[English] 日本語
Yorodumi
- EMDB-49175: Cryo-EM structure of the Fta RNAP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49175
TitleCryo-EM structure of the Fta RNAP complex
Map data
Sample
  • Complex: RNAP 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 beta'
    • Protein or peptide: RNA polymerase Rpb6
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsFta RNAP / RNA polymerase / RNA BINDING PROTEIN
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / 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
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 ...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 Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 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, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / RNA polymerase Rpb6 / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesFlagellimonas taeanensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsChang L / Sternberg SH / Xiao R / Hoffmann FT / Wiegand T / Xie D
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138675 United States
National Science Foundation (NSF, United States)2339799 United States
National Science Foundation (NSF, United States)2239685 United States
The Pew Charitable Trusts United States
CitationJournal: To Be Published
Title: Structural basis of RNA-guided transcription via Cas12f-Sigma factor association
Authors: Renjian X / Leifu C
History
DepositionFeb 11, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49175.png

Downloads & links

-
Map

FileDownload / File: emd_49175.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 315.648 Å		0.82 Å/pix.
x 384 pix.
= 315.648 Å		0.82 Å/pix.
x 384 pix.
= 315.648 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: 0.03
Minimum - Maximum-0.0017003887 - 2.1332304
Average (Standard dev.)0.0014467017 (±0.027256772)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 315.648 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_49175_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49175_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RNAP complex

EntireName: RNAP complex
Components
  • Complex: RNAP 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 beta'
    • Protein or peptide: RNA polymerase Rpb6
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

-
Supramolecule #1: RNAP complex

SupramoleculeName: RNAP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Flagellimonas taeanensis (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: Flagellimonas taeanensis (bacteria)
Molecular weightTheoretical: 37.228574 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MALLNFQKPD KVIMIDSTDF EGKFEFRPLE PGYGLTVGNA LRRVLLSSLE GFAITSVRID GVEHEFSVVP GVVEDVTEII LNLKQVRFK RQIDDVESET VSISVSGKEQ LTAGDFQKFI SGYQVLNPDL VICNMGPKVS INMEIVIEKG RGYVPAEENK K SNAPLGSI ...String:
MALLNFQKPD KVIMIDSTDF EGKFEFRPLE PGYGLTVGNA LRRVLLSSLE GFAITSVRID GVEHEFSVVP GVVEDVTEII LNLKQVRFK RQIDDVESET VSISVSGKEQ LTAGDFQKFI SGYQVLNPDL VICNMGPKVS INMEIVIEKG RGYVPAEENK K SNAPLGSI AVDSVYTPVK NVKYSIENYR VEQKTDYEKL VFEIITDGSI HPKDALTEAA KVLIHHFMLF SDERITLEAD EI AQTETYD EESLHMRQLL KTKLVDMDLS VRALNCLKAA EVDTLGDLVS FNKNDLMKFR NFGKKSLTEL EELVINKGLQ FGM DLSKYK LDKD

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: Flagellimonas taeanensis (bacteria)
Molecular weightTheoretical: 142.961375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFTNTIERVN FASAKNIPEY PDFLDIQIKS FQDFFQLETK SDERGNEGLY NTFMENFPIT DTRNQFVLEF LDYFIDPPRY SIQECIERG LTYSVPLKAR LKLYCTDPEH EDFETIVQDV YLGTIPYMTP SGTFVINGAE RVVVSQLHRS PGVFFGQSFH A NGTKLYSA ...String:
MFTNTIERVN FASAKNIPEY PDFLDIQIKS FQDFFQLETK SDERGNEGLY NTFMENFPIT DTRNQFVLEF LDYFIDPPRY SIQECIERG LTYSVPLKAR LKLYCTDPEH EDFETIVQDV YLGTIPYMTP SGTFVINGAE RVVVSQLHRS PGVFFGQSFH A NGTKLYSA RVIPFKGSWI EFATDINGVM YAYIDRKKKL PVTTLFRAIG FERDKDILEI FDLSEEVKVS KAGLKKVLGR KL AARVLNT WHEDFVDEDT GEVVSIERNE IILDRDTILE KEHIDEIIDA DVKTILLHKE NNAQSDYAII HNTLQKDPTN SEK EAVEHI YRQLRNAEPP DEETARGIIE KLFFSDQRYS LGEVGRYRMN KKLGLDIGMD KEVLTKEDII TIIKYLIELI NSKA EIDDI DHLSNRRVRT VGEQLSQQFG VGLARMARTI RERMNVRDNE VFTPIDLINA KTLSSVINSF FGTNQLSQFM DQTNP LAEI THKRRLSALG PGGLSRERAG FEVRDVHYTH YGRLCPIETP EGPNIGLISS LSVFAKVNSM GFLETPYRKV VDGKVD VKE HIYLSAEEEE GMKIAQANIP LKDDGTIDRE KVIARDEGDF PVVDPVEINY TDVAPNQIAS ISASLIPFLE HDDANRA LM GSNMMRQAVP LLRPESPIVG TGLERQVATD SRVLINAEGD GVVEYVDAQK ITIKYDRTEE ERLVSFEEDS KTYELVKF R KTNQGTSINL KPIVRKGDKV KKGQVLCEGY ATEKGELALG RNMKVAFMPW KGYNFEDAIV ISEKVVREDI FTSVHIDEY ALEVRDTKLG AEELTNDIPN VSEEATRDLD EYGMIRIGAE VKPGDILIGK ITPKGESDPT PEEKLLRAIF GDKAGDVKDA SLKASPSLR GVVIDKKLFS RSIKDKRKRS EDKEAISRLE MDYEVKFQQL KDVLIEKLFG LVNGKTSQGV INDLGEEVLP K GKKYTIKM LNAVDDFAHL VGGSWTTDED TNALVADLLH NYKIKLNDIQ GNLRRDKFTI SVGDELPAGI MKLAKVYIAK KR KLKVGDK MAGRHGNKGI VARIVRQEDM PFLEDGTPVD IVLNPLGVPS RMNIGQIYET VLGWAGLKLG QKYGTPIFDG ATL DDINEL TDKAGVPRFG HTYLYDGGTG QRFDQAATVG VIYMLKLGHM VDDKMHARSI GPYSLITQQP LGGKAQFGGQ RFGE MEVWA LEAYGASATL REILTVKSDD VIGRAKTYES IVKGETMPEP GLPESFNVLM HELKGLGLDI RLEE

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: Flagellimonas taeanensis (bacteria)
Molecular weightTheoretical: 160.063375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MARIKDNNAP KRFNKISIGL ASPESILAES RGEVLKPETI NYRTHKPERD GLFCERIFGP VKDYECACGK YKRIRYRGIV CDRCGVEVT EKKVRRDRVG HINLVVPVAH IWYFRSLPNK IGYLLGLPSK KLDMIIYYER YVVIQPGIAK GPEGEEIHKL D FLTEEEYL ...String:
MARIKDNNAP KRFNKISIGL ASPESILAES RGEVLKPETI NYRTHKPERD GLFCERIFGP VKDYECACGK YKRIRYRGIV CDRCGVEVT EKKVRRDRVG HINLVVPVAH IWYFRSLPNK IGYLLGLPSK KLDMIIYYER YVVIQPGIAK GPEGEEIHKL D FLTEEEYL NILESLPSEN QYLEENDPNK FIAKMGAECL IDLLARIDLE QLSYELRHKA NTETSKQRKT EALKRLQVVE AL RESQDNR ENNPEWMIMK VIPVIPPELR PLVPLDGGRF ATSDLNDLYR RVIIRNNRLK RLMEIKAPEV ILRNEKRMLQ EAV DSLFDN TRKASAVKTE SNRPLKSLSD SLKGKQGRFR QNLLGKRVDY SARSVIVVGP EMKLYECGLP KDMAAELYKP FIIR KLIER GIVKTVKSAK KIIDKKEPVV WDILENVLKG HPVLLNRAPT LHRLGIQAFQ PKLIEGKAIR LHPLACTAFN ADFDG DQMA VHLPLGPEAI LEAQLLMLAS QNILNPANGS PITVPSQDMV LGLYYMTKEK RSTPEEPVIG EGLTFYSSEE VEIAFN ERK VALNAIIKVR TKDFNEAGEL VNKIIETTVG RVLFNTVVPE QAGYINTVLN KKSLRNIIGD ILAVTDVPTT ADFLDKI KT MGYEFAFKGG LSFSLGDIII PKEKHEMIAE ANEQVDGIMM NYNMGLITFN ERYNQVIDVW TSTNAMLTEL AMKRIRED K QGFNSVYMML DSGARGSKEQ IRQLTGMRGL MAKPKKSTAG GGEIIENPIL SNFKEGLSIL EYFISTHGAR KGLADTALK TADAGYLTRR LVDVSQDVII NTEDCGTLRG IEVEALKKNE EVVETLGERI LGRVSLHDVY NPLTEELILK AGQEISEADV KKVEAAPIE KVEVRSPLTC EAAQGICAKC YGRNLATNKM VQRGEAVGVV AAQSIGEPGT QLTLRTFHVG GIAGNISEDS K LEAKFDGI AEIEDLRVVE GVDNGGGKSD IVISRTSEIK IVDAKTGITL STNNIPYGSQ LFVKNGEKIT KGTVICQWDP YN GVIVSEF TGQIAYENIE QGMTYQVEID EQTGFQEKVI SESRNKRLIP TLLIKDGKGE TIRSYNLPVG SHLMVDNGEK IKE GKILVK IPRKSAKAGD ITGGLPRVTE LFEARNPSNP AVVTEIDGVV SFGKIKRGNR EIIIESKAGE VKKYLVKLSN QILV QENDY VRAGMALSDG SITPEDILAI KGPSAVQQYL VNEVQEVYRL QGVKINDKHF EVVVRQMMRK VQIQDSGDTT FLENQ LVHK DDFINENDEI FGKKVVEDAG DSERLKPGQI VTARQLRDEN SILRREDKTL VTARDAVAAT ATPILQGITR ASLQTK SFI SAASFQETTK VLNEAAVNGK VDTLEGLKEN VIVGHKIPAG TGMRDYDSII VGSKEEYDEI MARKEEFKF

UniProtKB: DNA-directed RNA polymerase subunit beta'

-
Macromolecule #4: RNA polymerase Rpb6

MacromoleculeName: RNA polymerase Rpb6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flagellimonas taeanensis (bacteria)
Molecular weightTheoretical: 12.565037 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MQDLKNTKAP VSTATLNRNE FDSKTGNIYE AISIASKRAV QINSDIKKEL LEKLEEFATY SDSLEEVFEN KEQIEVSKFY EKLPKPHAL AVQEWLEDKI YYRNTEKDA

UniProtKB: RNA polymerase Rpb6

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171804
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