.0734-0.14750.922968.905-46.5272-9.6356
3911.11565.65626.48052.89373.06867.1661-0.1668-0.92110.24070.27550.0711-0.04280.2379-0.16310.09560.4573-0.0880.2016-0.032-0.19611.028570.552-50.14152.7038
4023.1083-1.7733.03450.136-0.23280.3985-0.031-1.01460.45380.9184-0.01790.3982-0.13241.17380.04891.10830.036-0.12931.2750.08161.418297.4683-48.60822.7367
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA7 - 157 - 15
22AA16 - 5916 - 59
33AA60 - 7460 - 74
44AA75 - 9675 - 96
55AA97 - 10997 - 109
66AA110 - 127110 - 127
77AA128 - 160128 - 160
88AA161 - 179161 - 179
99AA180 - 213180 - 213
1010AA214 - 228214 - 228
1111BB9 - 149 - 14
1212BB15 - 3015 - 30
1313BB31 - 5231 - 52
1414BB53 - 7353 - 73
1515BB74 - 9674 - 96
1616BB97 - 12697 - 126
1717BB127 - 164127 - 164
1818BB165 - 185165 - 185
1919BB186 - 215186 - 215
2020BB216 - 230216 - 230
2121CC5 - 145 - 14
2222CC15 - 2915 - 29
2323CC30 - 5230 - 52
2424CC53 - 7353 - 73
2525CC74 - 9674 - 96
2626CC97 - 13997 - 139
2727CC140 - 163140 - 163
2828CC164 - 179164 - 179
2929CC180 - 215180 - 215
3030CC216 - 230216 - 230
3131DD5 - 135 - 13
3232DD14 - 3614 - 36
3333DD37 - 5937 - 59
3434DD60 - 7260 - 72
3535DD73 - 9673 - 96
3636DD97 - 12697 - 126
3737DD127 - 163127 - 163
3838DD164 - 182164 - 182
3939DD183 - 215183 - 215
4040DD216 - 229216 - 229

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more