[English] 日本語
Yorodumi
- PDB-9ubw: The atomic coordinates of the mouse CatSper dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ubw
TitleThe atomic coordinates of the mouse CatSper dimer
Components
  • (Cation channel sperm-associated auxiliary subunit ...) x 7
  • (Cation channel sperm-associated protein ...) x 4
  • EF-hand calcium-binding domain-containing protein 9
  • Solute carrier organic anion transporter family member 6C1
  • Unknown protein
KeywordsPROTEIN TRANSPORT / sperm / hyperactivation / calcium channel
Function / homology
Function and homology information


Sperm Motility And Taxes / CatSper complex / fusion of sperm to egg plasma membrane involved in single fertilization / sperm principal piece / regulation of cilium beat frequency involved in ciliary motility / calcium ion sensor activity / male meiotic nuclear division / organic anion transport / flagellated sperm motility / : ...Sperm Motility And Taxes / CatSper complex / fusion of sperm to egg plasma membrane involved in single fertilization / sperm principal piece / regulation of cilium beat frequency involved in ciliary motility / calcium ion sensor activity / male meiotic nuclear division / organic anion transport / flagellated sperm motility / : / calcium-activated cation channel activity / fertilization / motile cilium / sodium ion transport / sperm capacitation / regulation of calcium ion transport / monoatomic ion channel complex / sperm flagellum / voltage-gated calcium channel activity / acrosomal vesicle / establishment of localization in cell / calcium ion transport / spermatogenesis / cell differentiation / calmodulin binding / cilium / calcium ion binding / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated auxiliary subunit gamma / Cation channel sperm-associated protein 4 / Cation channel sperm-associated protein 1 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Cation channel sperm-associated auxiliary subunit delta/epsilon / Cation channel sperm-associated auxiliary subunit TMEM262 / : / : ...Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated auxiliary subunit gamma / Cation channel sperm-associated protein 4 / Cation channel sperm-associated protein 1 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Cation channel sperm-associated auxiliary subunit delta/epsilon / Cation channel sperm-associated auxiliary subunit TMEM262 / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / CATSPERD, beta-propeller domain / CATSPERG beta-propeller domain / CATSPERB, C-terminal domain / Cation channel sperm-associated auxiliary subunit TMEM249 / CATSPER protein subunit beta protein 1st domain / CATSPER subunit beta protein 2nd domain / CATSPERB head domain / CATSPERB Ig-like domain / CATSPERG N-terminal domain / CATSPERE first N-terminal domain / CATSPERE second N-terminal domain / CATSPERE beta-propeller domain / CATSPERG C-terminal domain / CATSPERE Ig-like domain / CATSPERD/E C-terminal domain / CATSPERG Ig-like domain / CATSPERD Ig-like domain / Cation channel sperm-associated auxiliary subunit zeta / EF-hand calcium-binding domain-containing protein 9 / Organic anion transporter polypeptide / Organic Anion Transporter Polypeptide (OATP) family / Kazal-type serine protease inhibitor domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Voltage-dependent channel domain superfamily / MFS transporter superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
CHOLESTEROL / Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Cation channel sperm-associated auxiliary subunit gamma 2 / Cation channel sperm-associated auxiliary subunit TMEM262 / Cation channel sperm-associated auxiliary subunit delta / Cation channel sperm-associated auxiliary subunit epsilon / Cation channel sperm-associated protein 3 / Cation channel sperm-associated protein 4 ...CHOLESTEROL / Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Cation channel sperm-associated auxiliary subunit gamma 2 / Cation channel sperm-associated auxiliary subunit TMEM262 / Cation channel sperm-associated auxiliary subunit delta / Cation channel sperm-associated auxiliary subunit epsilon / Cation channel sperm-associated protein 3 / Cation channel sperm-associated protein 4 / Solute carrier organic anion transporter family member 6C1 / Cation channel sperm-associated protein 1 / Cation channel sperm-associated auxiliary subunit zeta / EF-hand calcium-binding domain-containing protein 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsXu, Q. / Lin, S. / Zhao, Q. / Yan, Z. / Wu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of the mouse CatSper dimer
Authors: Xu, Q. / Lin, S. / Zhao, Q. / Yan, Z. / Wu, J.
History
DepositionApr 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cation channel sperm-associated protein 1
B: Cation channel sperm-associated protein 2
C: Cation channel sperm-associated protein 3
D: Cation channel sperm-associated protein 4
E: Cation channel sperm-associated auxiliary subunit beta
F: Cation channel sperm-associated auxiliary subunit gamma 2
G: Cation channel sperm-associated auxiliary subunit delta
H: Cation channel sperm-associated auxiliary subunit epsilon
I: EF-hand calcium-binding domain-containing protein 9
J: Cation channel sperm-associated auxiliary subunit TMEM249
K: Cation channel sperm-associated auxiliary subunit zeta
L: Solute carrier organic anion transporter family member 6C1
M: Cation channel sperm-associated auxiliary subunit TMEM262
N: Unknown protein
a: Cation channel sperm-associated protein 1
b: Cation channel sperm-associated protein 2
c: Cation channel sperm-associated protein 3
d: Cation channel sperm-associated protein 4
e: Cation channel sperm-associated auxiliary subunit beta
f: Cation channel sperm-associated auxiliary subunit gamma 2
g: Cation channel sperm-associated auxiliary subunit delta
h: Cation channel sperm-associated auxiliary subunit epsilon
i: EF-hand calcium-binding domain-containing protein 9
j: Cation channel sperm-associated auxiliary subunit TMEM249
k: Cation channel sperm-associated auxiliary subunit zeta
l: Solute carrier organic anion transporter family member 6C1
m: Cation channel sperm-associated auxiliary subunit TMEM262
n: Unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,413,31268
Polymers1,394,23128
Non-polymers19,08040
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Cation channel sperm-associated protein ... , 4 types, 8 molecules AaBbCcDd

#1: Protein Cation channel sperm-associated protein 1 / CatSper1


Mass: 29080.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsper1 / Production host: Mus musculus (house mouse) / References: UniProt: Q91ZR5
#2: Protein Cation channel sperm-associated protein 2 / CatSper2


Mass: 33115.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsper2 / Production host: Mus musculus (house mouse) / References: UniProt: A2ARP9
#3: Protein Cation channel sperm-associated protein 3 / CatSper3


Mass: 32308.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsper3 / Production host: Mus musculus (house mouse) / References: UniProt: Q80W99
#4: Protein Cation channel sperm-associated protein 4 / CatSper4


Mass: 28880.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsper4 / Production host: Mus musculus (house mouse) / References: UniProt: Q8BVN3

-
Cation channel sperm-associated auxiliary subunit ... , 7 types, 14 molecules EeFfGgHhJjKkMm

#5: Protein Cation channel sperm-associated auxiliary subunit beta / CatSper-beta


Mass: 121580.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsperb / Production host: Mus musculus (house mouse) / References: UniProt: A2RTF1
#6: Protein Cation channel sperm-associated auxiliary subunit gamma 2


Mass: 119864.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsperg2, Catsperg / Production host: Mus musculus (house mouse) / References: UniProt: C6KI89
#7: Protein Cation channel sperm-associated auxiliary subunit delta / CatSper-delta / CatSperdelta / Transmembrane protein 146


Mass: 82834.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsperd, Tmem146 / Production host: Mus musculus (house mouse) / References: UniProt: E9Q9F6
#8: Protein Cation channel sperm-associated auxiliary subunit epsilon / CatSper-epsilon / CatSperepsilon / C1orf101-like protein


Mass: 107004.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catspere, Catspere1, Gm7068 / Production host: Mus musculus (house mouse) / References: UniProt: P0DP43
#10: Protein Cation channel sperm-associated auxiliary subunit TMEM249 / Transmembrane protein 249


Mass: 19898.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tmem249 / Production host: Mus musculus (house mouse) / References: UniProt: A0A2R8VHF7
#11: Protein Cation channel sperm-associated auxiliary subunit zeta / CatSper-zeta / CatSperzeta / Protein expressed in male leptotene and zygotene spermatocytes 622 / ...CatSper-zeta / CatSperzeta / Protein expressed in male leptotene and zygotene spermatocytes 622 / MLZ-622 / Testis-expressed protein 40


Mass: 17504.592 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Catsperz, Tex40 / Production host: Mus musculus (house mouse) / References: UniProt: Q9CQP8
#13: Protein Cation channel sperm-associated auxiliary subunit TMEM262 / Cation channel sperm-associated auxiliary subunit eta / Transmembrane protein 262


Mass: 13350.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tmem262, Catsperh / Production host: Mus musculus (house mouse) / References: UniProt: D3Z338

-
Protein , 2 types, 4 molecules IiLl

#9: Protein EF-hand calcium-binding domain-containing protein 9


Mass: 20942.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Efcab9 / Production host: Mus musculus (house mouse) / References: UniProt: Q9DAM2
#12: Protein Solute carrier organic anion transporter family member 6C1


Mass: 68349.680 Da / Num. of mol.: 2 / Mutation: A224G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slco6c1 / Production host: Mus musculus (house mouse) / References: UniProt: Q8C0X7

-
Protein/peptide / Non-polymers , 2 types, 4 molecules Nn

#14: Protein/peptide Unknown protein


Mass: 2400.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#21: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION

-
Sugars , 6 types, 38 molecules

#15: Polysaccharide beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-beta-D- ...beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpb1-3[DManpb1-3DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#16: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#17: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#18: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-[beta-D- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-6[DManpb1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#19: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#20: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mouse CatSper dimer / Type: COMPLEX / Entity ID: #1-#14 / Source: MULTIPLE SOURCES
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 459159 / Symmetry type: POINT

+
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