[English] 日本語
Yorodumi
- EMDB-27298: E.coli ATP synthase imaged in 10mM MgATP State1 "half-up" Fo clas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27298
TitleE.coli ATP synthase imaged in 10mM MgATP State1 "half-up" Fo classified
Map data
Sample
  • Complex: ATP synthase
    • Protein or peptide: x 8 types
  • Protein or peptide: x 1 types
  • Ligand: x 3 types
KeywordsEnergy / ATP hyrolysis / ATP synthesis / Motor / Membrane protein / cryoEM
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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, 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, F1 complex, alpha subunit nucleotide-binding domain / 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 / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain 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 beta / ATP synthase epsilon chain / ATP synthase subunit alpha / ATP synthase subunit a / ATP synthase gamma chain / ATP synthase subunit b / ATP synthase subunit c / ATP synthase subunit delta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSobti M / Stewart AG
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Commun Biol / Year: 2023
Title: Changes within the central stalk of E. coli FF ATP synthase observed after addition of ATP.
Authors: Meghna Sobti / Yi C Zeng / James L Walshe / Simon H J Brown / Robert Ishmukhametov / Alastair G Stewart /
Abstract: FF ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F motor that is transferred to the F motor to ...FF ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F motor that is transferred to the F motor to catalyze ATP production, with flexible F/F coupling required for efficient catalysis. FF ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli FF ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the F motor. This highlights the importance of the central rotor for flexible coupling of the F and F motors and provides further insight into the regulatory mechanism mediated by subunit ε.
History
DepositionJun 14, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27298.png

Downloads & links

-
Map

FileDownload / File: emd_27298.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 352 pix.
= 379.808 Å		1.08 Å/pix.
x 352 pix.
= 379.808 Å		1.08 Å/pix.
x 352 pix.
= 379.808 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.079 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.01
Minimum - Maximum-0.01810367 - 0.055085696
Average (Standard dev.)-0.00013236431 (±0.0027116698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 379.80798 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_27298_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_27298_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : ATP synthase

EntireName: ATP synthase
Components
  • Complex: ATP synthase
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase subunit b
  • Protein or peptide: ATP synthase subunit a
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: ATP synthase

SupramoleculeName: ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Escherichia coli (E. coli)

+
Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 55.022414 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QLNSTEISEL IKQRIAQFNV VSEAHNEGTI VSVSDGVIRI HGLADAMQGE MISLPGNRYA IALNLERDSV GAVVMGPYAD LAEGMKVKA TGRILEVPVG RGLLGRVVNT LGAPIDGKGP LDHDGFSAVE AIAPGVIERQ SVDQPVQTGY KAVDSMIPIG R GQRELIIG ...String:
QLNSTEISEL IKQRIAQFNV VSEAHNEGTI VSVSDGVIRI HGLADAMQGE MISLPGNRYA IALNLERDSV GAVVMGPYAD LAEGMKVKA TGRILEVPVG RGLLGRVVNT LGAPIDGKGP LDHDGFSAVE AIAPGVIERQ SVDQPVQTGY KAVDSMIPIG R GQRELIIG DRQTGKTALA IDAIINQRDS GIKAIYVAIG QKASTISNVV RKLEEHGALA NTIVVVATAS ESAALQYLAP YA GAAMGEY FRDRGEDALI IYDDLSKQAV AYRQISLLLR RPPGREAFPG DVFYLHSRLL ERAARVNAEY VEAFTKGEVK GKT GSLTAL PIIETQAGDV SAFVPTNVIS ITDGQIFLET NLFNAGIRPA VNPGISVSRV GGAAQTKIMK KLSGGIRTAL AQYR ELAAF SQFASDLDDA TRKQLDHGQK VTELLKQKQY APMSVAQQSL VLFAAERGYL ADVELSKIGS FEAALLAYVD RDHAP LMQE INQTGGYNDE IEGKLKGILD SFKATQSW

UniProtKB: ATP synthase subunit alpha

+
Macromolecule #2: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 54.94632 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QLNSTEISEL IKQRIAQFNV VSEAHNEGTI VSVSDGVIRI HGLADAMQGE MISLPGNRYA IALNLERDSV GAVVMGPYAD LAEGMKVKA TGRILEVPVG RGLLGRVVNT LGAPIDGKGP LDHDGFSAVE AIAPGVIERQ SVDQPVQTGY KAVDSMIPIG R GQRELIIG ...String:
QLNSTEISEL IKQRIAQFNV VSEAHNEGTI VSVSDGVIRI HGLADAMQGE MISLPGNRYA IALNLERDSV GAVVMGPYAD LAEGMKVKA TGRILEVPVG RGLLGRVVNT LGAPIDGKGP LDHDGFSAVE AIAPGVIERQ SVDQPVQTGY KAVDSMIPIG R GQRELIIG DRQTGKTALA IDAIINQRDS GIKAIYVAIG QKASTISNVV RKLEEHGALA NTIVVVATAS ESAALQYLAP YA GAAMGEY FRDRGEDALI IYDDLSKQAV AYRQISLLLR RPPGREAFPG DVFYLHSRLL ERAARVNAEY VEAFTKGEVK GKT GSLTAL PIIETQAGDV SAFVPTNVIS ITDGQIFLET NLFNAGIRPA VNPGISVSRV GGAAQTKIMK KLSGGIRTAL AQYR ELAAF SQAASDLDDA TRKQLDHGQK VTELLKQKQY APMSVAQQSL VLFAAERGYL ADVELSKIGS FEAALLAYVD RDHAP LMQE INQTGGYNDE IEGKLKGILD SFKATQSW

UniProtKB: ATP synthase subunit alpha

+
Macromolecule #3: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 50.346129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATGKIVQVI GAVVDVEFPQ DAVPRVYDAL EVQNGNERLV LEVQQQLGGG IVRTIAMGSS DGLRRGLDVK DLEHPIEVPV GKATLGRIM NVLGEPVDMK GEIGEEERWA IHRAAPSYEE LSNSQELLET GIKVIDLMAP FAKGGKVGLF GGAGVGKTVN M MELIRNIA ...String:
MATGKIVQVI GAVVDVEFPQ DAVPRVYDAL EVQNGNERLV LEVQQQLGGG IVRTIAMGSS DGLRRGLDVK DLEHPIEVPV GKATLGRIM NVLGEPVDMK GEIGEEERWA IHRAAPSYEE LSNSQELLET GIKVIDLMAP FAKGGKVGLF GGAGVGKTVN M MELIRNIA IEHSGYSVFA GVGERTREGN DFYHEMTDSN VIDKVSLVYG QMNEPPGNRL RVALTGLTMA EKFRDEGRDV LL FVDNIYR YTLAGTEVSA LLGRMPSAVG YQPTLAEEMG VLQERITSTK TGSITSVQAV YVPADDLTDP SPATTFAHLD ATV VLSRQI ASLGIYPAVD PLDSTSRQLD PLVVGQEHYD TARGVQSILQ RYQELKDIIA ILGMDELSEE DKLVVARARK IQRF LSQPF FVAEVFTGSP GKYVSLKDTI RGFKGIMEGE YDHLPEQAFY MVGSIEEAVE KAKKL

UniProtKB: ATP synthase subunit beta

+
Macromolecule #4: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 31.237883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AGAKDIRSKI ASVQNTQKIT KAMEMVAASK MRKSQDRMAA SRPYAETMRK VIGHLAHGNL EYKHPYLEDR DVKRVGYLVV STDRGLAGG LNINLFKKLL AEMKTWTDKG VQADLAMIGS KGVSFFNSVG GNVVAQVTGM GDNPSLSELI GPVKVMLQAY D EGRLDKLY ...String:
AGAKDIRSKI ASVQNTQKIT KAMEMVAASK MRKSQDRMAA SRPYAETMRK VIGHLAHGNL EYKHPYLEDR DVKRVGYLVV STDRGLAGG LNINLFKKLL AEMKTWTDKG VQADLAMIGS KGVSFFNSVG GNVVAQVTGM GDNPSLSELI GPVKVMLQAY D EGRLDKLY IVSNKFINTM SQVPTISQLL PLPASDDDDL KHKSWDYLYE PDPKALLDTL LRRYVESQVY QGVVENLASE QA ARMVAMK AATDNGGSLI KELQLVYNKA RQASITQELT EIVSGAA

UniProtKB: ATP synthase gamma chain

+
Macromolecule #5: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.012496 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TYHLDVVSAE QQMFSGLVEK IQVTGSEGEL GIYPGHAPLL TAIKPGMIRI VKQHGHEEFI YLSGGILEVQ PGNVTVLADT AIRGQDLDE ARAMEAKRKA EE

UniProtKB: ATP synthase epsilon chain

+
Macromolecule #6: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 6 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.998754 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NLNMDLLYMA AAVMMGLAAI GAAIGIGILG GKFLEGAARQ PDLIPLLRTQ FFIVMGLVDA IPMIAVGLGL YVMFAVA

UniProtKB: ATP synthase subunit c

+
Macromolecule #7: ATP synthase subunit delta

MacromoleculeName: ATP synthase subunit delta / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.855578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EFITVARPYA KAAFDFAVEH QSVERWQDML AFAAEVTKNE QMAELLSGAL APETLAESFI AVAGEQLDEN GQNLIRVMAE NGRLNALPD VLEQFIHLRA VSEATAEVDV ISAAALSEQQ LAKISAAMEK RLSRKVKLNA KIDKSVMAGV IIRAGDMVID G SVRGRLER LADVL

UniProtKB: ATP synthase subunit delta

+
Macromolecule #8: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 17.257889 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNLNATILGQ AIAFVLFVLF AMKYVWPPLM AAIEKRQKEI ADGLASAERA HKDLDLAKAS ATDQLKKAKA EAQVIIEQAN KRRSQILDE AKAEAEQERT KIVAQAQAEI EAERKRAREE LRKQVAILAV AGAEKIIERS VDEAANSDIV DKLVAEL

UniProtKB: ATP synthase subunit b

+
Macromolecule #9: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.767484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ENMTPQDYIG HHLNNLQLDL RTFSLVDPQN PPATFWTINI DSMFFSVVLG LLFLVLFRSV AKKATSGVPG KFQTAIELVI GFVNGSVKD MYHGKSKLIA PLALTIFVWV FLMNLMDLLP IDLLPYIAEH VLGLPALRVV PSADVNVTLS MALGVFILIL F YSIKMKGI ...String:
ENMTPQDYIG HHLNNLQLDL RTFSLVDPQN PPATFWTINI DSMFFSVVLG LLFLVLFRSV AKKATSGVPG KFQTAIELVI GFVNGSVKD MYHGKSKLIA PLALTIFVWV FLMNLMDLLP IDLLPYIAEH VLGLPALRVV PSADVNVTLS MALGVFILIL F YSIKMKGI GGFTKELTLQ PFNHWAFIPV NLILEGVSLL SKPVSLGLRL FGNMYAGELI FILIAGLLPW WSQWILNVPW AI FHILIIT LQAFIFMVLT IVYLSMASE

UniProtKB: ATP synthase subunit a

+
Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

+
Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9354
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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