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- EMDB-48802: Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L... -

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Basic information

Entry
Database: EMDB / ID: EMD-48802
TitleMfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state
Map data
Sample
  • Complex: Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state
    • Protein or peptide: Transcription-repair-coupling factor
    • 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
    • RNA: RNA (5'-R(P*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
    • DNA: DNA (49-MER)
    • DNA: DNA (55-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsRNA polymerase / MFD / Transcription-coupled repair / TCR / TRANSCRIPTION
Function / homology
Function and homology information


transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...transcription-coupled nucleotide-excision repair, DNA damage recognition / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex / DNA helicase activity / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / DNA-templated transcription initiation / cell motility / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein-containing complex assembly / damaged DNA binding / intracellular iron ion homeostasis / hydrolase activity / protein dimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
: / MFD, D3 domain / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain / TRCF domain / TRCF / : / UvrB, interaction domain / UvrB interaction domain ...: / MFD, D3 domain / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain / TRCF domain / TRCF / : / UvrB, interaction domain / UvrB interaction domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / 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 / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / Helicase conserved C-terminal domain / RNA polymerase Rpb2, domain 2 superfamily / 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 Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / 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 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transcription-repair-coupling factor / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit omega
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.29 Å
AuthorsBrewer JJ / Darst SA / Campbell EA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state
Authors: Brewer JJ / Darst SA / Campbell EA
History
DepositionJan 24, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48802.png

Downloads & links

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Map

FileDownload / File: emd_48802.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324.9 Å		1.08 Å/pix.
x 300 pix.
= 324.9 Å		1.08 Å/pix.
x 300 pix.
= 324.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168
Minimum - Maximum-0.3419469 - 0.7867045
Average (Standard dev.)0.0046432405 (±0.033651665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_48802_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48802_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48802_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L...

EntireName: Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state
Components
  • Complex: Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state
    • Protein or peptide: Transcription-repair-coupling factor
    • 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
    • RNA: RNA (5'-R(P*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
    • DNA: DNA (49-MER)
    • DNA: DNA (55-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L...

SupramoleculeName: Mfd-bound E.coli RNA polymerase elongation complex + ADP-BeF3 - L1.5 state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Transcription-repair-coupling factor

MacromoleculeName: Transcription-repair-coupling factor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 132.234703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSSGL EVLFQGPHMP EQYRYTLPVK AGEQRLLGEL TGAACATLVA EIAERHAGPV VLIAPDMQNA LRLHDEISQF TDQMVMNLA DWETLPYDSF SPHQDIISSR LSTLYQLPTM QRGVLIVPVN TLMQRVCPHS FLHGHALVMK KGQRLSRDAL R TQLDSAGY ...String:
HHHHHHSSGL EVLFQGPHMP EQYRYTLPVK AGEQRLLGEL TGAACATLVA EIAERHAGPV VLIAPDMQNA LRLHDEISQF TDQMVMNLA DWETLPYDSF SPHQDIISSR LSTLYQLPTM QRGVLIVPVN TLMQRVCPHS FLHGHALVMK KGQRLSRDAL R TQLDSAGY RHVDQVMEHG EYATRGALLD LFPMGSELPY RLDFFDDEID SLRVFDVDSQ RTLEEVEAIN LLPAHEFPTD KA AIELFRS QWRDTFEVKR DPEHIYQQVS KGTLPAGIEY WQPLFFSEPL PPLFSYFPAN TLLVNTGDLE TSAERFQADT LAR FENRGV DPMRPLLPPQ SLWLRVDELF SELKNWPRVQ LKTEHLPTKA ANANLGFQKL PDLAVQAQQK APLDALRKFL ETFD GPVVF SVESEGRREA LGELLARIKI APQRIMRLDE ASDRGRYLMI GAAEHGFVDT VRNLALICES DLLGERVARR RQDSR RTIN PDTLIRNLAE LHIGQPVVHL EHGVGRYAGM TTLEAGGITG EYLMLTYAND AKLYVPVSSL HLISRYAGGA EENAPL HKL GGDAWSRARQ KAAEKVRDVA AELLDIYAQR AAKEGFAFKH DREQYQLFCD SFPFETTPDQ AQAINAVLSD MCQPLAM DR LVCGDVGFGK TEVAMRAAFL AVDNHKQVAV LVPTTLLAQQ HYDNFRDRFA NWPVRIEMIS RFRSAKEQTQ ILAEVAEG K IDILIGTHKL LQSDVKFKDL GLLIVDEEHR FGVRHKERIK AMRANVDILT LTATPIPRTL NMAMSGMRDL SIIATPPAR RLAVKTFVRE YDSMVVREAI LREILRGGQV YYLYNDVENI QKAAERLAEL VPEARIAIGH GQMRERELER VMNDFHHQRF NVLVCTTII ETGIDIPTAN TIIIERADHF GLAQLHQLRG RVGRSHHQAY AWLLTPHPKA MTTDAQKRLE AIASLEDLGA G FALATHDL EIRGAGELLG EEQSGSMETI GFSLYMELLE NAVDALKAGR EPSLEDLTSQ QTEVELRMPS LLPDDFIPDV NT RLSFYKR IASAKTENEL EEIKVELIDR FGLLPDPART LLDIARLRQQ AQKLGIRKLE GNEKGGVIEF AEKNHVNPAW LIG LLQKQP QHYRLDGPTR LKFIQDLSER KTRIEWVRQF MRELEENAIA

UniProtKB: Transcription-repair-coupling factor

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Macromolecule #2: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.897453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SVTEFLKPRL VDIEQVSSTH AKVTLEPLER GFGHTLGNAL RRILLSSMPG CAVTEVEIDG VLHEYSTKEG VQEDILEILL NLKGLAVRV QGKDEVILTL NKSGIGPVTA ADITHDGDVE IVKPQHVICH LTDENASISM RIKVQRGRGY VPASTRIHSE E DERPIGRL ...String:
SVTEFLKPRL VDIEQVSSTH AKVTLEPLER GFGHTLGNAL RRILLSSMPG CAVTEVEIDG VLHEYSTKEG VQEDILEILL NLKGLAVRV QGKDEVILTL NKSGIGPVTA ADITHDGDVE IVKPQHVICH LTDENASISM RIKVQRGRGY VPASTRIHSE E DERPIGRL LVDACYSPVE RIAYNVEAAR VEQRTDLDKL VIEMETNGTI DPEEAIRRAA TILAEQLEAF VDLRDV

UniProtKB: DNA-directed RNA polymerase subunit alpha

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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
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 150.560562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VYSYTEKKRI RKDFGKRPQV LDVPYLLSIQ LDSFQKFIEQ DPEGQYGLEA AFRSVFPIQS YSGNSELQYV SYRLGEPVFD VQECQIRGV TYSAPLRVKL RLVIYEREAP EGTVKDIKEQ EVYMGEIPLM TDNGTFVING TERVIVSQLH RSPGVFFDSD K GKTHSSGK ...String:
VYSYTEKKRI RKDFGKRPQV LDVPYLLSIQ LDSFQKFIEQ DPEGQYGLEA AFRSVFPIQS YSGNSELQYV SYRLGEPVFD VQECQIRGV TYSAPLRVKL RLVIYEREAP EGTVKDIKEQ EVYMGEIPLM TDNGTFVING TERVIVSQLH RSPGVFFDSD K GKTHSSGK VLYNARIIPY RGSWLDFEFD PKDNLFVRID RRRKLPATII LRALNYTTEQ ILDLFFEKVI FEIRDNKLQM EL VPERLRG ETASFDIEAN GKVYVEKGRR ITARHIRQLE KDDVKLIEVP VEYIAGKVVA KDYIDESTGE LICAANMELS LDL LAKLSQ SGHKRIETLF TNDLDHGPYI SETLRVDPTN DRLSALVEIY RMMRPGEPPT REAAESLFEN LFFSEDRYDL SAVG RMKFN RSLLREEIEG SGILSKDDII DVMKKLIDIR NGKGEVDDID HLGNRRIRSV GEMAENQFRV GLVRVERAVK ERLSL GDLD TLMPQDMINA KPISAAVKEF FGSSQLSQFM DQNNPLSEIT HKRRISALGP GGLTRERAGF EVRDVHPTHY GRVCPI ETP EGPNIGLINS LSVYAQTNEY GFLETPYRKV TDGVVTDEIH YLSAIEEGNY VIAQANSNLD EEGHFVEDLV TCRSKGE SS LFSRDQVDYM DVSTQQVVSV GASLIPFLEH DDANRALMGA NMQRQAVPTL RADKPLVGTG MERAVAVDSG VTAVAKRG G VVQYVDASRI VIKVNEDEMY PGEAGIDIYN LTKYTRSNQN TCINQMPCVS LGEPVERGDV LADGPSTDLG ELALGQNMR VAFMPWNGYN FEDSILVSER VVQEDRFTTI HIQELACVSR DTKLGPEEIT ADIPNVGEAA LSKLDESGIV YIGAEVTGGD ILVGKVTPK GETQLTPEEK LLRAIFGEKA SDVKDSSLRV PNGVSGTVID VQVFTRDGVE KDKRALEIEE MQLKQAKKDL S EELQILEA GLFSRIRAVL VAGGVEAEKL DKLPRDRWLE LGLTDEEKQN QLEQLAEQYD ELKHEFEKKL EAKRRKITQG DD LAPGVLK IVKVYLAVKR RIQPGDKMAG RHGNKGVISK INPIEDMPYD ENGTPVDIVL NPLGVPSRMN IGQILETHLG MAA KGIGDK INAMLKQQQE VAKLREFIQR AYDLGADVRQ KVDLSTFSDE EVMRLAENLR KGMPIATPVF DGAKEAEIKE LLKL GDLPT SGQIRLYDGR TGEQFERPVT VGYMYMLKLN HLVDDKMHAR STGSYSLVTQ QPLGGKAQFG GQRFGEMEVW ALEAY GAAY TLQEMLTVKS DDVNGRTKMY KNIVDGNHQM EPGMPESFNV LLKEIRSLGI NIELED

UniProtKB: DNA-directed RNA polymerase subunit beta

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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
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 150.436344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EFDAIKIALA SPDMIRSWSF GEVKKPETIN YRTFKPERDG LFCARIFGPV KDYECLCGKY KRLKHRGVIC EKCGVEVTQT KVRRERMGH IELASPTAHI WFLKSLPSRI GLLLDMPLRD IERVLYFESY VVIEGGMTNL ERQQILTEEQ YLDALEEFGD E FDAKMGAE ...String:
EFDAIKIALA SPDMIRSWSF GEVKKPETIN YRTFKPERDG LFCARIFGPV KDYECLCGKY KRLKHRGVIC EKCGVEVTQT KVRRERMGH IELASPTAHI WFLKSLPSRI GLLLDMPLRD IERVLYFESY VVIEGGMTNL ERQQILTEEQ YLDALEEFGD E FDAKMGAE AIQALLKSMD LEQECEQLRE ELNETNSETK RKKLTKRIKL LEAFVQSGNK PEWMILTVLP VLPPDLRPLV PL DGGRFAT SDLNDLYRRV INRNNRLKRL LDLAAPDIIV RNEKRMLQEA VDALLDNGRR GRAITGSNKR PLKSLADMIK GKQ GRFRQN LLGKRVDYSG RSVITVGPYL RLHQCGLPKK MALELFKPFI YGKLELRGLA TTIKAAKKMV EREEAVVWDI LDEV IREHP VLLNRAPTLH RLGIQAFEPV LIEGKAIQLH PLVCAAYNAD FDGDQMAVHV PLTLEAQLEA RALMMSTNNI LSPAN GEPI IVPSQDVVLG LYYMTRDCVN AKGEGMVLTG PKEAERLYRS GLASLHARVK VRITEYEKDA NGELVAKTSL KDTTVG RAI LWMIVPKGLP YSIVNQALGK KAISKMLNTC YRILGLKPTV IFADQIMYTG FAYAARSGAS VGIDDMVIPE KKHEIIS EA EAEVAEIQEQ FQSGLVTAGE RYNKVIDIWA AANDRVSKAM MDNLQTETVI NRDGQEEKQV SFNSIYMMAD SGARGSAA Q IRQLAGMRGL MAKPDGSIIE TPITANFREG LNVLQYFIST HGARKGLADT ALKTANSGYL TRRLVDVAQD LVVTEDDCG THEGIMMTPV IEGGDVKEPL RDRVLGRVTA EDVLKPGTAD ILVPRNTLLH EQWCDLLEEN SVDAVKVRSV VSCDTDFGVC AHCYGRDLA RGHIINKGEA IGVIAAQSIG EPGTQLTMRT FHIGGAASRA AAESSIQVKN KGSIKLSNVK SVVNSSGKLV I TSRNTELK LIDEFGRTKE SYKVPYGAVL AKGDGEQVAG GETVANWDPH TMPVITEVSG FVRFTDMIDG QTITRQTDEL TG LSSLVVL DSAERTAGGK DLRPALKIVD AQGNDVLIPG TDMPAQYFLP GKAIVQLEDG VQISSGDTLA RIPQESGGTK DIT GGLPRV ADLFEARRPK EPAILAEISG IVSFGKETKG KRRLVITPVD GSDPYEEMIP KWRQLNVFEG ERVERGDVIS DGPE APHDI LRLRGVHAVT RYIVNEVQDV YRLQGVKIND KHIEVIVRQM LRKATIVNAG SSDFLEGEQV EYSRVKIANR ELEAN GKVG ATYSRDLLGI TKASLATESF ISAASFQETT RVLTEAAVAG KRDELRGLKE NVIVGRLIPA GTGYAYHQDR MRRR

UniProtKB: DNA-directed RNA polymerase subunit beta'

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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: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.249547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARVTVQDAV EKIGNRFDLV LVAARRARQM QVGGKDPLVP EENDKTTVIA LREIEEGLIN NQILDVRERQ EQQEQEAAEL QAVTAIAEG RR

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #6: RNA (5'-R(P*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')

MacromoleculeName: RNA (5'-R(P*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.509968 KDa
SequenceString:
GCAUUCAAAG CGGAGAGGUA

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Macromolecule #7: DNA (49-MER)

MacromoleculeName: DNA (49-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 19.748631 KDa
SequenceString: (DC)(DC)(DC)(DA)(DA)(DC)(DG)(DG)(DC)(DA) (DC)(DC)(DG)(DC)(DT)(DG)(DC)(DA)(DA)(DG) (DG)(DA)(DA)(DT)(DA)(DG)(DG)(DA)(DT) (DA)(DC)(DT)(DT)(DG)(DC)(DG)(DG)(DG)(DC) (DT) (DA)(DG)(DG)(DC)(DT)(DC) ...String:
(DC)(DC)(DC)(DA)(DA)(DC)(DG)(DG)(DC)(DA) (DC)(DC)(DG)(DC)(DT)(DG)(DC)(DA)(DA)(DG) (DG)(DA)(DA)(DT)(DA)(DG)(DG)(DA)(DT) (DA)(DC)(DT)(DT)(DG)(DC)(DG)(DG)(DG)(DC) (DT) (DA)(DG)(DG)(DC)(DT)(DC)(DT)(DT) (DA)(DT)(DG)(DG)(DC)(DG)(DG)(DC)(DG)(DA) (DA)(DT) (DA)(DC)(DC)(DC)

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Macromolecule #8: DNA (55-MER)

MacromoleculeName: DNA (55-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 19.630492 KDa
SequenceString: (DG)(DG)(DG)(DT)(DA)(DT)(DT)(DC)(DG)(DC) (DC)(DG)(DC)(DG)(DT)(DA)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DT)(DA)(DG)(DC)(DC)(DC) (DG)(DC)(DA)(DA)(DG)(DT)(DA)(DT)(DC)(DC) (DT) (DA)(DT)(DT)(DC)(DC)(DT) ...String:
(DG)(DG)(DG)(DT)(DA)(DT)(DT)(DC)(DG)(DC) (DC)(DG)(DC)(DG)(DT)(DA)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DT)(DA)(DG)(DC)(DC)(DC) (DG)(DC)(DA)(DA)(DG)(DT)(DA)(DT)(DC)(DC) (DT) (DA)(DT)(DT)(DC)(DC)(DT)(DT)(DG) (DC)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG)(DT) (DT)(DG)(DG)(DG)

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Macromolecule #9: MAGNESIUM ION

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

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
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: PDB ENTRY
PDB model - PDB ID:

6alh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13808
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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  • 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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