[English] 日本語
Yorodumi
- EMDB-38197: Cryo-EM structure of Bacillus RNAP and HelD complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38197
TitleCryo-EM structure of Bacillus RNAP and HelD complex
Map data
Sample
  • Complex: Cryo-EM structure of Bacillus RNAP and HelD complex
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit epsilon
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: DNA helicase IV
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit delta
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Keywordscomplex / TRANSCRIPTION
Function / homology
Function and homology information


recombinational repair / 3'-5' DNA helicase activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : ...recombinational repair / 3'-5' DNA helicase activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / protein dimerization activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
: / RNA polymerase epsilon subunit / RNA polymerase epsilon subunit / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain ...: / RNA polymerase epsilon subunit / RNA polymerase epsilon subunit / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit epsilon / DNA helicase IV / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesBacillus (Bacillus rRNA group 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsChen M / Jin Q / Yuan S / Liu B
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270151 China
National Natural Science Foundation of China (NSFC)32270172 China
CitationJournal: To Be Published
Title: A phage encoded sigA-dependent transcription inhibitor also attacks host HelD-mediated defence system
Authors: Chen M / Jin Q / Zhang K / Wang Y / Chen H / Yu Z / Matthews S / Yuan S / Liu B
History
DepositionDec 2, 2023-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_38197.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 400 pix.
= 380. Å
0.95 Å/pix.
x 400 pix.
= 380. Å
0.95 Å/pix.
x 400 pix.
= 380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.85542196 - 1.3075584
Average (Standard dev.)-0.00013514984 (±0.027448228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 380.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_38197_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_38197_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : Cryo-EM structure of Bacillus RNAP and HelD complex

EntireName: Cryo-EM structure of Bacillus RNAP and HelD complex
Components
  • Complex: Cryo-EM structure of Bacillus RNAP and HelD complex
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit epsilon
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: DNA helicase IV
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit delta
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: Cryo-EM structure of Bacillus RNAP and HelD complex

SupramoleculeName: Cryo-EM structure of Bacillus RNAP and HelD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)

+
Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 34.842387 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MIEIEKPKIE TVEISDDAKF GKFVVEPLER GYGTTLGNSL RRILLSSLPG AAVTSIQIDG VLHEFSTIEG VVEDVTTIIL HIKKLALKI YSDEEKTLEI DVQGEGTVTA ADITHDSDVE ILNPDLHIAT LGENASFRVR LTAQRGRGYT PADANKRDDQ P IGVIPIDS ...String:
MIEIEKPKIE TVEISDDAKF GKFVVEPLER GYGTTLGNSL RRILLSSLPG AAVTSIQIDG VLHEFSTIEG VVEDVTTIIL HIKKLALKI YSDEEKTLEI DVQGEGTVTA ADITHDSDVE ILNPDLHIAT LGENASFRVR LTAQRGRGYT PADANKRDDQ P IGVIPIDS IYTPVSRVSY QVENTRVGQV ANYDKLTLDV WTDGSTGPKE AIALGSKILT EHLNIFVGLT DEAQHAEIMV EK EEDQKEK VLEMTIEELD LSVRSYNCLK RAGINTVQEL ANKTEEDMMK VRNLGRKSLE EVKAKLEELG LGLRKDD

UniProtKB: DNA-directed RNA polymerase subunit alpha

+
Macromolecule #2: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 134.444953 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MLDVNNFEYM NIGLASPDKI RSWSFGEVKK PETINYRTLK PEKDGLFCER IFGPTKDWEC HCGKYKRVRY KGVVCDRCGV EVTRAKVRR ERMGHIELAA PVSHIWYFKG IPSRMGLVLD MSPRALEEVI YFASYVVTDP ANTPLEKKQL LSEKEYRAYL D KYGNKFQA ...String:
MLDVNNFEYM NIGLASPDKI RSWSFGEVKK PETINYRTLK PEKDGLFCER IFGPTKDWEC HCGKYKRVRY KGVVCDRCGV EVTRAKVRR ERMGHIELAA PVSHIWYFKG IPSRMGLVLD MSPRALEEVI YFASYVVTDP ANTPLEKKQL LSEKEYRAYL D KYGNKFQA SMGAEAIHKL LQDIDLVKEV DMLKEELKTS QGQRRTRAIK RLEVLEAFRN SGNKPSWMIL DVLPVIPPEL RP MVQLDGG RFATSDLNDL YRRVINRNNR LKRLLDLGAP SIIVQNEKRM LQEAVDALID NGRRGRPVTG PGNRPLKSLS HML KGKQGR FRQNLLGKRV DYSGRSVIVV GPHLKMYQCG LPKEMALELF KPFVMKELVE KGLAHNIKSA KRKIERVQPE VWDV LESVI KEHPVLLNRA PTLHRLGIQA FEPTLVEGRA IRLHPLVCTA YNADFDGDQM AVHVPLSAEA QAEARILMLA AQNIL NPKD GKPVVTPSQD MVLGNYYLTL ERAGAVGEGM VFKNTDEALL AYQNGYVHLH TRVAVAANSL KNVTFTEEQR SKLLIT TVG KLVFNEILPE SFPYMNEPTK SNIEEKTPDR FFLEKGADVK AVIAQQPINA PFKKGILGKI IAEIFKRFHI TETSKML DR MKNLGFKYST KAGITVGVSD IVVLDDKQEI LEEAQSKVDN VMKQFRRGLI TEEERYERVI SIWSAAKDVI QGKLMKSL D ELNPIYMMSD SGARGNASNF TQLAGMRGLM ANPAGRIIEL PIKSSFREGL TVLEYFISTH GARKGLADTA LKTADSGYL TRRLVDVAQD VIIRETDCGT DRGILAKPLK EGTETIERLE ERLIGRFARK QVKHPETGEV LVNENELIDE DKALEIVEAG IEEVWIRSA FTCNTPHGVC KRCYGRNLAT GSDVEVGEAV GIIAAQSIGE PGTQLTMRTF HTGGVAGDDI TQGLPRIQEL F EARNPKGQ ATITEIDGTV VEINEVRDKQ QEIVVQGAVE TRSYTAPYNS RLKVAEGDKI TRGQVLTEGS IDPKELLKVT DL TTVQEYL LHEVQKVYRM QGVEIGDKHV EVMVRQMLRK VRVIDAGDTD VLPGTLLDIH QFTEANKKVL LEGNRPATGR PVL LGITKA SLETDSFLSA ASFQETTRVL TDAAIKGKRD ELLGLKENVI IGKLVPAGTG MMKYRKVKPV SNVQPTDDMV PVE

UniProtKB: DNA-directed RNA polymerase subunit beta'

+
Macromolecule #3: DNA-directed RNA polymerase subunit epsilon

MacromoleculeName: DNA-directed RNA polymerase subunit epsilon / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 8.277386 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MIYKVFYQEK ADEVPVREKT DSLYIEGVSE RDIRTKLKEK KFNIEFITPV DGAFLEYEQQ SENFKVLEL

UniProtKB: DNA-directed RNA polymerase subunit epsilon

+
Macromolecule #4: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 7.766921 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MLDPSIDSLM NKLDSKYTLV TVSARRAREM QIKKDQMIEH TISHKYVGKA LEEIDAGLLS FEKEDRE

UniProtKB: DNA-directed RNA polymerase subunit omega

+
Macromolecule #5: DNA helicase IV

MacromoleculeName: DNA helicase IV / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 90.052516 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MNQQDKEWKE EQSRIDEVLK ELEKKERFLE TSAGGLKHDI IGLRKSFWED VKVNFDDAHE AIETMASIKQ QAELLSDREH NHRRMDQQL KRIHQLKKSP YFGRIDFIEN GEEQAERIYI GLASCLDEKE EHFLIYDWRA PISSLYYNYS PGKAEYEVPG E TIEGEMVL ...String:
MNQQDKEWKE EQSRIDEVLK ELEKKERFLE TSAGGLKHDI IGLRKSFWED VKVNFDDAHE AIETMASIKQ QAELLSDREH NHRRMDQQL KRIHQLKKSP YFGRIDFIEN GEEQAERIYI GLASCLDEKE EHFLIYDWRA PISSLYYNYS PGKAEYEVPG E TIEGEMVL KRQFMIKNGT LKAMFNTDMT IGDEMLQEVL SHHSDTQMKN IVSTIQKEQN QIIRNEKSKI LIVQGAAGSG KT SAALQRV AYLLYRHRGV IDAGQIVLFS PNFLFNSYVS SVLPELGEEN MEQATFQEYI EHRLGRKFKC ESPFDQLEYC LTE TKGGDF PTRLAGITWK AGLSFQQFIN EYVTRLSSEG MIFKNIIFRG QKLITKEQIQ SYFYSLDQNH SIPNRMEQTA KWLL SELNK LEKKERRKDW VVHEAELLDK EDYLDVYKKL QERKRFSEST FNDYQREQQL LAAIIVKKAF KPLKQAVRLL AFLDV TQLY LQLFSGWGGK FQHEKMDAIG ELTRSAFTDN KLLYEDAAPF LYMQDLIEGR KKNTKIKHLF IDEAQDYSPF QMAYMR SIF PAASMTVLGD INQSIYAHTI NGDQRMDACF EDEPAEYVRL KRTYRSTRQI VEFTKAMLQD GADIEPFNRS GEMPLVV KT EGHESLCQKL AQEIGRLKKK GHETIAVICK TAHQCIQAHA HMSEYTDVRL IHKENQPFQK GVCVIPVYLA KGIEFDAV L VYDASEEHYH TEHDRRLLYT ACTRAMHMLA VFYTGEASPF VTAVPPHLYQ IAE

UniProtKB: DNA helicase IV

+
Macromolecule #6: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 133.847938 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MTGQLVQYGR HRQRRSYARI SEVLELPNLI EIQTSSYQWF LDEGLREMFQ DISPIEDFTG NLSLEFIDYS LGEPKYPVEE SKERDVTYS APLRVKVRLI NKETGEVKDQ DVFMGDFPIM TDTGTFIING AERVIVSQLV RSPSVYFSGK VDKNGKKGFT A TVIPNRGA ...String:
MTGQLVQYGR HRQRRSYARI SEVLELPNLI EIQTSSYQWF LDEGLREMFQ DISPIEDFTG NLSLEFIDYS LGEPKYPVEE SKERDVTYS APLRVKVRLI NKETGEVKDQ DVFMGDFPIM TDTGTFIING AERVIVSQLV RSPSVYFSGK VDKNGKKGFT A TVIPNRGA WLEYETDAKD VVYVRIDRTR KLPVTVLLRA LGFGSDQEIL DLIGENEYLR NTLDKDNTEN SDKALLEIYE RL RPGEPPT VENAKSLLDS RFFDPKRYDL ANVGRYKINK KLHIKNRLFN QRLAETLVDP ETGEILAEKG QILDRRTLDK VLP YLENGI GFRKLYPNGG VVEDEVTLQS IKIFAPTDQE GEQVINVIGN AYIEEEIKNI TPADIISSIS YFFNLLHGVG DTDD IDHLG NRRLRSVGEL LQNQFRIGLS RMERVVRERM SIQDTNTITP QQLINIRPVI ASIKEFFGSS QLSQFMDQTN PLAEL THKR RLSALGPGGL TRERAGMEVR DVHYSHYGRM CPIETPEGPN IGLINSLSSY AKVNRFGFIE TPYRRVDPET GKVTGR IDY LTADEEDNYV VAQANARLDD EGAFIDDSIV ARFRGENTVV SRNRVDYMDV SPKQVVSAAT ACIPFLENDD SNRALMG AN MQRQAVPLMQ PEAPFVGTGM EYVSGKDSGA AVICKHPGIV ERVEAKNVWV RRYEEVDGQK VKGNLDKYSL LKFVRSNQ G TCYNQRPIVS VGDEVVKGEI LADGPSMELG ELALGRNVMV GFMTWDGYNY EDAIIMSERL VKDDVYTSIH IEEYESEAR DTKLGPEEIT RDIPNVGEDA LRNLDDRGII RIGAEVKDGD LLVGKVTPKG VTELTAEERL LHAIFGEKAR EVRDTSLRVP HGGGGIIHD VKVFNREDGD ELPPGVNQLV RVYIVQKRKI SEGDKMAGRH GNKGVISKIL PEEDMPYLPD GTPIDIMLNP L GVPSRMNI GQVLELHMGM AARYLGIHIA SPVFDGAREE DVWETLEEAG MSRDAKTVLY DGRTGEPFDN RVSVGIMYMI KL AHMVDDK LHARSTGPYS LVTQQPLGGK AQFGGQRFGE MEVWALEAYG AAYTLQEILT VKSDDVVGRV KTYEAIVKGD NVP EPGVPE SFKVLIKELQ SLGMDVKILS GDEEEIEMRD LEDEEDAKQA DGLALSGDEE PEETASADVE RDVVTKE

UniProtKB: DNA-directed RNA polymerase subunit beta

+
Macromolecule #7: DNA-directed RNA polymerase subunit delta

MacromoleculeName: DNA-directed RNA polymerase subunit delta / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Molecular weightTheoretical: 20.417891 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MGIKQYSQEE LKEMALVEIA HELFEEHKKP VPFQELLNEI ASLLGVKKEE LGDRIAQFYT DLNIDGRFLA LSDQTWGLRS WYPYDQLDE ETQPTVKAKK KKAKKAVEED LDLDEFEEID EDDLDLDEVE EELDLEADDF DEEDLDEDDD DLEIEEDIID E DDEDYDDE EEEIK

UniProtKB: DNA-directed RNA polymerase subunit delta

+
Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / 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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78265
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION
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