[English] 日本語
Yorodumi
- PDB-7moq: The structure of the Tetrahymena thermophila outer dynein arm on ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7moq
TitleThe structure of the Tetrahymena thermophila outer dynein arm on doublet microtubule
Components
  • (Docking complex ...) x 2
  • (Dynein light ...) x 10
  • (Outer dynein arm docking complex protein oda ...) x 2
  • Dynein heavy chain, outer arm protein
  • Dynein intermediate chain 2
  • Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative
  • Flagellar outer dynein arm intermediate protein, putative
  • Outer arm dynein beta heavy chain
  • Thioredoxin
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / cilia / doublet / axoneme / outer dynein arm / dynein
Function / homology
Function and homology information


outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / axonemal dynein complex / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex ...outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / axonemal dynein complex / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / motile cilium / dynein intermediate chain binding / microtubule-based movement / microtubule-based process / protein-disulfide reductase activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / cilium / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Outer dynein arm-docking complex subunit 3 / Kelch motif / Galactose oxidase, central domain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 ...Outer dynein arm-docking complex subunit 3 / Kelch motif / Galactose oxidase, central domain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / 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 / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / 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 / Thioredoxin / IPT/TIG domain / Kelch-type beta propeller / ig-like, plexins, transcription factors / Thioredoxin / IPT domain / Thioredoxin, conserved site / Thioredoxin family active site. / 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. / Thioredoxin domain profile. / 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 / Thioredoxin domain / Tubulin/FtsZ, GTPase domain superfamily / EF-hand domain pair / Immunoglobulin E-set / Thioredoxin-like superfamily / Trp-Asp (WD) repeats profile. / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / EF hand protein / Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative / Outer arm dynein beta heavy chain / Dynein light chain roadblock-type 2 protein ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / EF hand protein / Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative / Outer arm dynein beta heavy chain / Dynein light chain roadblock-type 2 protein / Tubulin alpha chain / Tubulin beta chain / Dynein light chain / Dynein light chain / Dynein light chain / Dynein light chain / Thioredoxin / Dynein light chain 2A / Dynein heavy chain, outer arm protein / Dynein light chain roadblock-type 2 protein / Dynein light chain / Uncharacterized protein / Outer dynein arm docking complex protein oda protein / Flagellar outer dynein arm intermediate protein, putative / Dynein light chain
Similarity search - Component
Biological speciesTetrahymena thermophila CU428 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsKubo, S. / Yang, S.K. / Ichikawa, M. / Bui, K.H.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-04954 Canada
Canadian Institutes of Health Research (CIHR)PJT-156354 Canada
CitationJournal: EMBO Rep / Year: 2021
Title: Remodeling and activation mechanisms of outer arm dyneins revealed by cryo-EM.
Authors: Shintaroh Kubo / Shun Kai Yang / Corbin S Black / Daniel Dai / Melissa Valente-Paterno / Jacek Gaertig / Muneyoshi Ichikawa / Khanh Huy Bui /
Abstract: Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the ...Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the trachea and protect the human body from viral infections. The main force generators of ciliary beating are the outer dynein arms (ODAs) which attach to the doublet microtubules. The bending of cilia is driven by the ODAs' conformational changes caused by ATP hydrolysis. Here, we report the native ODA complex structure attaching to the doublet microtubule by cryo-electron microscopy. The structure reveals how the ODA complex is attached to the doublet microtubule via the docking complex in its native state. Combined with coarse-grained molecular dynamic simulations, we present a model of how the attachment of the ODA to the doublet microtubule induces remodeling and activation of the ODA complex.
History
DepositionMay 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-23926
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-23926
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative
B: Outer arm dynein beta heavy chain
C: Dynein heavy chain, outer arm protein
D: Dynein intermediate chain 2
E: Flagellar outer dynein arm intermediate protein, putative
F: Dynein light chain roadblock-type 2 protein
G: Dynein light chain roadblock-type 2 protein
H: Dynein light chain
I: Dynein light chain
J: Dynein light chain
K: Dynein light chain
L: Dynein light chain
M: Dynein light chain
N: Dynein light chain 2A
O: Dynein light chain tctex-type 1 protein
P: Thioredoxin
Q: Tubulin beta chain
R: Tubulin alpha chain
S: Tubulin alpha chain
T: Outer dynein arm docking complex protein oda protein
U: Tubulin beta chain
V: Docking complex 1/2 protein
W: Tubulin alpha chain
X: Docking complex 1 protein
Y: Tubulin beta chain
Z: Outer dynein arm docking complex protein oda protein
d: Dynein intermediate chain 2
e: Flagellar outer dynein arm intermediate protein, putative
s: Tubulin alpha chain
u: Tubulin beta chain
r: Tubulin alpha chain
q: Tubulin beta chain
w: Tubulin alpha chain
y: Tubulin beta chain
x: Docking complex 1/2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,783,90156
Polymers2,776,59535
Non-polymers7,30621
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 7 types, 19 molecules ACDdEePQUYuqyRSWsrw

#1: Protein Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative


Mass: 475554.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: I7M6H4
#3: Protein Dynein heavy chain, outer arm protein


Mass: 534328.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q22A67
#4: Protein Dynein intermediate chain 2


Mass: 77888.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: I7M008
#5: Protein Flagellar outer dynein arm intermediate protein, putative


Mass: 77178.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q23FU1
#16: Protein Thioredoxin


Mass: 12855.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HFX5
#17: Protein
Tubulin beta chain / Beta-tubulin


Mass: 49617.676 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: P41352
#18: Protein
Tubulin alpha chain / Alpha-tubulin


Mass: 49639.035 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: P41351

-
Dynein light ... , 10 types, 10 molecules FGHIJKLMNO

#6: Protein Dynein light chain roadblock-type 2 protein


Mass: 14751.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: I7MHB1
#7: Protein Dynein light chain roadblock-type 2 protein


Mass: 18490.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q22MV2
#8: Protein Dynein light chain


Mass: 10780.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HFW2
#9: Protein Dynein light chain


Mass: 12348.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HFX0
#10: Protein Dynein light chain


Mass: 10973.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HFV9
#11: Protein Dynein light chain


Mass: 13336.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q22R86
#12: Protein Dynein light chain


Mass: 12516.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: W7XJB1
#13: Protein Dynein light chain


Mass: 10453.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HFW0
#14: Protein Dynein light chain 2A


Mass: 15608.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HGH8
#15: Protein Dynein light chain tctex-type 1 protein


Mass: 13202.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: A4VEB3

-
Outer dynein arm docking complex protein oda ... , 2 types, 2 molecules TZ

#19: Protein Outer dynein arm docking complex protein oda protein


Mass: 35237.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: I7M2C6
#22: Protein Outer dynein arm docking complex protein oda protein


Mass: 63455.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q233H6

-
Docking complex ... , 2 types, 3 molecules VxX

#20: Protein Docking complex 1/2 protein


Mass: 11081.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428
#21: Protein Docking complex 1 protein


Mass: 64756.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q22T00

-
Antibody , 1 types, 1 molecules B

#2: Antibody Outer arm dynein beta heavy chain


Mass: 530111.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: SB715 / References: UniProt: I7M9J2

-
Non-polymers , 5 types, 21 molecules

#23: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#24: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#25: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#26: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#27: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Outer dynein arm complex from Tetrahymena thermophila / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#22 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: YES
Source (natural)Organism: Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / Cellular location: cilia / Organelle: cilia
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: Blot force 3 for 5 seconds

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
Image scansMovie frames/image: 40 / Used frames/image: 1-40

-
Processing

SoftwareName: PHENIX / Version: dev_3699: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.8image acquisition
4RELION3CTF correction
7UCSF Chimera1model fitting
9SPIDER19.02initial Euler assignment
10RELION3final Euler assignment
11FREALIGN9.03final Euler assignment
12FREALIGN9.03classification
13RELION33D reconstruction
14Coot0.8.7model refinement
15PHENIX1.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139548 / Symmetry type: POINT
Atomic model buildingB value: 179 / Protocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006132552
ELECTRON MICROSCOPYf_angle_d0.888179275
ELECTRON MICROSCOPYf_dihedral_angle_d12.19617676
ELECTRON MICROSCOPYf_chiral_restr0.0519867
ELECTRON MICROSCOPYf_plane_restr0.00523039

+
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