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- PDB-7kzm: Outer dynein arm bound to doublet microtubules from C. reinhardtii -

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Entry
Database: PDB / ID: 7kzm
TitleOuter dynein arm bound to doublet microtubules from C. reinhardtii
Components
  • (Dynein light chain ...) x 4
  • (Flagellar outer dynein arm ...) x 2
  • (Outer dynein arm-docking complex ...) x 2
  • DC1
  • DC2
  • Dynein 11 kDa light chain, flagellar outer arm
  • Dynein 18 kDa light chain, flagellar outer arm
  • Dynein 8 kDa light chain, flagellar outer arm
  • Dynein gamma chain, flagellar outer arm
  • Dynein, 70 kDa intermediate chain, flagellar outer arm
  • Dynein, 78 kDa intermediate chain, flagellar outer arm
  • Heavy chain alpha
  • Outer dynein arm protein 1
  • Tubulin alpha
  • Tubulin beta
KeywordsMOTOR PROTEIN / dynein / microtubule / cilia
Function / homology
Function and homology information


outer dynein arm / outer dynein arm assembly / cilium movement involved in cell motility / 9+2 motile cilium / dynein light chain binding / cilium movement / motile cilium assembly / dynein heavy chain binding / cell projection organization / dynein complex ...outer dynein arm / outer dynein arm assembly / cilium movement involved in cell motility / 9+2 motile cilium / dynein light chain binding / cilium movement / motile cilium assembly / dynein heavy chain binding / cell projection organization / dynein complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / ciliary plasm / motile cilium / dynein intermediate chain binding / microtubule-based movement / axoneme / microtubule-based process / enzyme regulator activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / calcium ion binding / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / ODAD1 central coiled coil region / Kelch repeat type 2 / Kelch motif / Galactose oxidase, central domain / Dynein light chain roadblock-type 1/2 / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Phospholipase D/Transphosphatidylase ...: / ODAD1 central coiled coil region / Kelch repeat type 2 / Kelch motif / Galactose oxidase, central domain / Dynein light chain roadblock-type 1/2 / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Dynein heavy chain 3, AAA+ lid domain / AAA+ lid domain / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / Galactose oxidase/kelch, beta-propeller / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / IPT/TIG domain / Kelch-type beta propeller / IPT domain / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin E-set / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / PLD phosphodiesterase domain-containing protein / Uncharacterized protein / Dynein light chain roadblock / Uncharacterized protein / Dynein light chain / Outer dynein arm protein 1 / Mr19,000 outer arm dynein light chain / Tubulin beta-1/beta-2 chain ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / PLD phosphodiesterase domain-containing protein / Uncharacterized protein / Dynein light chain roadblock / Uncharacterized protein / Dynein light chain / Outer dynein arm protein 1 / Mr19,000 outer arm dynein light chain / Tubulin beta-1/beta-2 chain / Tubulin alpha-1 chain / Dynein, 70 kDa intermediate chain, flagellar outer arm / Dynein light chain 9 / Dynein gamma chain, flagellar outer arm / Dynein, 78 kDa intermediate chain, flagellar outer arm / Dynein 11 kDa light chain, flagellar outer arm / Dynein 8 kDa light chain, flagellar outer arm / Dynein 18 kDa light chain, flagellar outer arm / Outer dynein arm-docking complex protein DC3 / Dynein light chain roadblock
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsWalton, T. / Wu, H. / Brown, A.B.
CitationJournal: Nat Commun / Year: 2021
Title: Structure of a microtubule-bound axonemal dynein.
Authors: Travis Walton / Hao Wu / Alan Brown /
Abstract: Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily ...Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily and biochemically distinct from cytoplasmic dyneins that transport cargo, and the mechanisms regulating their localization and function are poorly understood. Here, we report a single-particle cryo-EM reconstruction of a three-headed axonemal dynein natively bound to doublet microtubules isolated from cilia. The slanted conformation of the axonemal dynein causes interaction of its motor domains with the neighboring dynein complex. Our structure shows how a heterotrimeric docking complex specifically localizes the linear array of axonemal dyneins to the doublet microtubule by directly interacting with the heavy chains. Our structural analysis establishes the arrangement of conserved heavy, intermediate and light chain subunits, and provides a framework to understand the roles of individual subunits and the interactions between dyneins during ciliary waveform generation.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A1: Tubulin beta
A2: Tubulin alpha
A3: Tubulin beta
A4: Tubulin alpha
A5: Tubulin beta
A6: Tubulin alpha
A7: Tubulin beta
B1: Tubulin beta
B2: Tubulin alpha
B3: Tubulin beta
B4: Tubulin alpha
B5: Tubulin beta
B6: Tubulin alpha
B7: Tubulin beta
A: Heavy chain alpha
B: Flagellar outer dynein arm heavy chain beta
C: Dynein gamma chain, flagellar outer arm
D: Dynein, 78 kDa intermediate chain, flagellar outer arm
E: Dynein, 70 kDa intermediate chain, flagellar outer arm
F: Flagellar outer dynein arm light chain 2
G: Dynein 18 kDa light chain, flagellar outer arm
H: Dynein 11 kDa light chain, flagellar outer arm
I: Dynein light chain roadblock LC7a
J: Dynein light chain roadblock LC7b
K: Dynein 8 kDa light chain, flagellar outer arm
L: Dynein 8 kDa light chain, flagellar outer arm
M: Dynein 8 kDa light chain, flagellar outer arm
N: Dynein 8 kDa light chain, flagellar outer arm
O: Dynein light chain 9
P: Dynein light chain 10
X: Outer dynein arm-docking complex subunit 1
X0: DC1
X1: Outer dynein arm-docking complex subunit 1
Y: Outer dynein arm protein 1
Y0: DC2
Y1: Outer dynein arm protein 1
Z: Outer dynein arm-docking complex protein DC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,859,92859
Polymers2,852,55037
Non-polymers7,37822
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 12 types, 28 molecules A1A3A5A7B1B3B5B7A2A4A6B2B4B6ACDEGHKLMNX0YY1Y0

#1: Protein
Tubulin beta / Tubulin beta-1/beta-2 chain / Beta-tubulin


Mass: 49665.809 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P04690
#2: Protein
Tubulin alpha / Tubulin alpha-1 chain


Mass: 49638.008 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P09204
#3: Protein Heavy chain alpha


Mass: 504949.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DV97
#5: Protein Dynein gamma chain, flagellar outer arm


Mass: 513491.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39575
#6: Protein Dynein, 78 kDa intermediate chain, flagellar outer arm / / IC78


Mass: 76628.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39578
#7: Protein Dynein, 70 kDa intermediate chain, flagellar outer arm / / IC69 / IC70


Mass: 63594.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P27766
#9: Protein Dynein 18 kDa light chain, flagellar outer arm


Mass: 17807.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39584
#10: Protein Dynein 11 kDa light chain, flagellar outer arm


Mass: 13876.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39579
#13: Protein
Dynein 8 kDa light chain, flagellar outer arm


Mass: 10336.775 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q39580
#17: Protein DC1


Mass: 13805.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#18: Protein Outer dynein arm protein 1 / Docking complex component 2


Mass: 62292.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JF70
#19: Protein DC2


Mass: 14315.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)

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Dynein light chain ... , 4 types, 4 molecules IJOP

#11: Protein Dynein light chain roadblock LC7a


Mass: 11946.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9SWQ6
#12: Protein Dynein light chain roadblock LC7b


Mass: 11132.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IY95
#14: Protein Dynein light chain 9


Mass: 12993.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q2VIY5
#15: Protein Dynein light chain 10


Mass: 12101.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J5C4

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Outer dynein arm-docking complex ... , 2 types, 3 molecules XX1Z

#16: Protein Outer dynein arm-docking complex subunit 1


Mass: 83518.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: A8IPZ5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#20: Protein Outer dynein arm-docking complex protein DC3 / Outer dynein arm-docking complex subunit 3


Mass: 21371.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q7Y0H2

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Antibody / Flagellar outer dynein arm ... , 2 types, 2 molecules BF

#4: Antibody Flagellar outer dynein arm heavy chain beta


Mass: 520510.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J1M5
#8: Protein Flagellar outer dynein arm light chain 2 / Mr19 / 000 outer arm dynein light chain


Mass: 15903.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: O04355

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Non-polymers , 3 types, 22 molecules

#21: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#22: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#23: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: ODA complex / Type: COMPLEX
Details: ODA complex natively bound to doublet microtubules from C. reinhardtii
Entity ID: #1-#20 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.4
Details: Buffer also contained 1x Protease Arrest (G-Biosciences)
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMHEPES1
225 mMKCl1
35 mMMgSO41
40.5 mMEGTA1
510 mMATPAdenosine triphosphate1
60.75 mMCaCl21
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Splayed axonemes isolated from Chlamydomonas reinhardtii flagella.
Specimen supportDetails: 15 mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K
Details: 2.5 ul of splayed axoneme solution was then dispensed onto glow-discharged C-Flat 1.2/1.3-4Cu grids inside a Vitrobot Mark IV under 100% humidity. After a 10 s delay time, cryo-EM samples ...Details: 2.5 ul of splayed axoneme solution was then dispensed onto glow-discharged C-Flat 1.2/1.3-4Cu grids inside a Vitrobot Mark IV under 100% humidity. After a 10 s delay time, cryo-EM samples were prepared by first blotting for 10 s with blot force set to 16 and immediately plunged into liquid ethane.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.7 sec. / Electron dose: 61.48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 20524
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 25 eV

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEM3.6 and 3.7image acquisition
4CTFFIND4CTF correction
7Coot0.9.1model fitting
9PHENIX1.18.2model refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionDetails: The composite map was assembled on a box 700 reference map (7.5 A) using the ODA-DC and ODA core composite maps (deposited separately), and maps targeting the aHC AAA+ domain (4.5 A), bHC ...Details: The composite map was assembled on a box 700 reference map (7.5 A) using the ODA-DC and ODA core composite maps (deposited separately), and maps targeting the aHC AAA+ domain (4.5 A), bHC AAA+ domain (6.2 A), aHC AAA+ domain (11.4 A), and aHC tail domain (5.3 A). A second conformation of bHC AAA+ domain (9.8 A) is also provided.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0 ° / Axial rise/subunit: 82 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 5584147
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 485694
Details: The composite map varies in resolution from 3.5 to 12 A. The reference map is 7.5 A.
Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Correlation coefficient

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