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- EMDB-51273: Cryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bo... -

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Basic information

Entry
Database: EMDB / ID: EMD-51273
TitleCryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bound to an ompU promoter DNA fragment
Map dataompU Open Promoter Complex raw map
Sample
  • Complex: Virulent transcription complex #1
    • Complex: DNA-directed RNA polymerase
      • 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 beta'
      • Protein or peptide: DNA-directed RNA polymerase subunit omega
      • Protein or peptide: RNA polymerase sigma factor RpoD
    • Complex: Double stranded DNA
      • DNA: ompU promoter template DNA strand
      • DNA: ompU promoter non-template DNA strand
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsRNA polymerase / Open promoter complex / ompU / Vibrio cholerae / TRANSCRIPTION
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 ...RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / 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, 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / 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, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsAlcaide-Jimenez A / Baudin F / Canals A / Machon C / Murciano B / Fabrega-Ferrer M / Bantysh O / Perez-Luque R / Krukonis ES / Muller CW / Coll M
Funding support Spain, 2 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-12141GB-100 Spain
Generalitat de Catalunya2021SGR00423 Spain
CitationJournal: Sci Adv / Year: 2026
Title: Structures of transcription complexes reveal how ToxR and TcpP recruit the RNA polymerase and activate virulence genes.
Authors: Adrià Alcaide-Jiménez / Albert Canals / Florence Baudin / Cristina Machón / Montserrat Fàbrega-Ferrer / Olga Bantysh / Rosa Pérez-Luque / Brice Murciano / Ali A Mohammad / Michael J ...Authors: Adrià Alcaide-Jiménez / Albert Canals / Florence Baudin / Cristina Machón / Montserrat Fàbrega-Ferrer / Olga Bantysh / Rosa Pérez-Luque / Brice Murciano / Ali A Mohammad / Michael J Rowse / Joseph M Ferracciolo / Eric S Krukonis / Christoph W Müller / Miquel Coll /
Abstract: Activation of virulence in , the etiological agent of cholera disease, is mediated by two transmembrane one-component signal-transduction proteins, ToxR and TcpP, which are also transcription factors. ...Activation of virulence in , the etiological agent of cholera disease, is mediated by two transmembrane one-component signal-transduction proteins, ToxR and TcpP, which are also transcription factors. Using cryo-electron microscopy, we have solved five structures of the and transcription activation complexes, including the RNA polymerase (RNAP) holoenzyme, promoter DNAs, transcribed RNA, and their corresponding transcription factors, ToxR or TcpP and ToxR-TcpP, respectively. Activation is achieved through the interaction of ToxR or TcpP with the α-C-terminal repeat domain of RNAP where a single residue of the activator, a phenylalanine, appears to be the most critical contact, as confirmed by mutagenesis. No interactions of the transcription factors were observed with other subunits of the RNAP, i.e., the σ subunit as it occurs in the structurally related PhoB family of two-component transcription factors. The structures, and their comparison with our previously solved DNA promoter-ToxR x-ray structures, unveil the molecular mechanism of cholera virulence gene activation.
History
DepositionAug 6, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51273.png

Downloads & links

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Map

FileDownload / File: emd_51273.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationompU Open Promoter Complex raw map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00455
Minimum - Maximum-0.023198346 - 1.6902776
Average (Standard dev.)0.0022925823 (±0.032394763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: ompU Open Promoter Complex raw map

Fileemd_51273_additional_1.map
AnnotationompU Open Promoter Complex raw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ompU Open Promoter Complex raw map

Fileemd_51273_half_map_1.map
AnnotationompU Open Promoter Complex raw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ompU Open Promoter Complex raw map

Fileemd_51273_half_map_2.map
AnnotationompU Open Promoter Complex raw 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 : Virulent transcription complex #1

EntireName: Virulent transcription complex #1
Components
  • Complex: Virulent transcription complex #1
    • Complex: DNA-directed RNA polymerase
      • 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 beta'
      • Protein or peptide: DNA-directed RNA polymerase subunit omega
      • Protein or peptide: RNA polymerase sigma factor RpoD
    • Complex: Double stranded DNA
      • DNA: ompU promoter template DNA strand
      • DNA: ompU promoter non-template DNA strand
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Virulent transcription complex #1

SupramoleculeName: Virulent transcription complex #1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Supramolecule #2: DNA-directed RNA polymerase

SupramoleculeName: DNA-directed RNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#7
Source (natural)Organism: Vibrio cholerae O395 (bacteria)

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Supramolecule #3: Double stranded DNA

SupramoleculeName: Double stranded DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Vibrio cholerae O395 (bacteria)

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Macromolecule #1: ompU promoter template DNA strand

MacromoleculeName: ompU promoter template DNA strand / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 21.146613 KDa
SequenceString: (DG)(DC)(DC)(DA)(DT)(DT)(DT)(DT)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DT)(DG)(DT)(DG)(DA) (DA)(DA)(DA)(DA)(DC)(DT)(DC)(DC)(DC) (DA)(DA)(DA)(DG)(DT)(DT)(DC)(DC)(DG)(DC) (DT) (DA)(DT)(DC)(DA)(DG)(DT) ...String:
(DG)(DC)(DC)(DA)(DT)(DT)(DT)(DT)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DT)(DG)(DT)(DG)(DA) (DA)(DA)(DA)(DA)(DC)(DT)(DC)(DC)(DC) (DA)(DA)(DA)(DG)(DT)(DT)(DC)(DC)(DG)(DC) (DT) (DA)(DT)(DC)(DA)(DG)(DT)(DT)(DA) (DG)(DT)(DA)(DA)(DA)(DA)(DT)(DG)(DA)(DT) (DA)(DT) (DA)(DA)(DA)(DT)(DC)(DC)(DA) (DA)(DC)

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Macromolecule #2: ompU promoter non-template DNA strand

MacromoleculeName: ompU promoter non-template DNA strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 21.408746 KDa
SequenceString: (DG)(DT)(DT)(DG)(DG)(DA)(DT)(DT)(DT)(DA) (DT)(DA)(DT)(DC)(DA)(DT)(DT)(DT)(DT)(DA) (DC)(DT)(DA)(DA)(DC)(DT)(DG)(DA)(DT) (DA)(DG)(DC)(DG)(DG)(DA)(DA)(DC)(DT)(DT) (DT) (DG)(DG)(DG)(DA)(DG)(DT) ...String:
(DG)(DT)(DT)(DG)(DG)(DA)(DT)(DT)(DT)(DA) (DT)(DA)(DT)(DC)(DA)(DT)(DT)(DT)(DT)(DA) (DC)(DT)(DA)(DA)(DC)(DT)(DG)(DA)(DT) (DA)(DG)(DC)(DG)(DG)(DA)(DA)(DC)(DT)(DT) (DT) (DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA) (DA)(DA)(DG)(DA)(DG)(DT)(DC)(DT)(DC)(DC) (DG)(DC) (DG)(DA)(DA)(DA)(DA)(DT)(DG) (DG)(DC)

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Macromolecule #3: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 36.461473 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MQGSVTEFLK PRLVDIEQIS TTHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IEGVLHEYST KEGVQEDILE ILLNLKGLA VRVAEGKDEV FITLNKSGSG PVVAGDITHD GDVEIVNPEH VICHLTSDNA AIAMRIKVER GRGYVPASAR I HTEEDERP ...String:
MQGSVTEFLK PRLVDIEQIS TTHAKVTLEP LERGFGHTLG NALRRILLSS MPGCAVTEVE IEGVLHEYST KEGVQEDILE ILLNLKGLA VRVAEGKDEV FITLNKSGSG PVVAGDITHD GDVEIVNPEH VICHLTSDNA AIAMRIKVER GRGYVPASAR I HTEEDERP IGRLLVDATF SPVDKIAYSV EAARVEQRTD LDKLVIDMET NGTLEPEEAI RRAATILAEQ LDAFVDLRDV RV PEEKEEK PEFDPILLRP VDDLELTVRS ANCLKAEAIH YIGDLVQRTE VELLKTPNLG KKSLTEIKDV LASRGLSLGM RLE NWPPAS IAED

UniProtKB: DNA-directed RNA polymerase subunit alpha

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Macromolecule #4: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 149.696531 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVYSYTEKKR IRKDFGTRPQ VLDIPYLLSI QLDSFEKFIE QDPEGQYGLE AAFRSVFPIQ SYNGNSELQY VSYRLGEPVF DVKECQIRG VTYSKPLRVK LRLVIFDKDA PAGTVKDIKE QEVYMGEIPL MTENGTFVIN GTERVIVSQL HRSPGVFFDS D KGKTHSSG ...String:
MVYSYTEKKR IRKDFGTRPQ VLDIPYLLSI QLDSFEKFIE QDPEGQYGLE AAFRSVFPIQ SYNGNSELQY VSYRLGEPVF DVKECQIRG VTYSKPLRVK LRLVIFDKDA PAGTVKDIKE QEVYMGEIPL MTENGTFVIN GTERVIVSQL HRSPGVFFDS D KGKTHSSG KVLYNARIIP YRGSWLDFEF DPKDNLYVRI DRRRKLPASI ILRVLGKTSA EILDIFFEKV NFEVKDQTLM ME LVPERLR GETATFDIEA DGKVYVEKGR RVTARHIRQL EKDGVNFIEV PVEYIVGKVS AKDYVNEATG ELIITANQEI SLE ALANLS QAGYKKLEVL FTNDLDHGPF MSETLRVDST TDRISALVEI YRMMRPGEPP TKEAAESLFE SLFFSAERYD LSTV GRMKF NSSIGREDAE EQGTLDEVDI IEVMKKLISI RNGKGEVDDI DHLGNRRIRS VGEMAENQFR VGLVRVERAV KERLS LGDL DNVMPQDLIN AKPISAAVKE FFGSSQLSQF MDQNNPLSEV THKRRISALG PGGLTRERAG FEVRDVHVTH YGRLCP IET PEGPNIGLIN SLSAFARCNE YGFLETPYRR VVNGVVTDEV DYLSAIEEGQ FVIAQANAKL TEEGGFADEL VTARQKG ES GLHPREHVDY MDVATNQVVS IAASLIPFLE HDDANRALMG ANMQRQAVPT LRSEKPLVGT GIERNVAVDS GVTAVAKR G GVIQSVDASR IVVKVNEEEL IPGEAGIDIY NLTKYTRSNQ NTCINQRPCV MPGEPVARGD VLADGPSTDL GELALGQNM RIAFMPWNGY NFEDSILVSE RVVQDDRFTT IHIQELSCVA RDTKLGAEEI TADIPNVGEA ALSKLDESGI VYIGAEVKGG DILVGKVTP KGETQLTPEE KLLRAIFGEK ASDVKDTSLR VPNSVAGTVI DVQVFTRDGV EKDKRALEIE QMQLKEAKKD L TEEFQILE GGLLARVRSV LLAGGYTEAK LSSIERKKWL EQTLENEELQ NQLEQLAEQY DELKADFDKK FEAKRRKITQ GD DLAPGVL KIVKVYLAVK RRIQPGDKMA GRHGNKGVIS KINPVEDMPY DENGQPVDIV LNPLGVPSRM NIGQILEVHL GLA AKGIGD KINQMIKEQQ ELAKLREFLQ KVYDLGDTRQ RVDISELSDE DVRTLAHNLR AGLPVATPVF DGAPESSIKA MLEL ADLPA SGQLTLFDGR TGDAFERPVT VGYMYMLKLN HLVDDKMHAR STGSYSLVTQ QPLGGKAQFG GQRFGEMEVW ALEAY GAAY TLQEMLTVKS DDVNGRTKMY KNIVDGNHAM EPGMPESFNV LLKEIRSLGI NIELEDE

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #5: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 155.234281 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKDLLNFLKA QHKTEEFDAI KIGLASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCG VEVTQTKVRR DRMGHIELAS PVAHIWFLKS LPSRIGLLMD MPLRDIERVL YFEMYVVTEP GMTDLERGQM L TEEEYLDR ...String:
MKDLLNFLKA QHKTEEFDAI KIGLASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR IFGPVKDYEC LCGKYKRLKH RGVICEKCG VEVTQTKVRR DRMGHIELAS PVAHIWFLKS LPSRIGLLMD MPLRDIERVL YFEMYVVTEP GMTDLERGQM L TEEEYLDR LEEWGDEFTA KMGAEAIKDL LASMDLPAEA EQMREELDTT NSETKRKKLT KRLKLVEAFV ASGNKPEWMI LT VLPVLPP DLRPLVPLDG GRFATSDLND LYRRVINRNN RLKRLLELAA PDIIVRNEKR MLQESVDALL DNGRRGRAIT GSN KRPLKS LADMIKGKQG RFRQNLLGKR VDYSGRSVIT VGPYLRLHQC GLPKKMALEL FKPFIYSKLE TRGLATTIKA AKKM VEREE AVVWDILDEV IREHPVLLNR APTLHRLGIQ AFEPVLIEGK AIQLHPLVCA AYNADFDGDQ MAVHVPLTLE AQLEA RTLM MSTNNILSPA SGDPIIVPSQ DVVLGLYYMT REKINAKGEG MYLTGPAEAE KAYRTKTAEL HARVKVRITE TIKHEN GKL TTETKMIDTT VGRAMLWQIV PKGLPYSLVN QKLGKKQISN LLNEAYRKLG LKDTVIFADQ IMYTGFAYAA LSGVSVG ID DMVVPAAKYT EIAEAEEEVR EIQEQFQSGL VTAGERYNKV IDIWASTNDR VAKAMMENLS SEQVINRQGE QEKQESFN S IYMMADSGAR GSAAQIRQLA GMRGLMARPD GSIIETPITA NFKEGLNVLQ YFISTHGARK GLADTALKTA NSGYLTRRL VDVAQDVVVT EHDCGTLEGV VMTPHIEGGD VKVALTELAL GRVVSEDILK PGTDEVLIPR NTLLDEKWCK VINDNSVDQI KVRSVVTCD SDFGCCAQCY GRDLARGHLV NQGEAVGVIA AQSIGEPGTQ LTMRTFHIGG AASTAAAENS IQAKNNGSVK L HNAKFVTN KDGKLVITSR ASELTIIDEF GRTKEKHKLP YGSMLSKADG DAVAAGETVA NWEAHTMPII TEVAGRVQFV DM IDGVTVS RQTDDLTGLS SSEVTEAAAR PAAGKDMRPA IKLVDANGKD VLIPGTDMPA QYFLPGKAIV NLDDGAEVNV GDT LARIPQ KSGGNKDITG GLPRVADLFE ARKPKEPAIL AEHSGTVSFG KETKGKRRLI ITRDSGDTYE EMIPKHRQLN VFEG ERIER GDVIADGPES PHDILRLRGI HAVTTYIANE VQEVYRLQGV KINDKHIETI VRQMLRKCTI TFAGDSEFLP GETVE YSQV KIANRKLVEE GKEPARFERE LLGITKASLA TESFISAASF QETTRVLTEA AVSGKRDDLR GLKENVIVGR LIPAGT GFA YHQDRQAKRA QEQQGPSAEQ ATDNLAALLN AGFSSDDE

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #6: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 10.068355 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARVTVQDAV EKIGNRFDLV LVAARRARQM QSGGKDALVP EENDKPTVIA LREIEEGLIT KDVLDARERQ EQQEQEAAEL AAVSSIMHN R

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #7: RNA polymerase sigma factor RpoD

MacromoleculeName: RNA polymerase sigma factor RpoD / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O395 (bacteria)
Molecular weightTheoretical: 70.749648 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDQNPQSQLK QLVLRGKEQG YLTYAEVNDH LPAEIVDSEQ VEDIIQMIND MGIKVVETAP DADDLALSDD TTITDEDAAE AAAAALSSV ESEIGRTTDP VRMYMREMGT VELLTREGEI DIAKRIEDGI NQVQSAIAEY PGTIPYILEQ FDRVQAEELR L TDLISGFV ...String:
MDQNPQSQLK QLVLRGKEQG YLTYAEVNDH LPAEIVDSEQ VEDIIQMIND MGIKVVETAP DADDLALSDD TTITDEDAAE AAAAALSSV ESEIGRTTDP VRMYMREMGT VELLTREGEI DIAKRIEDGI NQVQSAIAEY PGTIPYILEQ FDRVQAEELR L TDLISGFV DPNDMETEAP TATHIGSELS EADLADEDDA VVEDEDEDGD GESSDSEEEV GIDPELAREK FNELRGKFQN LQ LAVNEFG RDSHQASEAS DLVLDIFREF RLTPKQFDHL VETLRTSMDR VRTQERLVMK AVVEVAKMPK KSFIALFTGN ESN EEWLDK VLASDKPYVA KVREQEEEIR RSIQKLQMIE QETSLSVERI KDISHRMSIG EAKARRAKKE MVEANLRLVI SIAK KYTNR GLQFLDLIQE GNIGLMKAVD KFEYRRGYKF STYATWWIRQ AITRSIADQA RTIRIPVHMI ETINKLNRIS RQMLQ EMGR EPLPEELAER MQMPEDKIRK VLKIAKEPIS METPIGDDED SHLGDFIEDT TLELPLDSAT ATSLKAATRD VLAGLT PRE AKVLRMRFGI DMNTDHTLEE VGKQFDVTRE RIRQIEAKAL RKLRHPSRSE VLRSFLDE

UniProtKB: RNA polymerase sigma factor RpoD

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / 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

Concentration3.0 mg/mL
BufferpH: 8
Details: 10 mM HEPES pH 8.0, 500 mM NaCl, 1 mM DTT and 0.1 mM EDTA, CHAPSO 4mM
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.11 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199680
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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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

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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

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