[English] 日本語
Yorodumi
- EMDB-43903: PS3 F1 ATPase Wild type -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43903
TitlePS3 F1 ATPase Wild type
Map data
Sample
  • Complex: PS3 F1 ATPase Wild type
    • Protein or peptide: ATP synthase subunit alpha
    • 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 subunit beta
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsATPase / electron transfer / ATP hydrolysis / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / 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 / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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, 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 / 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 alpha / ATP synthase gamma chain / ATP synthase subunit beta
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsSobti M / Stewart AG
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2024
Title: The molecular structure of an axle-less F-ATPase.
Authors: Emily J Furlong / Ian-Blaine P Reininger-Chatzigiannakis / Yi C Zeng / Simon H J Brown / Meghna Sobti / Alastair G Stewart /
Abstract: FF ATP synthase is a molecular rotary motor that can generate ATP using a transmembrane proton motive force. Isolated F-ATPase catalytic cores can hydrolyse ATP, passing through a series of ...FF ATP synthase is a molecular rotary motor that can generate ATP using a transmembrane proton motive force. Isolated F-ATPase catalytic cores can hydrolyse ATP, passing through a series of conformational states involving rotation of the central γ rotor subunit and the opening and closing of the catalytic β subunits. Cooperativity in F-ATPase has long thought to be conferred through the γ subunit, with three key interaction sites between the γ and β subunits being identified. Single molecule studies have demonstrated that the F complexes lacking the γ axle still "rotate" and hydrolyse ATP, but with less efficiency. We solved the cryogenic electron microscopy structure of an axle-less Bacillus sp. PS3 F-ATPase. The unexpected binding-dwell conformation of the structure in combination with the observed lack of interactions between the axle-less γ and the open β subunit suggests that the complete γ subunit is important for coordinating efficient ATP binding of F-ATPase.
History
DepositionMar 3, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43903.png

Downloads & links

-
Map

FileDownload / File: emd_43903.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 256 pix.
= 252.416 Å		0.99 Å/pix.
x 256 pix.
= 252.416 Å		0.99 Å/pix.
x 256 pix.
= 252.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.986 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.37997955 - 0.8036986
Average (Standard dev.)-0.0033310961 (±0.036909085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 252.416 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #2

Fileemd_43903_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_43903_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43903_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43903_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : PS3 F1 ATPase Wild type

EntireName: PS3 F1 ATPase Wild type
Components
  • Complex: PS3 F1 ATPase Wild type
    • Protein or peptide: ATP synthase subunit alpha
    • 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 subunit beta
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: PS3 F1 ATPase Wild type

SupramoleculeName: PS3 F1 ATPase Wild type / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Bacillus sp. PS3 (bacteria)

+
Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 51.689055 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDVGTVIQVG DGIARAHGLD NVMSGELVEF ANGVMGMALN LEENNVGIVI LGPYTGIKEG DEVRRTGRIM EVPVGEALIG RVVNPLGQP VDGLGPVETT ETRPIESRAP GVMDRRSVHE PLQTGIKAID ALVPIGRGQR ELIIGDRQTG KTSVAIDTII N QKDQNMIS ...String:
SDVGTVIQVG DGIARAHGLD NVMSGELVEF ANGVMGMALN LEENNVGIVI LGPYTGIKEG DEVRRTGRIM EVPVGEALIG RVVNPLGQP VDGLGPVETT ETRPIESRAP GVMDRRSVHE PLQTGIKAID ALVPIGRGQR ELIIGDRQTG KTSVAIDTII N QKDQNMIS IYVAIGQKES TVRTVVETLR KHGALDYTIV VTASASQPAP LLFLAPYAGV AMGEYFMYKG KHVLVVYDDL SK QAAAYRE LSLLLRRPPG REAYPGDIFY LHSRLLERAA KLSDAKGGGS LTALPFVETQ AGDISAYIPT NVISITDGQI FLQ SDLFFS GVRPAINAGL SVSRVGGAAQ IKAMKKVAGT LRLDLAAYRE LEAFAQFGSD LDKATQAKLA RGARTVEVLK QDLH QPIPV EKQVLIIYAL TRGFLDDIPV EDVRRFEKEF YLFLDQNGQH LLEHIRTTKD LPNEDDLNKA IEAFKKTFV

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: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 51.788184 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DVGTVIQVGD GIARAHGLDN VMSGELVEFA NGVMGMALNL EENNVGIVIL GPYTGIKEGD EVRRTGRIME VPVGEALIGR VVNPLGQPV DGLGPVETTE TRPIESRAPG VMDRRSVHEP LQTGIKAIDA LVPIGRGQRE LIIGDRQTGK TSVAIDTIIN Q KDQNMISI ...String:
DVGTVIQVGD GIARAHGLDN VMSGELVEFA NGVMGMALNL EENNVGIVIL GPYTGIKEGD EVRRTGRIME VPVGEALIGR VVNPLGQPV DGLGPVETTE TRPIESRAPG VMDRRSVHEP LQTGIKAIDA LVPIGRGQRE LIIGDRQTGK TSVAIDTIIN Q KDQNMISI YVAIGQKEST VRTVVETLRK HGALDYTIVV TASASQPAPL LFLAPYAGVA MGEYFMYKGK HVLVVYDDLS KQ AAAYREL SLLLRRPPGR EAYPGDIFYL HSRLLERAAK LSDAKGGGSL TALPFVETQA GDISAYIPTN VISITDGQIF LQS DLFFSG VRPAINAGLS VSRVGGAAQI KAMKKVAGTL RLDLAAYREL EAFAQFGSDL DKATQAKLAR GARTVEVLKQ DLHQ PIPVE KQVLIIYALT RGFLDDIPVE DVRRFEKEFY LFLDQNGQHL LEHIRTTKDL PNEDDLNKAI EAFKKTFVVS

UniProtKB: ATP synthase subunit alpha

+
Macromolecule #3: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 51.875262 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDVGTVIQVG DGIARAHGLD NVMSGELVEF ANGVMGMALN LEENNVGIVI LGPYTGIKEG DEVRRTGRIM EVPVGEALIG RVVNPLGQP VDGLGPVETT ETRPIESRAP GVMDRRSVHE PLQTGIKAID ALVPIGRGQR ELIIGDRQTG KTSVAIDTII N QKDQNMIS ...String:
SDVGTVIQVG DGIARAHGLD NVMSGELVEF ANGVMGMALN LEENNVGIVI LGPYTGIKEG DEVRRTGRIM EVPVGEALIG RVVNPLGQP VDGLGPVETT ETRPIESRAP GVMDRRSVHE PLQTGIKAID ALVPIGRGQR ELIIGDRQTG KTSVAIDTII N QKDQNMIS IYVAIGQKES TVRTVVETLR KHGALDYTIV VTASASQPAP LLFLAPYAGV AMGEYFMYKG KHVLVVYDDL SK QAAAYRE LSLLLRRPPG REAYPGDIFY LHSRLLERAA KLSDAKGGGS LTALPFVETQ AGDISAYIPT NVISITDGQI FLQ SDLFFS GVRPAINAGL SVSRVGGAAQ IKAMKKVAGT LRLDLAAYRE LEAFAQFGSD LDKATQAKLA RGARTVEVLK QDLH QPIPV EKQVLIIYAL TRGFLDDIPV EDVRRFEKEF YLFLDQNGQH LLEHIRTTKD LPNEDDLNKA IEAFKKTFVV S

UniProtKB: ATP synthase subunit alpha

+
Macromolecule #4: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 51.552531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TRGRVIQVMG PVVDVKFENG HLPAIYNALK IQHKARNENE VDIDLTLEVA LHLGDDTVRT IAMASTDGLI RGMEVIDTGA PISVPVGEV TLGRVFNVLG EPIDLEGDIP ADARRDPIHR PAPKFEELAT EVEILETGIK VVDLLAPYIK GGKIGLFGGA G VGKTVLIQ ...String:
TRGRVIQVMG PVVDVKFENG HLPAIYNALK IQHKARNENE VDIDLTLEVA LHLGDDTVRT IAMASTDGLI RGMEVIDTGA PISVPVGEV TLGRVFNVLG EPIDLEGDIP ADARRDPIHR PAPKFEELAT EVEILETGIK VVDLLAPYIK GGKIGLFGGA G VGKTVLIQ ELIHNIAQEH GGISVFAGVG ERTREGNDLY HEMKDSGVIS KTAMVFGQMN EPPGARMRVA LTGLTMAEYF RD EQGQDVL LFIDNIFRFT QAGSEVSALL GRMPSAVGYQ PTLATEMGQL QERITSTAKG SITSIQAIYV PADDYTDPAP ATT FSHLDA TTNLERKLAE MGIYPAVDPL ASTSRALAPE IVGEEHYQVA RKVQQTLQRY KELQDIIAIL GMDELSDEDK LVVH RARRI QFFLSQNFHV AEQFTGQPGS YVPVKETVRG FKEILEGKYD HLPEDAFRLV GRIEEVVEKA KAMGV

UniProtKB: ATP synthase subunit beta

+
Macromolecule #5: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 51.584598 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTRGRVIQVM GPVVDVKFEN GHLPAIYNAL KIQHKARNEN EVDIDLTLEV ALHLGDDTVR TIAMASTDGL IRGMEVIDTG APISVPVGE VTLGRVFNVL GEPIDLEGDI PADARRDPIH RPAPKFEELA TEVEILETGI KVVDLLAPYI KGGKIGLFGG A GVGKTVLI ...String:
MTRGRVIQVM GPVVDVKFEN GHLPAIYNAL KIQHKARNEN EVDIDLTLEV ALHLGDDTVR TIAMASTDGL IRGMEVIDTG APISVPVGE VTLGRVFNVL GEPIDLEGDI PADARRDPIH RPAPKFEELA TEVEILETGI KVVDLLAPYI KGGKIGLFGG A GVGKTVLI QELIHNIAQE HGGISVFAGV GERTREGNDL YHEMKDSGVI SKTAMVFGQM NEPPGARMRV ALTGLTMAEY FR DEQGQDV LLFIDNIFRF TQAGSEVSAL LGRMPSAVGY QPTLATEMGQ LQERITSTAK GSITSIQAIY VPADDYTDPA PAT TFSHLD ATTNLERKLA EMGIYPAVDP LASTSRALAP EIVGEEHYQV ARKVQQTLQR YKELQDIIAI LGMDELSDED KLVV HRARR IQFFLSQNFH VAEQFTGQPG SYVPVKETVR GFKEILEGKY DHLPEDAFRL VGRIEEVVEK AKAMG

UniProtKB: ATP synthase subunit beta

+
Macromolecule #6: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 51.669703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTRGRVIQVM GPVVDVKFEN GHLPAIYNAL KIQHKARNEN EVDIDLTLEV ALHLGDDTVR TIAMASTDGL IRGMEVIDTG APISVPVGE VTLGRVFNVL GEPIDLEGDI PADARRDPIH RPAPKFEELA TEVEILETGI KVVDLLAPYI KGGKIGLFGG A GVGKTVLI ...String:
MTRGRVIQVM GPVVDVKFEN GHLPAIYNAL KIQHKARNEN EVDIDLTLEV ALHLGDDTVR TIAMASTDGL IRGMEVIDTG APISVPVGE VTLGRVFNVL GEPIDLEGDI PADARRDPIH RPAPKFEELA TEVEILETGI KVVDLLAPYI KGGKIGLFGG A GVGKTVLI QELIHNIAQE HGGISVFAGV GDRTREGNDL YHEMKDSGVI SKTAMVFGQM NEPPGARMRV ALTGLTMAEY FR DEQGQDV LLFIDNIFRF TQAGSEVSAL LGRMPSAVGY QPTLATEMGQ LQERITSTAK GSITSIQAIY VPADDYTDPA PAT TFSHLD ATTNLERKLA EMGIYPAVDP LASTSRALAP EIVGEEHYQV ARKVQQTLQR YKELQDIIAI LGMDELSDED KLVV HRARR IQFFLSQNFH VAEQFTGQPG SYVPVKETVR GFKEILEGKY DHLPEDAFRL VGRIEEVVEK AKAMGV

UniProtKB: ATP synthase subunit beta

+
Macromolecule #7: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 31.547225 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SLRDIKTRIN ATKKTSQITK AMEMVSTSKL NRAEQNAKSF VPYMEKIQEV VANVALGAGG ASHPMLVSRP VKKTGYLVIT SDRGLAGAY NSNVLRLVYQ TIQKRHACPD EYAIIVIGRV GLSFFRKRNM PVILDITRLP DQPSFADIKE IARKTVGLFA D GTFDELYM ...String:
SLRDIKTRIN ATKKTSQITK AMEMVSTSKL NRAEQNAKSF VPYMEKIQEV VANVALGAGG ASHPMLVSRP VKKTGYLVIT SDRGLAGAY NSNVLRLVYQ TIQKRHACPD EYAIIVIGRV GLSFFRKRNM PVILDITRLP DQPSFADIKE IARKTVGLFA D GTFDELYM YYNHYVSAIQ QEVTERKLLP LCDLAENKQR TVYEFEPSQE EILDVLLPQY AESLIYGALL DAKASEHAAR MT AMKNATD NANELIRTLT LSYNRARQAA ITQEITEIVA GANAL

UniProtKB: ATP synthase gamma chain

+
Macromolecule #8: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 8 / Number of copies: 5 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

+
Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7l1r

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153828
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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