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- EMDB-36897: The cryo-EM map of close TIEA-TIC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-36897
TitleThe cryo-EM map of close TIEA-TIC complex
Map dataThe cryo-EM map of close TIEA-TIC complex
Sample
  • Complex: The cryo-EM map of closed TIEA-TIC complex
    • 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: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: 15 kDa RNA polymerase-binding protein
    • DNA: DNA (29-MER)
    • DNA: DNA (29-MER)
    • RNA: RNA (5'-R(*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
Keywordsbacteriophage T4 / RNA polymerase / transcription / inhibitor / elongation accelerator / complex / TRANSCRIPTION/DNA/RNA / TRANSCRIPTION-DNA-RNA complex
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 / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / DNA replication / protein dimerization activity / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Bacteriophage T4, P15K, RNA polymerase binding / Phage RNA polymerase binding, RpbA / 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 ...Bacteriophage T4, P15K, RNA polymerase binding / Phage RNA polymerase binding, RpbA / 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 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
15 kDa RNA polymerase-binding protein / 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 (strain K12) (bacteria) / Escherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsZhang KN / Liu Y / Chen M / Wang Y / Lin W / Li M / Zhang X / Gao Y / Gong Q / Chen H ...Zhang KN / Liu Y / Chen M / Wang Y / Lin W / Li M / Zhang X / Gao Y / Gong Q / Chen H / Steve M / Li S / Zhang K / Liu B
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: TIEA inhibits Sigma70-dependent transcriptions, accelerates elongation speed and elevates transcription error
Authors: Zhang KN / Liu Y / Chen M / Wang Y / Lin W / Li M / Zhang X / Gao Y / Gong Q / Chen H / Steve M / Li S / Zhang K / Liu B
History
DepositionJul 21, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36897.png

Downloads & links

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Map

FileDownload / File: emd_36897.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM map of close TIEA-TIC complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.82156855 - 1.3778464
Average (Standard dev.)0.0008513479 (±0.02849009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 275.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The cryo-EM map of close TIEA-TIC complex

Fileemd_36897_additional_1.map
AnnotationThe cryo-EM map of close TIEA-TIC complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The cryo-EM map of close TIEA-TIC complex

Fileemd_36897_half_map_1.map
AnnotationThe cryo-EM map of close TIEA-TIC complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The cryo-EM map of close TIEA-TIC complex

Fileemd_36897_half_map_2.map
AnnotationThe cryo-EM map of close TIEA-TIC complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The cryo-EM map of closed TIEA-TIC complex

EntireName: The cryo-EM map of closed TIEA-TIC complex
Components
  • Complex: The cryo-EM map of closed TIEA-TIC complex
    • 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: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: 15 kDa RNA polymerase-binding protein
    • DNA: DNA (29-MER)
    • DNA: DNA (29-MER)
    • RNA: RNA (5'-R(*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')

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Supramolecule #1: The cryo-EM map of closed TIEA-TIC complex

SupramoleculeName: The cryo-EM map of closed TIEA-TIC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 150.590547 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: YSYTEKKRIR KDFGKRPQVL DVPYLLSIQL DSFQKFIEQD PEGQYGLEAA FRSVFPIQSY SGNSELQYVS YRLGEPVFDV QECQIRGVT YSAPLRVKLR LVIYEREAPE GTVKDIKEQE VYMGEIPLMT DNGTFVINGT ERVIVSQLHR SPGVFFDSDK G KTHSSGKV ...String:
YSYTEKKRIR KDFGKRPQVL DVPYLLSIQL DSFQKFIEQD PEGQYGLEAA FRSVFPIQSY SGNSELQYVS YRLGEPVFDV QECQIRGVT YSAPLRVKLR LVIYEREAPE GTVKDIKEQE VYMGEIPLMT DNGTFVINGT ERVIVSQLHR SPGVFFDSDK G KTHSSGKV LYNARIIPYR GSWLDFEFDP KDNLFVRIDR RRKLPATIIL RALNYTTEQI LDLFFEKVIF EIRDNKLQME LV PERLRGE TASFDIEANG KVYVEKGRRI TARHIRQLEK DDVKLIEVPV EYIAGKVVAK DYIDESTGEL ICAANMELSL DLL AKLSQS GHKRIETLFT NDLDHGPYIS ETLRVDPTND RLSALVEIYR MMRPGEPPTR EAAESLFENL FFSEDRYDLS AVGR MKFNR SLLREEIEGS GILSKDDIID VMKKLIDIRN GKGEVDDIDH LGNRRIRSVG EMAENQFRVG LVRVERAVKE RLSLG DLDT LMPQDMINAK PISAAVKEFF GSSQLSQFMD QNNPLSEITH KRRISALGPG GLTRERAGFE VRDVHPTHYG RVCPIE TPE GPNIGLINSL SVYAQTNEYG FLETPYRKVT DGVVTDEIHY LSAIEEGNYV IAQANSNLDE EGHFVEDLVT CRSKGES SL FSRDQVDYMD VSTQQVVSVG ASLIPFLEHD DANRALMGAN MQRQAVPTLR ADKPLVGTGM ERAVAVDSGV TAVAKRGG V VQYVDASRIV IKVNEDEMYP GEAGIDIYNL TKYTRSNQNT CINQMPCVSL GEPVERGDVL ADGPSTDLGE LALGQNMRV AFMPWNGYNF EDSILVSERV VQEDRFTTIH IQELACVSRD TKLGPEEITA DIPNVGEAAL SKLDESGIVY IGAEVTGGDI LVGKVTPKG ETQLTPEEKL LRAIFGEKAS DVKDSSLRVP NGVSGTVIDV QVFTRDGVEK DKRALEIEEM QLKQAKKDLS E ELQILEAG LFSRIRAVLV AGGVEAEKLD KLPRDRWLEL GLTDEEKQNQ LEQLAEQYDE LKHEFEKKLE AKRRKITQGD DL APGVLKI VKVYLAVKRR IQPGDKMAGR HGNKGVISKI NPIEDMPYDE NGTPVDIVLN PLGVPSRMNI GQILETHLGM AAK GIGDKI NAMLKQQQEV AKLREFIQRA YDLGADVRQK VDLSTFSDEE VMRLAENLRK GMPIATPVFD GAKEAEIKEL LKLG DLPTS GQIRLYDGRT GEQFERPVTV GYMYMLKLNH LVDDKMHARS TGSYSLVTQQ PLGGKAQFGG QRFGEMEVWA LEAYG AAYT LQEMLTVKSD DVNGRTKMYK NIVDGNHQME PGMPESFNVL LKEIRSLGIN IELEDE

UniProtKB: DNA-directed RNA polymerase subunit beta

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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 / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 150.865766 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: TEEFDAIKIA LASPDMIRSW SFGEVKKPET INYRTFKPER DGLFCARIFG PVKDYECLCG KYKRLKHRGV ICEKCGVEVT QTKVRRERM GHIELASPTA HIWFLKSLPS RIGLLLDMPL RDIERVLYFE SYVVIEGGMT NLERQQILTE EQYLDALEEF G DEFDAKMG ...String:
TEEFDAIKIA LASPDMIRSW SFGEVKKPET INYRTFKPER DGLFCARIFG PVKDYECLCG KYKRLKHRGV ICEKCGVEVT QTKVRRERM GHIELASPTA HIWFLKSLPS RIGLLLDMPL RDIERVLYFE SYVVIEGGMT NLERQQILTE EQYLDALEEF G DEFDAKMG AEAIQALLKS MDLEQECEQL REELNETNSE TKRKKLTKRI KLLEAFVQSG NKPEWMILTV LPVLPPDLRP LV PLDGGRF ATSDLNDLYR RVINRNNRLK RLLDLAAPDI IVRNEKRMLQ EAVDALLDNG RRGRAITGSN KRPLKSLADM IKG KQGRFR QNLLGKRVDY SGRSVITVGP YLRLHQCGLP KKMALELFKP FIYGKLELRG LATTIKAAKK MVEREEAVVW DILD EVIRE HPVLLNRAPT LHRLGIQAFE PVLIEGKAIQ LHPLVCAAYN ADFDGDQMAV HVPLTLEAQL EARALMMSTN NILSP ANGE PIIVPSQDVV LGLYYMTRDC VNAKGEGMVL TGPKEAERLY RSGLASLHAR VKVRITEYEK DANGELVAKT SLKDTT VGR AILWMIVPKG LPYSIVNQAL GKKAISKMLN TCYRILGLKP TVIFADQIMY TGFAYAARSG ASVGIDDMVI PEKKHEI IS EAEAEVAEIQ EQFQSGLVTA GERYNKVIDI WAAANDRVSK AMMDNLQTET VINRDGQEEK QVSFNSIYMM ADSGARGS A AQIRQLAGMR GLMAKPDGSI IETPITANFR EGLNVLQYFI STHGARKGLA DTALKTANSG YLTRRLVDVA QDLVVTEDD CGTHEGIMMT PVIEGGDVKE PLRDRVLGRV TAEDVLKPGT ADILVPRNTL LHEQWCDLLE ENSVDAVKVR SVVSCDTDFG VCAHCYGRD LARGHIINKG EAIGVIAAQS IGEPGTQLTM RTFHIGGAAS RAAAESSIQV KNKGSIKLSN VKSVVNSSGK L VITSRNTE LKLIDEFGRT KESYKVPYGA VLAKGDGEQV AGGETVANWD PHTMPVITEV SGFVRFTDMI DGQTITRQTD EL TGLSSLV VLDSAERTAG GKDLRPALKI VDAQGNDVLI PGTDMPAQYF LPGKAIVQLE DGVQISSGDT LARIPQESGG TKD ITGGLP RVADLFEARR PKEPAILAEI SGIVSFGKET KGKRRLVITP VDGSDPYEEM IPKWRQLNVF EGERVERGDV ISDG PEAPH DILRLRGVHA VTRYIVNEVQ DVYRLQGVKI NDKHIEVIVR QMLRKATIVN AGSSDFLEGE QVEYSRVKIA NRELE ANGK VGATYSRDLL GITKASLATE SFISAASFQE TTRVLTEAAV AGKRDELRGL KENVIVGRLI PAGTGYAYHQ DRMRRR AAG

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #3: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 8.649695 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ARVTVQDAVE KIGNRFDLVL VAARRARQMQ VGGKDPLVPE ENDKTTVIAL REIEEGLINN QILDVRERQE QQEQEA

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #4: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 25.612111 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: TEFLKPRLVD IEQVSSTHAK VTLEPLERGF GHTLGNALRR ILLSSMPGCA VTEVEIDGVL HEYSTKEGVQ EDILEILLNL KGLAVRVQG KDEVILTLNK SGIGPVTAAD ITHDGDVEIV KPQHVICHLT DENASISMRI KVQRGRGYVP ASTRIHSEED E RPIGRLLV ...String:
TEFLKPRLVD IEQVSSTHAK VTLEPLERGF GHTLGNALRR ILLSSMPGCA VTEVEIDGVL HEYSTKEGVQ EDILEILLNL KGLAVRVQG KDEVILTLNK SGIGPVTAAD ITHDGDVEIV KPQHVICHLT DENASISMRI KVQRGRGYVP ASTRIHSEED E RPIGRLLV DACYSPVERI AYNVEAARVE QRTDLDKLVI EMETNGTIDP EEAIRRAATI LAEQLEAFVD LRD

UniProtKB: DNA-directed RNA polymerase subunit alpha

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Macromolecule #5: 15 kDa RNA polymerase-binding protein

MacromoleculeName: 15 kDa RNA polymerase-binding protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 14.731656 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTKITVNYTV DVKDIQPKHV RSESNPQNQN KIRRAWVLSL SDNAMEVIQN KIKSAPARHA YYEAIDREVS NKWIELMRKH TTESLNAGA KFIMTSCGER LEDDYCGNAD ERLIVAAQIV AETIAADFNR

UniProtKB: 15 kDa RNA polymerase-binding protein

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Macromolecule #6: DNA (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 8.915744 KDa
SequenceString:
(DG)(DG)(DG)(DC)(DT)(DA)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DA)(DT)(DG)(DA)(DC)(DG)(DG) (DC)(DG)(DA)(DA)(DT)(DA)(DC)(DC)(DC)

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Macromolecule #7: DNA (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 8.813646 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)(DA)(DG)(DC)(DC)(DC)

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Macromolecule #8: RNA (5'-R(*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')

MacromoleculeName: RNA (5'-R(*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') / type: rna / ID: 8 / Number of copies: 1
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 3.280036 KDa
SequenceString:
CGGAGAGGUA

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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

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number real images: 8645 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3465772
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 414172
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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