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- EMDB-19079: Cryo-EM structure of bacterial RNA polymerase-sigma54 initial tra... -

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Basic information

Entry
Database: EMDB / ID: EMD-19079
TitleCryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex
Map data
Sample
  • Complex: RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase
    • Protein or peptide: RNA polymerase sigma-54 factor
    • DNA: DNA (47-MER)
    • RNA: RNA (5'-R(P*GP*CP*CP*GP*C)-3')
    • DNA: DNA (50-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
Keywordsinitiation / rna polymerase / sigma54 / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation ...RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / 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 / RNA polymerase Rpb6 ...DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / 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 / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Klebsiella oxytoca (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGao F / Zhang X
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/M011178/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural basis of σ displacement and promoter escape in bacterial transcription.
Authors: Forson Gao / Fuzhou Ye / Bowen Zhang / Nora Cronin / Martin Buck / Xiaodong Zhang /
Abstract: Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated, and in bacteria, transcription initiation is mediated by sigma ...Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP). Transcription initiation is highly regulated, and in bacteria, transcription initiation is mediated by sigma (σ) factors. σ recruits RNAP to the promoter DNA region, located upstream of the transcription start site (TSS) and facilitates open complex formation, where double-stranded DNA is opened up into a transcription bubble and template strand DNA is positioned inside RNAP for initial RNA synthesis. During initial transcription, RNAP remains bound to σ and upstream DNA, presumably with an enlarging transcription bubble. The release of RNAP from upstream DNA is required for promoter escape and processive transcription elongation. Bacteria sigma factors can be broadly separated into two classes with the majority belonging to the σ class, represented by the σ that regulates housekeeping genes. σ forms a class on its own and regulates stress response genes. Extensive studies on σ have revealed the molecular mechanisms of the σ dependent process while how σ transitions from initial transcription to elongation is currently unknown. Here, we present a series of cryo-electron microscopy structures of the RNAP-σ initial transcribing complexes with progressively longer RNA, which reveal structural changes that lead to promoter escape. Our data show that initially, the transcription bubble enlarges, DNA strands scrunch, reducing the interactions between σ and DNA strands in the transcription bubble. RNA extension and further DNA scrunching help to release RNAP from σ and upstream DNA, enabling the transition to elongation.
History
DepositionDec 10, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19079.png

Downloads & links

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Map

FileDownload / File: emd_19079.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.011662933 - 0.046605278
Average (Standard dev.)0.000010888012 (±0.0029793414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19079_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19079_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA polymerase-sigma54 initial transcribing complex - 5nt pre-tra...

EntireName: RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex
Components
  • Complex: RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase
    • Protein or peptide: RNA polymerase sigma-54 factor
    • DNA: DNA (47-MER)
    • RNA: RNA (5'-R(P*GP*CP*CP*GP*C)-3')
    • DNA: DNA (50-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: RNA polymerase-sigma54 initial transcribing complex - 5nt pre-tra...

SupramoleculeName: RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1
Details: Residues missing between Chain A and B due to missing densities
Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 35.726789 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: SVTEFLKPRL VDIEQVSSTH AKVTLEPLER GFGHTLGNAL RRILLSSMPG CAVTEVEIDG VLHEYSTKEG VQEDILEILL NLKGLAVRV QGKDEVILTL NKSGIGPVTA ADITHDGDVE IVKPQHVICH LTDENASISM RIKVQRGRGY VPASTRIHSE E DERPIGRL ...String:
SVTEFLKPRL VDIEQVSSTH AKVTLEPLER GFGHTLGNAL RRILLSSMPG CAVTEVEIDG VLHEYSTKEG VQEDILEILL NLKGLAVRV QGKDEVILTL NKSGIGPVTA ADITHDGDVE IVKPQHVICH LTDENASISM RIKVQRGRGY VPASTRIHSE E DERPIGRL LVDACYSPVE RIAYNVEAAR VEQRTDLDKL VIEMETNGTI DPEEAIRRAA TILAEQLEAF VDLRDVRQPE VK EEKPEFD PILLRPVDDL ELTVRSANCL KAEAIHYIGD LVQRTEVELL KTPNLGKKSL TEIKDVLASR GLSLGMRLEN WPP A

UniProtKB: DNA-directed RNA polymerase subunit alpha

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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: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 150.69175 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ SYSGNSELQY VSYRLGEPVF DVQECQIRG VTYSAPLRVK LRLVIYEREA PEGTVKDIKE QEVYMGEIPL MTDNGTFVIN GTERVIVSQL HRSPGVFFDS D KGKTHSSG ...String:
MVYSYTEKKR IRKDFGKRPQ VLDVPYLLSI QLDSFQKFIE QDPEGQYGLE AAFRSVFPIQ SYSGNSELQY VSYRLGEPVF DVQECQIRG VTYSAPLRVK LRLVIYEREA PEGTVKDIKE QEVYMGEIPL MTDNGTFVIN GTERVIVSQL HRSPGVFFDS D KGKTHSSG KVLYNARIIP YRGSWLDFEF DPKDNLFVRI DRRRKLPATI ILRALNYTTE QILDLFFEKV IFEIRDNKLQ ME LVPERLR GETASFDIEA NGKVYVEKGR RITARHIRQL EKDDVKLIEV PVEYIAGKVV AKDYIDESTG ELICAANMEL SLD LLAKLS QSGHKRIETL FTNDLDHGPY ISETLRVDPT NDRLSALVEI YRMMRPGEPP TREAAESLFE NLFFSEDRYD LSAV GRMKF NRSLLREEIE GSGILSKDDI IDVMKKLIDI RNGKGEVDDI DHLGNRRIRS VGEMAENQFR VGLVRVERAV KERLS LGDL DTLMPQDMIN AKPISAAVKE FFGSSQLSQF MDQNNPLSEI THKRRISALG PGGLTRERAG FEVRDVHPTH YGRVCP IET PEGPNIGLIN SLSVYAQTNE YGFLETPYRK VTDGVVTDEI HYLSAIEEGN YVIAQANSNL DEEGHFVEDL VTCRSKG ES SLFSRDQVDY MDVSTQQVVS VGASLIPFLE HDDANRALMG ANMQRQAVPT LRADKPLVGT GMERAVAVDS GVTAVAKR G GVVQYVDASR IVIKVNEDEM YPGEAGIDIY NLTKYTRSNQ NTCINQMPCV SLGEPVERGD VLADGPSTDL GELALGQNM RVAFMPWNGY NFEDSILVSE RVVQEDRFTT IHIQELACVS RDTKLGPEEI TADIPNVGEA ALSKLDESGI VYIGAEVTGG DILVGKVTP KGETQLTPEE KLLRAIFGEK ASDVKDSSLR VPNGVSGTVI DVQVFTRDGV EKDKRALEIE EMQLKQAKKD L SEELQILE AGLFSRIRAV LVAGGVEAEK LDKLPRDRWL ELGLTDEEKQ NQLEQLAEQY DELKHEFEKK LEAKRRKITQ GD DLAPGVL KIVKVYLAVK RRIQPGDKMA GRHGNKGVIS KINPIEDMPY DENGTPVDIV LNPLGVPSRM NIGQILETHL GMA AKGIGD KINAMLKQQQ EVAKLREFIQ RAYDLGADVR QKVDLSTFSD EEVMRLAENL RKGMPIATPV FDGAKEAEIK ELLK LGDLP TSGQIRLYDG RTGEQFERPV TVGYMYMLKL NHLVDDKMHA RSTGSYSLVT QQPLGGKAQF GGQRFGEMEV WALEA YGAA YTLQEMLTVK SDDVNGRTKM YKNIVDGNHQ MEPGMPESFN VLLKEIRSLG INIELED

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 152.040266 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: LLKFLKAQTK TEEFDAIKIA LASPDMIRSW SFGEVKKPET INYRTFKPER DGLFCARIFG PVKDYECLCG KYKRLKHRGV ICEKCGVEV TQTKVRRERM GHIELASPTA HIWFLKSLPS RIGLLLDMPL RDIERVLYFE SYVVIEGGMT NLERQQILTE E QYLDALEE ...String:
LLKFLKAQTK TEEFDAIKIA LASPDMIRSW SFGEVKKPET INYRTFKPER DGLFCARIFG PVKDYECLCG KYKRLKHRGV ICEKCGVEV TQTKVRRERM GHIELASPTA HIWFLKSLPS RIGLLLDMPL RDIERVLYFE SYVVIEGGMT NLERQQILTE E QYLDALEE FGDEFDAKMG AEAIQALLKS MDLEQECEQL REELNETNSE TKRKKLTKRI KLLEAFVQSG NKPEWMILTV LP VLPPDLR PLVPLDGGRF ATSDLNDLYR RVINRNNRLK RLLDLAAPDI IVRNEKRMLQ EAVDALLDNG RRGRAITGSN KRP LKSLAD MIKGKQGRFR QNLLGKRVDY SGRSVITVGP YLRLHQCGLP KKMALELFKP FIYGKLELRG LATTIKAAKK MVER EEAVV WDILDEVIRE HPVLLNRAPT LHRLGIQAFE PVLIEGKAIQ LHPLVCAAYN ADFDGDQMAV HVPLTLEAQL EARAL MMST NNILSPANGE PIIVPSQDVV LGLYYMTRDC VNAKGEGMVL TGPKEAERLY RSGLASLHAR VKVRITEYEK DANGEL VAK TSLKDTTVGR AILWMIVPKG LPYSIVNQAL GKKAISKMLN TCYRILGLKP TVIFADQIMY TGFAYAARSG ASVGIDD MV IPEKKHEIIS EAEAEVAEIQ EQFQSGLVTA GERYNKVIDI WAAANDRVSK AMMDNLQTET VINRDGQEEK QVSFNSIY M MADSGARGSA AQIRQLAGMR GLMAKPDGSI IETPITANFR EGLNVLQYFI STHGARKGLA DTALKTANSG YLTRRLVDV AQDLVVTEDD CGTHEGIMMT PVIEGGDVKE PLRDRVLGRV TAEDVLKPGT ADILVPRNTL LHEQWCDLLE ENSVDAVKVR SVVSCDTDF GVCAHCYGRD LARGHIINKG EAIGVIAAQS IGEPGTQLTM RTFHIGGAAS RAAAESSIQV KNKGSIKLSN V KSVVNSSG KLVITSRNTE LKLIDEFGRT KESYKVPYGA VLAKGDGEQV AGGETVANWD PHTMPVITEV SGFVRFTDMI DG QTITRQT DELTGLSSLV VLDSAERTAG GKDLRPALKI VDAQGNDVLI PGTDMPAQYF LPGKAIVQLE DGVQISSGDT LAR IPQESG GTKDITGGLP RVADLFEARR PKEPAILAEI SGIVSFGKET KGKRRLVITP VDGSDPYEEM IPKWRQLNVF EGER VERGD VISDGPEAPH DILRLRGVHA VTRYIVNEVQ DVYRLQGVKI NDKHIEVIVR QMLRKATIVN AGSSDFLEGE QVEYS RVKI ANRELEANGK VGATYSRDLL GITKASLATE SFISAASFQE TTRVLTEAAV AGKRDELRGL KENVIVGRLI PAGTGY AYH QDRMRRRAAG

UniProtKB: DNA-directed RNA polymerase subunit beta'

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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 / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 8.449504 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
ARVTVQDAVE KIGNRFDLVL VAARRARQMQ VGGKDPLVPE ENDKTTVIAL REIEEGLINN QILDVRERQE QQEQ

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #5: RNA polymerase sigma-54 factor

MacromoleculeName: RNA polymerase sigma-54 factor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella oxytoca (bacteria)
Molecular weightTheoretical: 42.687988 KDa
Recombinant expressionOrganism: Klebsiella oxytoca (bacteria)
SequenceString: TAGTPSGNGV DYQDDELPVY QGETTQSLQD YLMWQVELTP FTDTDRAIAT SIVDAVDDTG YLTIQIEDIV DSIGDDEIGL EEVEAVLKR IQRFDPVGVA AKDLRDCLLI QLSQFAKETP WLEEARLIIS DHLDLLANHD FRTLMRVTRL KEEVLKEAVN L IQSLDPRP ...String:
TAGTPSGNGV DYQDDELPVY QGETTQSLQD YLMWQVELTP FTDTDRAIAT SIVDAVDDTG YLTIQIEDIV DSIGDDEIGL EEVEAVLKR IQRFDPVGVA AKDLRDCLLI QLSQFAKETP WLEEARLIIS DHLDLLANHD FRTLMRVTRL KEEVLKEAVN L IQSLDPRP GQSIQTGEPE YVIPDVLVRK VNDRWVVELN SDSLPRLKIN QQYAAMGNSA RNDADGQFIR SNLQEARWLI KS LESANDT LLRVSRCIVE QQQAFFEQGE EYMKPMVLAD IAQAVEMHES TISRVTTQKY LHSPRGIFEL KYFFSSHVNT EGG GEASST AIRALVKKLI AAENPAKPLS DSKLTSMLSE QGIMVARRTV AKYRESLSIP PSNQ

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Macromolecule #6: DNA (47-MER)

MacromoleculeName: DNA (47-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Klebsiella oxytoca (bacteria)
Molecular weightTheoretical: 14.429279 KDa
SequenceString:
(DG)(DC)(DT)(DG)(DG)(DC)(DA)(DC)(DG)(DA) (DC)(DT)(DT)(DT)(DT)(DG)(DC)(DA)(DC)(DT) (DC)(DT)(DA)(DA)(DA)(DT)(DA)(DA)(DT) (DA)(DG)(DA)(DT)(DC)(DA)(DT)(DG)(DC)(DT) (DG) (DT)(DT)(DG)(DC)(DA)(DC)(DA)

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Macromolecule #8: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Klebsiella oxytoca (bacteria)
Molecular weightTheoretical: 15.461913 KDa
SequenceString:
(DT)(DG)(DT)(DG)(DC)(DA)(DA)(DC)(DA)(DG) (DC)(DA)(DT)(DG)(DA)(DT)(DC)(DG)(DC)(DG) (DG)(DC)(DA)(DA)(DG)(DC)(DT)(DG)(DA) (DT)(DC)(DG)(DT)(DG)(DC)(DA)(DA)(DA)(DA) (DG) (DT)(DC)(DG)(DT)(DG)(DC)(DC)(DA) (DG)(DC)

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Macromolecule #7: RNA (5'-R(P*GP*CP*CP*GP*C)-3')

MacromoleculeName: RNA (5'-R(P*GP*CP*CP*GP*C)-3') / type: rna / ID: 7 / Details: GCCGC / Number of copies: 1
Source (natural)Organism: Klebsiella oxytoca (bacteria)
Molecular weightTheoretical: 1.561 KDa
SequenceString:
GCCGC

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

0001

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 570815

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