[English] 日本語
Yorodumi
- EMDB-34849: Cryo-EM structure of E. coli RNAP sigma32 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34849
TitleCryo-EM structure of E. coli RNAP sigma32 complex
Map data
Sample
  • Complex: Cryo-EM structure of E. coli RNAP sigma32 complex
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: RNA polymerase sigma factor RpoH
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • DNA: DNA (54-MER)
    • DNA: DNA (54-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Keywordstranscription / RNA polymerase / sigma factor / heat shock response / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


site-specific recombinase activity / invertasome / bacterial-type RNA polymerase core enzyme binding / DNA-binding transcription activator activity / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly ...site-specific recombinase activity / invertasome / bacterial-type RNA polymerase core enzyme binding / DNA-binding transcription activator activity / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / core promoter sequence-specific DNA binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / regulation of gene expression / DNA recombination / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RNA polymerase sigma factor RpoH, proteobacteria / Sigma-70 factors family signature 1. / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 ...RNA polymerase sigma factor RpoH, proteobacteria / Sigma-70 factors family signature 1. / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / 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 Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 beta' / DNA-directed RNA polymerase subunit beta / RNA polymerase sigma factor RpoH
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsWu S / Ma LX
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomolecules / Year: 2023
Title: Structural Insight into the Mechanism of σ32-Mediated Transcription Initiation of Bacterial RNA Polymerase.
Authors: Qiang Lu / Taiyu Chen / Jiening Wang / Feng Wang / Wenlong Ye / Lixin Ma / Shan Wu /
Abstract: Bacterial RNA polymerases (RNAP) form distinct holoenzymes with different σ factors to initiate diverse gene expression programs. In this study, we report a cryo-EM structure at 2.49 Å of RNA ...Bacterial RNA polymerases (RNAP) form distinct holoenzymes with different σ factors to initiate diverse gene expression programs. In this study, we report a cryo-EM structure at 2.49 Å of RNA polymerase transcription complex containing a temperature-sensitive bacterial σ factor, σ (σ-RPo). The structure of σ-RPo reveals key interactions essential for the assembly of σ-RNAP holoenzyme and for promoter recognition and unwinding by σ. Specifically, a weak interaction between σ and -35/-10 spacer is mediated by T128 and K130 in σ. A histidine in σ, rather than a tryptophan in σ, acts as a wedge to separate the base pair at the upstream junction of the transcription bubble, highlighting the differential promoter-melting capability of different residue combinations. Structure superimposition revealed relatively different orientations between βFTH and σ from other σ-engaged RNAPs and biochemical data suggest that a biased σ-βFTH configuration may be adopted to modulate binding affinity to promoter so as to orchestrate the recognition and regulation of different promoters. Collectively, these unique structural features advance our understanding of the mechanism of transcription initiation mediated by different σ factors.
History
DepositionNov 25, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34849.png

Downloads & links

-
Map

FileDownload / File: emd_34849.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.851 Å
Density
Contour LevelBy AUTHOR: 0.0112
Minimum - Maximum-0.03969181 - 0.10768588
Average (Standard dev.)0.000051800573 (±0.003647174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_34849_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34849_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34849_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of E. coli RNAP sigma32 complex

EntireName: Cryo-EM structure of E. coli RNAP sigma32 complex
Components
  • Complex: Cryo-EM structure of E. coli RNAP sigma32 complex
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: RNA polymerase sigma factor RpoH
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • DNA: DNA (54-MER)
    • DNA: DNA (54-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Cryo-EM structure of E. coli RNAP sigma32 complex

SupramoleculeName: Cryo-EM structure of E. coli RNAP sigma32 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #6, #3-#5
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
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 / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 36.801016 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLA VRVQGKDEVI LTLNKSGIGP VTAADITHDG DVEIVKPQHV ICHLTDENAS ISMRIKVQRG RGYVPASTRI H SEEDERPI ...String:
MQGSVTEFLK PRLVDIEQVS STHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IDGVLHEYST KEGVQEDILE ILLNLKGLA VRVQGKDEVI LTLNKSGIGP VTAADITHDG DVEIVKPQHV ICHLTDENAS ISMRIKVQRG RGYVPASTRI H SEEDERPI GRLLVDACYS PVERIAYNVE AARVEQRTDL DKLVIEMETN GTIDPEEAIR RAATILAEQL EAFVDLRDVR QP EVKEEKP EFDPILLRPV DDLELTVRSA NCLKAEAIHY IGDLVQRTEV ELLKTPNLGK KSLTEIKDVL ASRGLSLGMR LEN WPPASI ADEKL

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 / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 151.341406 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEFVYSYTEK KRIRKDFGKR PQVLDVPYLL SIQLDSFQKF IEQDPEGQYG LEAAFRSVFP IQSYSGNSEL QYVSYRLGEP VFDVQECQI RGVTYSAPLR VKLRLVIYER EAPEGTVKDI KEQEVYMGEI PLMTDNGTFV INGTERVIVS QLHRSPGVFF D SDKGKTHS ...String:
MEFVYSYTEK KRIRKDFGKR PQVLDVPYLL SIQLDSFQKF IEQDPEGQYG LEAAFRSVFP IQSYSGNSEL QYVSYRLGEP VFDVQECQI RGVTYSAPLR VKLRLVIYER EAPEGTVKDI KEQEVYMGEI PLMTDNGTFV INGTERVIVS QLHRSPGVFF D SDKGKTHS SGKVLYNARI IPYRGSWLDF EFDPKDNLFV RIDRRRKLPA TIILRALNYT TEQILDLFFE KVIFEIRDNK LQ MELVPER LRGETASFDI EANGKVYVEK GRRITARHIR QLEKDDVKLI EVPVEYIAGK VVAKDYIDES TGELICAANM ELS LDLLAK LSQSGHKRIE TLFTNDLDHG PYISETLRVD PTNDRLSALV EIYRMMRPGE PPTREAAESL FENLFFSEDR YDLS AVGRM KFNRSLLREE IEGSGILSKD DIIDVMKKLI DIRNGKGEVD DIDHLGNRRI RSVGEMAENQ FRVGLVRVER AVKER LSLG DLDTLMPQDM INAKPISAAV KEFFGSSQLS QFMDQNNPLS EITHKRRISA LGPGGLTRER AGFEVRDVHP THYGRV CPI ETPEGPNIGL INSLSVYAQT NEYGFLETPY RKVTDGVVTD EIHYLSAIEE GNYVIAQANS NLDEEGHFVE DLVTCRS KG ESSLFSRDQV DYMDVSTQQV VSVGASLIPF LEHDDANRAL MGANMQRQAV PTLRADKPLV GTGMERAVAV DSGVTAVA K RGGVVQYVDA SRIVIKVNED EMYPGEAGID IYNLTKYTRS NQNTCINQMP CVSLGEPVER GDVLADGPST DLGELALGQ NMRVAFMPWN GYNFEDSILV SERVVQEDRF TTIHIQELAC VSRDTKLGPE EITADIPNVG EAALSKLDES GIVYIGAEVT GGDILVGKV TPKGETQLTP EEKLLRAIFG EKASDVKDSS LRVPNGVSGT VIDVQVFTRD GVEKDKRALE IEEMQLKQAK K DLSEELQI LEAGLFSRIR AVLVAGGVEA EKLDKLPRDR WLELGLTDEE KQNQLEQLAE QYDELKHEFE KKLEAKRRKI TQ GDDLAPG VLKIVKVYLA VKRRIQPGDK MAGRHGNKGV ISKINPIEDM PYDENGTPVD IVLNPLGVPS RMNIGQILET HLG MAAKGI GDKINAMLKQ QQEVAKLREF IQRAYDLGAD VRQKVDLSTF SDEEVMRLAE NLRKGMPIAT PVFDGAKEAE IKEL LKLGD LPTSGQIRLY DGRTGEQFER PVTVGYMYML KLNHLVDDKM HARSTGSYSL VTQQPLGGKA QFGGQRFGEM EVWAL EAYG AAYTLQEMLT VKSDDVNGRT KMYKNIVDGN HQMEPGMPES FNVLLKEIRS LGINIELEDE SR

UniProtKB: DNA-directed RNA polymerase subunit beta

-
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 / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 157.613078 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSKDLLKFL KAQTKTEEFD AIKIALASPD MIRSWSFGEV KKPETINYRT FKPERDGLFC ARIFGPVKDY ECLCGKYKRL KHRGVICEK CGVEVTQTKV RRERMGHIEL ASPTAHIWFL KSLPSRIGLL LDMPLRDIER VLYFESYVVI EGGMTNLERQ Q ILTEEQYL ...String:
MTSKDLLKFL KAQTKTEEFD AIKIALASPD MIRSWSFGEV KKPETINYRT FKPERDGLFC ARIFGPVKDY ECLCGKYKRL KHRGVICEK CGVEVTQTKV RRERMGHIEL ASPTAHIWFL KSLPSRIGLL LDMPLRDIER VLYFESYVVI EGGMTNLERQ Q ILTEEQYL DALEEFGDEF DAKMGAEAIQ ALLKSMDLEQ ECEQLREELN ETNSETKRKK LTKRIKLLEA FVQSGNKPEW MI LTVLPVL PPDLRPLVPL DGGRFATSDL NDLYRRVINR NNRLKRLLDL AAPDIIVRNE KRMLQEAVDA LLDNGRRGRA ITG SNKRPL KSLADMIKGK QGRFRQNLLG KRVDYSGRSV ITVGPYLRLH QCGLPKKMAL ELFKPFIYGK LELRGLATTI KAAK KMVER EEAVVWDILD EVIREHPVLL NRAPTLHRLG IQAFEPVLIE GKAIQLHPLV CAAYNADFDG DQMAVHVPLT LEAQL EARA LMMSTNNILS PANGEPIIVP SQDVVLGLYY MTRDCVNAKG EGMVLTGPKE AERLYRSGLA SLHARVKVRI TEYEKD ANG ELVAKTSLKD TTVGRAILWM IVPKGLPYSI VNQALGKKAI SKMLNTCYRI LGLKPTVIFA DQIMYTGFAY AARSGAS VG IDDMVIPEKK HEIISEAEAE VAEIQEQFQS GLVTAGERYN KVIDIWAAAN DRVSKAMMDN LQTETVINRD GQEEKQVS F NSIYMMADSG ARGSAAQIRQ LAGMRGLMAK PDGSIIETPI TANFREGLNV LQYFISTHGA RKGLADTALK TANSGYLTR RLVDVAQDLV VTEDDCGTHE GIMMTPVIEG GDVKEPLRDR VLGRVTAEDV LKPGTADILV PRNTLLHEQW CDLLEENSVD AVKVRSVVS CDTDFGVCAH CYGRDLARGH IINKGEAIGV IAAQSIGEPG TQLTMRTFHI GGAASRAAAE SSIQVKNKGS I KLSNVKSV VNSSGKLVIT SRNTELKLID EFGRTKESYK VPYGAVLAKG DGEQVAGGET VANWDPHTMP VITEVSGFVR FT DMIDGQT ITRQTDELTG LSSLVVLDSA ERTAGGKDLR PALKIVDAQG NDVLIPGTDM PAQYFLPGKA IVQLEDGVQI SSG DTLARI PQESGGTKDI TGGLPRVADL FEARRPKEPA ILAEISGIVS FGKETKGKRR LVITPVDGSD PYEEMIPKWR QLNV FEGER VERGDVISDG PEAPHDILRL RGVHAVTRYI VNEVQDVYRL QGVKINDKHI EVIVRQMLRK ATIVNAGSSD FLEGE QVEY SRVKIANREL EANGKVGATY SRDLLGITKA SLATESFISA ASFQETTRVL TEAAVAGKRD ELRGLKENVI VGRLIP AGT GYAYHQDRMR RRAAGEAPAA PQVTAEDASA SLAELLNAGL GGSDNELEHH HHHHHHHHHH GT

UniProtKB: DNA-directed RNA polymerase subunit beta'

-
Macromolecule #6: RNA polymerase sigma factor RpoH

MacromoleculeName: RNA polymerase sigma factor RpoH / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 32.513836 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDKMQSLAL APVGNLDSYI RAANAWPMLS ADEERALAEK LHYHGDLEAA KTLILSHLRF VVHIARNYAG YGLPQADLIQ EGNIGLMKA VRRFNPEVGV RLVSFAVHWI KAEIHEYVLR NWRIVKVATT KAQRKLFFNL RKTKQRLGWF NQDEVEMVAR E LGVTSKDV ...String:
MTDKMQSLAL APVGNLDSYI RAANAWPMLS ADEERALAEK LHYHGDLEAA KTLILSHLRF VVHIARNYAG YGLPQADLIQ EGNIGLMKA VRRFNPEVGV RLVSFAVHWI KAEIHEYVLR NWRIVKVATT KAQRKLFFNL RKTKQRLGWF NQDEVEMVAR E LGVTSKDV REMESRMAAQ DMTFDLSSDD DSDSQPMAPV LYLQDKSSNF ADGIEDDNWE EQAANRLTDA MQGLDERSQD II RARWLDE DNKSTLQELA DRYGVSAERV RQLEKNAMKK LRAAIEA

UniProtKB: RNA polymerase sigma factor RpoH

-
Macromolecule #4: DNA (54-MER)

MacromoleculeName: DNA (54-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.614637 KDa
SequenceString: (DC)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DA)(DA) (DG)(DA)(DC)(DG)(DT)(DG)(DG)(DT)(DT)(DT) (DA)(DC)(DG)(DA)(DC)(DC)(DC)(DC)(DA) (DT)(DT)(DT)(DA)(DG)(DT)(DA)(DG)(DT)(DC) (DA) (DA)(DC)(DC)(DG)(DC)(DA) ...String:
(DC)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DA)(DA) (DG)(DA)(DC)(DG)(DT)(DG)(DG)(DT)(DT)(DT) (DA)(DC)(DG)(DA)(DC)(DC)(DC)(DC)(DA) (DT)(DT)(DT)(DA)(DG)(DT)(DA)(DG)(DT)(DC) (DA) (DA)(DC)(DC)(DG)(DC)(DA)(DG)(DT) (DG)(DA)(DG)(DT)(DG)(DG)

-
Macromolecule #5: DNA (54-MER)

MacromoleculeName: DNA (54-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.663676 KDa
SequenceString: (DC)(DC)(DA)(DC)(DT)(DC)(DA)(DC)(DT)(DG) (DC)(DG)(DG)(DT)(DT)(DG)(DA)(DC)(DT)(DA) (DC)(DT)(DA)(DA)(DA)(DT)(DG)(DG)(DG) (DG)(DT)(DC)(DG)(DT)(DA)(DA)(DA)(DC)(DC) (DA) (DC)(DG)(DT)(DC)(DT)(DT) ...String:
(DC)(DC)(DA)(DC)(DT)(DC)(DA)(DC)(DT)(DG) (DC)(DG)(DG)(DT)(DT)(DG)(DA)(DC)(DT)(DA) (DC)(DT)(DA)(DA)(DA)(DT)(DG)(DG)(DG) (DG)(DT)(DC)(DG)(DT)(DA)(DA)(DA)(DC)(DC) (DA) (DC)(DG)(DT)(DC)(DT)(DT)(DC)(DA) (DA)(DG)(DG)(DG)(DG)(DG)

-
Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / 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: 7.9
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

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

6alh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 641734
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://pdbjlvh1.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