[English] 日本語
Yorodumi
- PDB-9vpb: Cryo-EM structure of the IF1 bound bovine F-ATP synthase planar dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vpb
TitleCryo-EM structure of the IF1 bound bovine F-ATP synthase planar dimer
Components
  • (ATP synthase ...) x 15
  • ATPase inhibitor, mitochondrial
KeywordsMEMBRANE PROTEIN / ATP synthase/hydrolase / oligomer / membrane bending / mammalian mitochondria
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / negative regulation of hydrolase activity / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / Mitochondrial translation termination / proton channel activity ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / negative regulation of hydrolase activity / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / Mitochondrial translation termination / proton channel activity / heme biosynthetic process / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / MHC class I protein binding / positive regulation of blood vessel endothelial cell migration / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / aerobic respiration / erythrocyte differentiation / ADP binding / mitochondrial membrane / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f ...ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f / Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit alpha / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase F(0) complex subunit a / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(0) complex subunit 8 / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial ...ATP synthase subunit alpha / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase F(0) complex subunit a / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(0) complex subunit 8 / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase F(0) complex subunit e, mitochondrial / ATP synthase F(0) complex subunit f, mitochondrial / ATP synthase F(0) complex subunit g, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsNakano, A. / Jiko, C. / Yamashita, E. / Yokoyama, K. / Gerle, C.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22ama 121003 Japan
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
CitationJournal: Biorxiv / Year: 2025
Title: A planar dimer of bovine ATP synthase
Authors: Jiko, C. / Nakano, A. / Teshirogi, Y. / Yamashita, E. / Kurisu, G. / Standley, D. / Terada, T. / Mitsuoka, K. / Yokoyama, K. / Gerle, C.
History
DepositionJul 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data 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
8: ATP synthase F(0) complex subunit 8
A: ATP synthase subunit alpha
A8: ATP synthase F(0) complex subunit 8
AA: ATP synthase subunit alpha
AB: ATP synthase subunit alpha
AC: ATP synthase subunit alpha
AD: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
AE: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
AF: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
AG: ATP synthase F(1) complex subunit gamma, mitochondrial
AH: ATP synthase F(1) complex subunit delta, mitochondrial
AI: ATP synthase F(1) complex subunit epsilon, mitochondrial
AJ: ATPase inhibitor, mitochondrial
AK: ATP synthase F(0) complex subunit C2, mitochondrial
AL: ATP synthase F(0) complex subunit C2, mitochondrial
AM: ATP synthase F(0) complex subunit C2, mitochondrial
AN: ATP synthase F(0) complex subunit C2, mitochondrial
AO: ATP synthase F(0) complex subunit C2, mitochondrial
AP: ATP synthase F(0) complex subunit C2, mitochondrial
AQ: ATP synthase F(0) complex subunit C2, mitochondrial
AR: ATP synthase F(0) complex subunit C2, mitochondrial
AS: ATP synthase peripheral stalk subunit OSCP, mitochondrial
Aa: ATP synthase F(0) complex subunit a
Ab: ATP synthase peripheral stalk subunit b, mitochondrial
Ad: ATP synthase peripheral stalk subunit d, mitochondrial
Ae: ATP synthase F(0) complex subunit e, mitochondrial
Af: ATP synthase F(0) complex subunit f, mitochondrial
Ag: ATP synthase F(0) complex subunit g, mitochondrial
Ah: ATP synthase peripheral stalk subunit F6, mitochondrial
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
E: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
F: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
G: ATP synthase F(1) complex subunit gamma, mitochondrial
H: ATP synthase F(1) complex subunit delta, mitochondrial
I: ATP synthase F(1) complex subunit epsilon, mitochondrial
J: ATPase inhibitor, mitochondrial
K: ATP synthase F(0) complex subunit C2, mitochondrial
L: ATP synthase F(0) complex subunit C2, mitochondrial
M: ATP synthase F(0) complex subunit C2, mitochondrial
N: ATP synthase F(0) complex subunit C2, mitochondrial
O: ATP synthase F(0) complex subunit C2, mitochondrial
P: ATP synthase F(0) complex subunit C2, mitochondrial
Q: ATP synthase F(0) complex subunit C2, mitochondrial
R: ATP synthase F(0) complex subunit C2, mitochondrial
S: ATP synthase peripheral stalk subunit OSCP, mitochondrial
a: ATP synthase F(0) complex subunit a
b: ATP synthase peripheral stalk subunit b, mitochondrial
d: ATP synthase peripheral stalk subunit d, mitochondrial
e: ATP synthase F(0) complex subunit e, mitochondrial
f: ATP synthase F(0) complex subunit f, mitochondrial
g: ATP synthase F(0) complex subunit g, mitochondrial
h: ATP synthase peripheral stalk subunit F6, mitochondrial


Theoretical massNumber of molelcules
Total (without water)1,367,64654
Polymers1,367,64654
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
ATP synthase ... , 15 types, 52 molecules 8A8AAAABACBCADAEAFDEFAGGAHHAIIAKALAMANAOAPAQARKL...

#1: Protein ATP synthase F(0) complex subunit 8 / A6L / F-ATPase subunit 8 / ATP synthase subunit A6L


Mass: 7944.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P03929
#2: Protein
ATP synthase subunit alpha


Mass: 59765.469 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: F1MLB8
#3: Protein
ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase subunit beta / ATP synthase F1 subunit beta


Mass: 56340.199 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P00829, H+-transporting two-sector ATPase
#4: Protein ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase subunit gamma / ATP synthase F1 subunit gamma / F-ATPase gamma subunit


Mass: 33119.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05631
#5: Protein ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase subunit delta / ATP synthase F1 subunit delta / F-ATPase delta subunit


Mass: 17626.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05630
#6: Protein ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase subunit epsilon / ATPase subunit epsilon / ATP synthase F1 subunit epsilon


Mass: 5793.889 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05632
#8: Protein
ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase subunit c / ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus ...ATP synthase subunit c / ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 2 / ATP synthase proteolipid P2 / ATPase protein 9 / ATPase subunit c


Mass: 15041.492 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07926
#9: Protein ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase oligomycin sensitivity conferral protein (OSCP) / ATP synthase subunit O / Oligomycin ...ATP synthase oligomycin sensitivity conferral protein (OSCP) / ATP synthase subunit O / Oligomycin sensitivity conferral protein / OSCP


Mass: 23351.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13621
#10: Protein ATP synthase F(0) complex subunit a / ATP synthase subunit a / F-ATPase protein 6 / Proton-conducting channel / ATP synthase F(0) complex subunit a


Mass: 24801.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00847
#11: Protein ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase subunit b / ATP synthase F(0) complex subunit B1 / mitochondrial / ATP synthase ...ATP synthase subunit b / ATP synthase F(0) complex subunit B1 / mitochondrial / ATP synthase peripheral stalk-membrane subunit b / ATP synthase subunit b / ATPase subunit b


Mass: 28859.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13619
#12: Protein ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase subunit d / ATPase subunit d / ATP synthase peripheral stalk subunit d


Mass: 18719.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13620
#13: Protein ATP synthase F(0) complex subunit e, mitochondrial / ATP synthase subunit e / ATPase subunit e / ATP synthase membrane subunit e


Mass: 8336.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q00361
#14: Protein ATP synthase F(0) complex subunit f, mitochondrial / ATP synthase subunit f / ATP synthase membrane subunit f


Mass: 10315.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q28851
#15: Protein ATP synthase F(0) complex subunit g, mitochondrial / ATP synthase subunit g / ATPase subunit g / ATP synthase membrane subunit g


Mass: 11429.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q28852
#16: Protein ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase subunit F6 / ATPase subunit F6 / ATP synthase peripheral stalk subunit F6


Mass: 12549.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02721

-
Protein , 1 types, 2 molecules AJJ

#7: Protein ATPase inhibitor, mitochondrial / ATPase inhibitory factor 1 (IF1) / ATP synthase F1 subunit epsilon / Inhibitor of F(1)F(o)-ATPase / ...ATPase inhibitory factor 1 (IF1) / ATP synthase F1 subunit epsilon / Inhibitor of F(1)F(o)-ATPase / IF(1) / IF1


Mass: 12326.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: heart / Tissue: muscle / References: UniProt: P01096

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Bovine F-ATP synthase in the oligomeric form of an IF1 bound planar dimer
Type: COMPLEX
Details: Oligomer fractions of bovine F-ATP synthase obtained from heart muscle tissue mitochondria.
Entity ID: all / Source: NATURAL
Molecular weightValue: 1.2 MDa / Experimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: heart / Organelle: mitochondria / Tissue: muscle
Buffer solutionpH: 7.3
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameCategory
1Topazparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22478 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16ZIU

6ziu

16ZIU1PDBexperimental model
26Z1U

6z1u

16Z1U2PDBexperimental model

+
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://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