[English] 日本語
Yorodumi
- EMDB-21850: F. tularensis RNAPs70-iglA DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21850
TitleF. tularensis RNAPs70-iglA DNA complex
Map dataF. tularensis RNAPs70-iglA sharpened map
Sample
  • Complex: Francisella RNAPs70-iglA complex
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha 1Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha 2Polymerase
    • 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
    • DNA: DNA NT-strand
    • DNA: DNA T-strand
    • RNA: RNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsRNA polymerase complex / TRANSCRIPTION
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / 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 beta / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha 2 / DNA-directed RNA polymerase subunit alpha 1
Similarity search - Component
Biological speciesFrancisella tularensis subsp. holarctica LVS (bacteria) / Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsTravis BA / Brennan RG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Mol Cell / Year: 2021
Title: Structural Basis for Virulence Activation of Francisella tularensis.
Authors: Brady A Travis / Kathryn M Ramsey / Samantha M Prezioso / Thomas Tallo / Jamie M Wandzilak / Allen Hsu / Mario Borgnia / Alberto Bartesaghi / Simon L Dove / Richard G Brennan / Maria A Schumacher /
Abstract: The bacterium Francisella tularensis (Ft) is one of the most infectious agents known. Ft virulence is controlled by a unique combination of transcription regulators: the MglA-SspA heterodimer, PigR, ...The bacterium Francisella tularensis (Ft) is one of the most infectious agents known. Ft virulence is controlled by a unique combination of transcription regulators: the MglA-SspA heterodimer, PigR, and the stress signal, ppGpp. MglA-SspA assembles with the σ-associated RNAP holoenzyme (RNAPσ), forming a virulence-specialized polymerase. These factors activate Francisella pathogenicity island (FPI) gene expression, which is required for virulence, but the mechanism is unknown. Here we report FtRNAPσ-promoter-DNA, FtRNAPσ-(MglA-SspA)-promoter DNA, and FtRNAPσ-(MglA-SspA)-ppGpp-PigR-promoter DNA cryo-EM structures. Structural and genetic analyses show MglA-SspA facilitates σ binding to DNA to regulate virulence and virulence-enhancing genes. Our Escherichia coli RNAPσhomodimeric EcSspA structure suggests this is a general SspA-transcription regulation mechanism. Strikingly, our FtRNAPσ-(MglA-SspA)-ppGpp-PigR-DNA structure reveals ppGpp binding to MglA-SspA tethers PigR to promoters. PigR in turn recruits FtRNAP αCTDs to DNA UP elements. Thus, these studies unveil a unique mechanism for Ft pathogenesis involving a virulence-specialized RNAP that employs two (MglA-SspA)-based strategies to activate virulence genes.
History
DepositionApr 21, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wmp
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21850.png

Downloads & links

-
Map

FileDownload / File: emd_21850.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationF. tularensis RNAPs70-iglA sharpened map
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.1106589 - 0.19803844
Average (Standard dev.)0.000011170372 (±0.0048588035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 376.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z376.640376.640376.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.1110.1980.000

-
Supplemental data

-
Additional map: F. tularensis RNAPs70-iglA unsharpened map

Fileemd_21850_additional_1.map
AnnotationF. tularensis RNAPs70-iglA unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Francisella RNAPs70-iglA complex

EntireName: Francisella RNAPs70-iglA complex
Components
  • Complex: Francisella RNAPs70-iglA complex
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha 1Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha 2Polymerase
    • 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
    • DNA: DNA NT-strand
    • DNA: DNA T-strand
    • RNA: RNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

+
Supramolecule #1: Francisella RNAPs70-iglA complex

SupramoleculeName: Francisella RNAPs70-iglA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)

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

MacromoleculeName: DNA-directed RNA polymerase subunit alpha 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Strain: LVS
Molecular weightTheoretical: 35.393387 KDa
SequenceString: MSNNNSKLEF VPNIQLKEDL GAFSYKVQLS PVEKGMAHIL GNSIRRVLLS SLSGASIIKV NIANVLHEYS TLEDVKEDVV EIVSNLKKV AIKLDTGIDR LDLELSVNKS GVVSAGDFKT TQGVEIINKD QPIATLTNQR AFSLTATVSV GRNVGILSAI P TELERVGD ...String:
MSNNNSKLEF VPNIQLKEDL GAFSYKVQLS PVEKGMAHIL GNSIRRVLLS SLSGASIIKV NIANVLHEYS TLEDVKEDVV EIVSNLKKV AIKLDTGIDR LDLELSVNKS GVVSAGDFKT TQGVEIINKD QPIATLTNQR AFSLTATVSV GRNVGILSAI P TELERVGD IAVDADFNPI KRVAFEVFDN GDSETLEVFV KTNGTIEPLA AVTKALEYFC EQISVFVSLR VPSNGKTGDV LI DSNIDPI LLKPIDDLEL TVRSSNCLRA ENIKYLGDLV QYSESQLMKI PNLGKKSLNE IKQILIDNNL SLGVQIDNFR ELV EGK

UniProtKB: DNA-directed RNA polymerase subunit alpha 1

+
Macromolecule #2: DNA-directed RNA polymerase subunit alpha 2

MacromoleculeName: DNA-directed RNA polymerase subunit alpha 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Strain: LVS
Molecular weightTheoretical: 35.113031 KDa
SequenceString: MALENLLHPT NIKIDEYAKN ATKFSFEALE RGVGYTLGFA LKQTMLYSIA GACVTSIKIN DGKVTSLEDV IPCDETVADI ILNVKSLSV TLAEDVETGT ITFELSGSEE EIFSEEAKLS EGLAITEEVF ICSYNGGKKL KIEAKVEKGV GFRPAQDNFK D GEFLLDAT ...String:
MALENLLHPT NIKIDEYAKN ATKFSFEALE RGVGYTLGFA LKQTMLYSIA GACVTSIKIN DGKVTSLEDV IPCDETVADI ILNVKSLSV TLAEDVETGT ITFELSGSEE EIFSEEAKLS EGLAITEEVF ICSYNGGKKL KIEAKVEKGV GFRPAQDNFK D GEFLLDAT FSPVVFCDFE IKDARVGRRT DLDKLELNIK TNGNVNCEEA LRLAATKIQN QLRNIVDIEE INKGIFVEDP KD INPILLK HVEELNLTAR SSNCLKAVNI RLIGELVQKT ENELLKAPNF GKKSLTEIKD KLSELGLSLG TLIENWPQDL

UniProtKB: DNA-directed RNA polymerase subunit alpha 2

+
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: Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Strain: LVS
Molecular weightTheoretical: 151.536141 KDa
SequenceString: MSYSYAEKKR IRKEFGVLPH ILDVPYLLSI QTESYKKFLT VDAAKGRLHS GLEIVLKQSF PVESKNGQYE LHYVDYQIGE PTFDETECQ VRGATYDAPL NVKLRLVVYN KDALPNEKIV EDIREEYVYM GDIPLMTTNG TFIINGTERV VVSQLHRSPG A FFSKDDSE ...String:
MSYSYAEKKR IRKEFGVLPH ILDVPYLLSI QTESYKKFLT VDAAKGRLHS GLEIVLKQSF PVESKNGQYE LHYVDYQIGE PTFDETECQ VRGATYDAPL NVKLRLVVYN KDALPNEKIV EDIREEYVYM GDIPLMTTNG TFIINGTERV VVSQLHRSPG A FFSKDDSE EGAFSARIIP YRGSWLDFEF DSKGIIWARI DRKRKFCATV ILKALGYTQE QILENFSESK TITFNSKGFA LR LDNLSNM KGELLKFDIV DAQDNVIVKK NKKLTSRDVK KIKDAGVDSV AIDFDLVSTL RVAKDIVNEA TGEVIAYAND DVT ESLLKS CVEVGMLELE VIDFITTERG RYISDTLKYD LTRNTDEALV EIYKVLRPGD PPAAASVKAL FEGLFFIESR YSLS DIGRM KLNARLGSDK VSKDIYTLEN SDIVGVIEEL INIRDGKGKV DDIDHLGNRR VRSVGEMVEN QFRIGLYRVE KGIRE SMSL VHKDKLMPKD IVNSKPITAA IKEFFTSGAL SQFMDQDNPL SEVTHKRRIS ALGPGGLSRD RAGFEVRDVH ATHYGR LCP IETPEGPNIG LINSLASYAR VNDYGFLEAP YRKVVDGKVT DEIEYLSAID EDNYVIAQAS TKLDENNHFV EDIIQCR SG GEAIFTESSR VQYMDVSAKQ MVSAAAALIP FLEHDDANRV LMGANMQRQA VPTLKSEKPL VGTGMEKIVA RDSGNCII A RNVGEVAEVD SNRIVIKVDT EKSQTSNLVD IYSLTKFKRS NKNTCINQRP IVNVGDKVEA GDILADGFAT DFGELSLGH NLMVAFMPWN GYNFEDSILL SERIVKDDKY TSIHIEEFTC VARDTKLGPE EITADIPNVS ESSLAKLDES GIVHIGANVE AGDILVAKI TPKAEQQLTP EERLLRAIFN EKASNVVDSS LRMPSGTSGT VINVQVFEND KGGKSKRALK IEKELIDKAR K DFDEEFAV IESVVKSSIE QEVVGAKIQK AKGLKKGAIL TKEFLATLPL SKWLEISFED EKLEEKVQNA REYYEEAKIA ID AKFEAKK KSITQSNELS PGVLKTVKVF VAIKKRIQPG DKMAGRHGNK GVVSRVLPVE DMPYMEDGTP VDVCLNPLGI PSR MNIGQI LEAHLGLASY GLGKKIEKTL EKTRKAAELR KTLEEVYNSV GDKKVNLEAL NDEEILTLCD NLKGGVPIAT PVFD GAKEE DIKSLLKIGG FATNGQMKLF DGRTGKPFDR HVTVGYMYML KLDHLVDDKM HARSTGSYSL VTQQPLGGKA QFGGQ RFGE MEVWALQAYG AAYTLREMLT VKSDDIAGRS KMYKNIVDGK LTMNVDVPES FNVLRNEVRA LGIDMDFDYS SEEE

UniProtKB: DNA-directed RNA polymerase subunit beta

+
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: Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Strain: LVS
Molecular weightTheoretical: 178.4455 KDa
SequenceString: MNNGILHQNY NSKKFDIIKI SLASPEVIRS WSHGEVKKPE TINYRTFKPE RDGLFCAKIF GPIKDYECLC GKYKRLKHRG VVCERCGVE VEQAKVRRER MGHIDLVCPV VHIWYLKSLP SRIGLFLDMP LKNVEKVLYF ESYIVTDPGM TPLEKKQLLT D EEYAEALE ...String:
MNNGILHQNY NSKKFDIIKI SLASPEVIRS WSHGEVKKPE TINYRTFKPE RDGLFCAKIF GPIKDYECLC GKYKRLKHRG VVCERCGVE VEQAKVRRER MGHIDLVCPV VHIWYLKSLP SRIGLFLDMP LKNVEKVLYF ESYIVTDPGM TPLEKKQLLT D EEYAEALE NYGYEFEASM GAEAIRDLLA DTDIESEIEL LQAECEESKS TAKKEKAIKR LRLLETFQAS GNKPEWMVMT VL PVLPPDL RPLVPIEGGR FATSDLNDLY RRVINRNNRL KKLLDLNAPD IIVRNEKRML QEAVDALLDN GRRGRAVTGS NKR PLKSLA DMIKGKQGRF RQNLLGKRVD YSGRSVITVG PSLRLHECGL PKKMALELFK PFVYSKLRLG GHATTIKQAK RMVE LEEAV VWDILETVIN EHPVLLNRAP TLHRLGIQAF EPRLIEGKAI QLHPLVCAAF NADFDGDQMA VHVPLTVESQ LEARV LMMS TNNILSPASG QPIITPTQDI VLGLYYITRE KEGARGEGKL FSSYEDVSRA YNSGTIDIHA KIKLRIDRQV FDTKGN TYN EKGVVNTTVG RALLLNILPE GLSFSLLNKV LVKKEISKII NQAFRVLGGK ATVVLADKLM YAGFKYSTLS GVSVGVD DM TIPDNKEAKI EEAEKEIKQI TEQYQSSLIT ENERYNNIIN IWSKTSDEVG ASMMDAISKD TVSINGEKKE IESFNSVY M MAKSGARGSY NQMRQLAGMR GLMAKPDGTM IETAITANFR EGLSVLQYFT STHGARKGLA DTALKTANAG YLTRRLVDV AQDLVVIEED CGTDDGLMFS AIVEDGEVKV PLVERALGRT LAADVVTEKG VVLLEAGTLL DENLVELLDD NGIDMIKVRS PITCKTRRG LCAKCYGRDL ARERQVNVGE SVGVIAAQSI GEPGTQLTMR TFHTGGAASL GITVSDIKVK TAGKIKFKNI R TVTNKEGQ EIVISRAGEI IVSDTMGRVR EQHKIPMGAV VPLASGKAVE IGDVIATWDP HAQPLITDVA GKVVLEDVID GI TSKHTYD DLTGQQTIEI TSISQRTTSK NLKPVVKIVD EKGAELKSIP LAVGAVLNVA DDSILEVGDI VAKIPLEGSK NKD ITGGLP RVAELFEARR PKDAAILSPC DGMVRLGNRD TKEKQRIEII DKNGHIVEEI LLPKSRHLVV FDGEQVSRGD VLAD GPTDP HDLLKYKGLE EFADYILIEA QSVYRMQGVV INDKHIETIV RQMLRKAVIL DEGDSKFVKD ESIELVRILE ENDKL RKQG KKEVEYELVL MGITRSSLST ESFLSAASFQ ETTRVLTEAS INSQIDNLRG LKENVLIGRL IPAGTGLAVR KESAKI EKM REELGVEDNM VFTDLSSFNP EEISFDSIQS QKEDKDINED IEESLRNALE SLDFAAASME KRRWKKNFIA VSAANRF KK ISSSGALDYD IPTTASENLY FQGELKTAAL AQHDEAVDNK FNKEQQNAFY EILHLPNLNE EQRNAFIQSL KDDPSQSA N LLAEAKKLND AQAPKVDNKF NKEQQNAFYE ILHLPNLNEE QRNAFIQSLK DDPSQSANLL AEAKKLNGAQ APKVDANSA GKST

+
Macromolecule #5: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Francisella tularensis subsp. holarctica (strain LVS) (bacteria)
Strain: LVS
Molecular weightTheoretical: 8.184333 KDa
SequenceString:
MARVTVEDCL DKVETRFDLV VLASMRANKI LKNGYSESME NEKKEKATVV ALREIAESEI TSEQILRNEI EG

UniProtKB: DNA-directed RNA polymerase subunit omega

+
Macromolecule #6: DNA NT-strand

MacromoleculeName: DNA NT-strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 3.945589 KDa
SequenceString:
(DA)(DC)(DG)(DG)(DC)(DG)(DA)(DA)(DT)(DA) (DC)(DC)(DC)

+
Macromolecule #7: DNA T-strand

MacromoleculeName: DNA T-strand / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 7.303687 KDa
SequenceString:
(DG)(DG)(DG)(DT)(DA)(DT)(DT)(DC)(DG)(DC) (DC)(DG)(DT)(DG)(DT)(DA)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DT)

+
Macromolecule #8: RNA

MacromoleculeName: RNA / type: rna / ID: 8 / Number of copies: 1
Source (natural)Organism: Francisella tularensis subsp. holarctica LVS (bacteria)
Molecular weightTheoretical: 3.30406 KDa
SequenceString:
AGGAGAGGUA

+
Macromolecule #9: MAGNESIUM ION

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

+
Macromolecule #10: ZINC ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
Details: RNAPs70-(MglA-SspA)-iglA map low-pass filtered to 60 angstroms.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 137682
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6wmp:
F. tularensis RNAPs70-iglA DNA complex

+
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