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- EMDB-50715: Ap4A bound in de novo transcription initiation T. thermophilus RN... -

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Basic information

Entry
Database: EMDB / ID: EMD-50715
TitleAp4A bound in de novo transcription initiation T. thermophilus RNA polymerase complex with aTT DNA template
Map data
Sample
  • Complex: heteropentamer 2:1:1:1 in complex with DNA duplex and nucleoside phosphates
    • Complex: RNA polymerase
      • Protein or peptide: x 4 types
    • Complex: RNA polymerase sigma factor SigA
      • Protein or peptide: x 1 types
    • Complex: DNA duplex
      • DNA: x 2 types
  • Ligand: x 4 types
KeywordsTRANSCRIPTION-DNA complex / non-canonical cap / 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
: / DNA-directed RNA polymerase subunit beta', hybrid domain / 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. ...: / DNA-directed RNA polymerase subunit beta', hybrid domain / 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 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, 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
DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsSkerlova J / Dubankova A / Svachova H / Kouba T
Funding support Czech Republic, 2 items
OrganizationGrant numberCountry
Other governmentCZ.02.01.01/00/22_008/0004575 Czech Republic
Other government101041374
CitationJournal: Nat Chem Biol / Year: 2026
Title: Molecular insight into 5' RNA capping with NpNs by bacterial RNA polymerase.
Authors: Valentina M Serianni / Jana Škerlová / Anna Knopp Dubánková / Anton Škríba / Hana Šváchová / Tereza Vučková / Anatolij Filimoněnko / Milan Fábry / Pavlína Řezáčová / Tomáš Kouba / Hana Cahova
Abstract: RNA capped with dinucleoside polyphosphates has been discovered in bacteria and eukaryotes only recently. The likely mechanism of this specific capping involves direct incorporation of dinucleoside ...RNA capped with dinucleoside polyphosphates has been discovered in bacteria and eukaryotes only recently. The likely mechanism of this specific capping involves direct incorporation of dinucleoside polyphosphates by RNA polymerase as noncanonical initiating nucleotides. However, how these compounds bind into the active site of RNA polymerase during transcription initiation is unknown. Here, we explored transcription initiation in vitro, using a series of DNA templates in combination with dinucleoside polyphosphates and model RNA polymerase from Thermus thermophilus. We observed that the transcription start site can vary on the basis of the compatibility of the specific template and dinucleoside polyphosphate. Cryo-electron microscopy structures of transcription initiation complexes with dinucleoside polyphosphates revealed that both nucleobase moieties can pair with the DNA template. The first encoded nucleotide pairs in a canonical Watson-Crick manner, whereas the second nucleobase pairs noncanonically in a reverse Watson-Crick manner. Our work provides a structural explanation of how dinucleoside polyphosphates initiate RNA transcription.
History
DepositionJun 18, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50715.png

Downloads & links

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Map

FileDownload / File: emd_50715.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 520 pix.
= 433.472 Å		0.83 Å/pix.
x 520 pix.
= 433.472 Å		0.83 Å/pix.
x 520 pix.
= 433.472 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.19379956 - 0.7976786
Average (Standard dev.)0.00096865644 (±0.014182214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 433.472 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50715_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_50715_additional_1.map
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Half map: #2

Fileemd_50715_half_map_1.map
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Half map: #1

Fileemd_50715_half_map_2.map
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Sample components

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Entire : heteropentamer 2:1:1:1 in complex with DNA duplex and nucleoside ...

EntireName: heteropentamer 2:1:1:1 in complex with DNA duplex and nucleoside phosphates
Components
  • Complex: heteropentamer 2:1:1:1 in complex with DNA duplex and nucleoside phosphates
    • Complex: 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
    • Complex: RNA polymerase sigma factor SigA
      • Protein or peptide: RNA polymerase sigma factor SigA
    • Complex: DNA duplex
      • DNA: DNA (52-MER)
      • DNA: DNA (52-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
  • Ligand: BIS(ADENOSINE)-5'-TETRAPHOSPHATE

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Supramolecule #1: heteropentamer 2:1:1:1 in complex with DNA duplex and nucleoside ...

SupramoleculeName: heteropentamer 2:1:1:1 in complex with DNA duplex and nucleoside phosphates
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Supramolecule #2: RNA polymerase

SupramoleculeName: RNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)

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Supramolecule #3: RNA polymerase sigma factor SigA

SupramoleculeName: RNA polymerase sigma factor SigA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)

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Supramolecule #4: DNA duplex

SupramoleculeName: DNA duplex / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: synthetic construct (others)

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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: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 35.056164 KDa
SequenceString: MLDSKLKAPV FTVRTQGREY GEFVLEPLER GFGVTLGNPL RRILLSSIPG TAVTSVYIED VLHEFSTIPG VKEDVVEIIL NLKELVVRF LNPSLQTVTL LLKAEGPKEV KARDFLPVAD VEIMNPDLHI ATLEEGGRLN MEVRVDRGVG YVPAEKHGIK D RINAIPVD ...String:
MLDSKLKAPV FTVRTQGREY GEFVLEPLER GFGVTLGNPL RRILLSSIPG TAVTSVYIED VLHEFSTIPG VKEDVVEIIL NLKELVVRF LNPSLQTVTL LLKAEGPKEV KARDFLPVAD VEIMNPDLHI ATLEEGGRLN MEVRVDRGVG YVPAEKHGIK D RINAIPVD AVFSPVRRVA FQVEDTRLGQ RTDLDKLTLR IWTDGSVTPL EALNQAVEIL REHLTYFSNP QAAAVAAPEE AK EPEAPPE QEEELDLPLE ELGLSTRVLH SLKEEGIESV RALLALNLKD LKNIPGIGER SLEEIKEALE KKGFTLKE

UniProtKB: DNA-directed RNA polymerase subunit alpha

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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: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 125.436539 KDa
SequenceString: MEIKRFGRIR EVIPLPPLTE IQVESYRRAL QADVPPEKRE NVGIQAAFRE TFPIEEEDKG KGGLVLDFLE YRLGEPPFPQ DECREKDLT YQAPLYARLQ LIHKDTGLIK EDEVFLGHIP LMTEDGSFII NGADRVIVSQ IHRSPGVYFT PDPARPGRYI A SIIPLPKR ...String:
MEIKRFGRIR EVIPLPPLTE IQVESYRRAL QADVPPEKRE NVGIQAAFRE TFPIEEEDKG KGGLVLDFLE YRLGEPPFPQ DECREKDLT YQAPLYARLQ LIHKDTGLIK EDEVFLGHIP LMTEDGSFII NGADRVIVSQ IHRSPGVYFT PDPARPGRYI A SIIPLPKR GPWIDLEVEP NGVVSMKVNK RKFPLVLLLR VLGYDQETLA RELGAYGELV QGLMDESVFA MRPEEALIRL FT LLRPGDP PKRDKAVAYV YGLIADPRRY DLGEAGRYKA EEKLGIRLSG RTLARFEDGE FKDEVFLPTL RYLFALTAGV PGH EVDDID HLGNRRIRTV GELMTDQFRV GLARLARGVR ERMLMGSEDS LTPAKLVNSR PLEAAIREFF SRSQLSQFKD ETNP LSSLR HKRRISALGP GGLTRERAGF DVRDVHRTHY GRICPVETPE GANIGLITSL AAYARVDELG FIRTPYRRVV GGVVT DEVV YMTATEEDRY TIAQANTPLE GNRIAAERVV ARRKGEPVIV SPEEVEFMDV SPKQVFSVNT NLIPFLEHDD ANRALM GSN MQTQAVPLIR AQAPVVMTGL EERVVRDSLA ALYAEEDGEV AKVDGNRIVV RYEDGRLVEY PLRRFYRSNQ GTALDQR PR VVVGQRVRKG DLLADGPASE NGFLALGQNV LVAIMPFDGY NFEDAIVISE ELLKRDFYTS IHIERYEIEA RDTKLGPE R ITRDIPHLSE AALRDLDEEG VVRIGAEVKP GDILVGRTSF KGESEPTPEE RLLRSIFGEK ARDVKDTSLR VPPGEGGIV VRTVRLRRGD PGVELKPGVR EVVRVYVAQK RKLQVGDKLA NRHGNKGVVA KILPVEDMPH LPDGTPVDVI LNPLGVPSRM NLGQILETH LGLAGYFLGQ RYISPIFDGA KEPEIKELLA QAFEVYFGKR KGEGFGVDKR EVEVLRRAEK LGLVTPGKTP E EQLKELFL QGKVVLYDGR TGEPIEGPIV VGQMFIMKLY HMVEDKMHAR STGPYSLITQ QPLGGKAQFG GQRFGEMEVW AL EAYGAAH TLQEMLTLKS DDIEGRNAAY EAIIKGEDVP EPSVPESFRV LVKELQALAL DVQTLDEKDN PVDIFEGLAS KR

UniProtKB: DNA-directed RNA polymerase subunit beta

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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 / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 170.997391 KDa
SequenceString: MKKEVRKVRI ALASPEKIRS WSYGEVEKPE TINYRTLKPE RDGLFDERIF GPIKDYECAC GKYKRQRFEG KVCERCGVEV TKSIVRRYR MGHIELATPA AHIWFVKDVP SKIGTLLDLS ATELEQVLYF SKYIVLDPKG AILNGVPVEK RQLLTDEEYR E LRYGKQET ...String:
MKKEVRKVRI ALASPEKIRS WSYGEVEKPE TINYRTLKPE RDGLFDERIF GPIKDYECAC GKYKRQRFEG KVCERCGVEV TKSIVRRYR MGHIELATPA AHIWFVKDVP SKIGTLLDLS ATELEQVLYF SKYIVLDPKG AILNGVPVEK RQLLTDEEYR E LRYGKQET YPLPPGVDAL VKDGEEVVKG QELAPGVVSR LDGVALYRFP RRVRVEYVKK ERAGLRLPLA AWVEKEAYKP GE ILAELPE PYLFRAEEEG VVELKELEEG AFLVLRREDE PVATYFLPVG MTPLVVHGEI VEKGQPLAEA KGLLRMPRQV RAA QVEAEE EGETVYLTLF LEWTEPKDYR VQPHMNVVVP EGARVEAGDK IVAAIDPEEE VIAEAEGVVH LHEPASILVV KARV YPFED DVEVSTGDRV APGDVLADGG KVKSDVYGRV EVDLVRNVVR VVESYDIDAR MGAEAIQQLL KELDLEALEK ELLEE MKHP SRARRAKARK RLEVVRAFLD SGNRPEWMIL EAVPVLPPDL RPMVQVDGGR FATSDLNDLY RRLINRNNRL KKLLAQ GAP EIIIRNEKRM LQEAVDALLD NGRRGAPVTN PGSDRPLRSL TDILSGKQGR FRQNLLGKRV DYSGRSVIVV GPQLKLH QC GLPKRMALEL FKPFLLKKME EKGIAPNVKA ARRMLERQRD IKDEVWDALE EVIHGKVVLL NRAPTLHRLG IQAFQPVL V EGQSIQLHPL VCEAFNADFD GDQMAVHVPL SSFAQAEARI QMLSAHNLLS PASGEPLAKP SRDIILGLYY ITQVRKEKK GAGLEFATPE EALAAHERGE VALNAPIKVA GRETSVGRLK YVFANPDEAL LAVAHGIVDL QDVVTVRYMG KRLETSPGRI LFARIVAEA VEDEKVAWEL IQLDVPQEKN SLKDLVYQAF LRLGMEKTAR LLDALKYYGF TFSTTSGITI GIDDAVIPEE K KQYLEEAD RKLLQIEQAY EMGFLTDRER YDQILQLWTE TTEKVTQAVF KNFEENYPFN PLYVMAQSGA RGNPQQIRQL CG LRGLMQK PSGETFEVPV RSSFREGLTV LEYFISSHGA RKGGADTALR TADSGYLTRK LVDVTHEIVV READCGTTNY ISV PLFQPD EVTRSLRLRK RADIEAGLYG RVLAREVEVL GVRLEEGRYL SMDDVHLLIK AAEAGEIQEV PVRSPLTCQT RYGV CQKCY GYDLSMARPV SIGEAVGIVA AQSIGEPGTQ LTMRTFHTGG VAGAADITQG LPRVIELFEA RRPKAKAVIS EIDGV VRIE ETEEKLSVFV ESEGFSKEYK LPKEARLLVK DGDYVEAGQP LTRGAIDPHQ LLEAKGPEAV ERYLVEEIQK VYRAQG VKL HDKHIEIVVR QMMKYVEVTD PGDSRLLEGQ VLEKWDVEAL NERLIAEGKT PVAWKPLLMG VTKSALSTKS WLSAASF QN TTHVLTEAAI AGKKDELIGL KENVILGRLI PAGTGSDFVR FTQVVDQKTL KAIEEARKEA VEAKERPAAR RGVKREQP G KQA

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #4: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 11.533316 KDa
SequenceString:
MAEPGIDKLF GMVDSKYRLT VVVAKRAQQL LRHGFKNTVL EPEERPKMQT LEGLFDDPNA VTWAMKELLT GRLVFGENLV PEDRLQKEM ERLYPVEREE

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #5: RNA polymerase sigma factor SigA

MacromoleculeName: RNA polymerase sigma factor SigA / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 51.470086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHSSG VDLGTENLYF QSNAASMKKS KRKNAQAQEA QETEVLVQEE AEELPEFPEG EPDPDLEDPD LALEDDLLDL PEEGEGLDL EEEEEDLPIP KISTSDPVRQ YLHEIGQVPL LTLEEEVELA RKVEEGMEAI KKLSEITGLD PDLIREVVRA K ILGSARVR ...String:
MHHHHHHSSG VDLGTENLYF QSNAASMKKS KRKNAQAQEA QETEVLVQEE AEELPEFPEG EPDPDLEDPD LALEDDLLDL PEEGEGLDL EEEEEDLPIP KISTSDPVRQ YLHEIGQVPL LTLEEEVELA RKVEEGMEAI KKLSEITGLD PDLIREVVRA K ILGSARVR HIPGLKETLD PKTVEEIDQK LKSLPKEHKR YLHIAREGEA ARQHLIEANL RLVVSIAKKY TGRGLSFLDL IQ EGNQGLI RAVEKFEYKR RFKFSTYATW WIRQAINRAI ADQARTIRIP VHMVETINKL SRTARQLQQE LGREPTYEEI AEA MGPGWD AKRVEETLKI AQEPVSLETP IGDEKDSFYG DFIPDEHLPS PVDAATQSLL SEELEKALSK LSEREAMVLK LRKG LIDGR EHTLEEVGAF FGVTRERIRQ IENKALRKLK YHESRTRKLR DFLD

UniProtKB: RNA polymerase sigma factor SigA

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Macromolecule #6: DNA (52-MER)

MacromoleculeName: DNA (52-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 16.06134 KDa
SequenceString: (DC)(DC)(DT)(DG)(DC)(DA)(DT)(DC)(DC)(DG) (DA)(DG)(DA)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DA)(DA)(DT)(DA)(DA)(DC)(DC)(DC) (DA)(DA)(DC)(DC)(DA)(DT)(DA)(DT)(DG)(DG) (DA) (DT)(DT)(DA)(DT)(DG)(DT) ...String:
(DC)(DC)(DT)(DG)(DC)(DA)(DT)(DC)(DC)(DG) (DA)(DG)(DA)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DA)(DA)(DT)(DA)(DA)(DC)(DC)(DC) (DA)(DA)(DC)(DC)(DA)(DT)(DA)(DT)(DG)(DG) (DA) (DT)(DT)(DA)(DT)(DG)(DT)(DC)(DA) (DA)(DG)(DA)(DG)

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Macromolecule #7: DNA (52-MER)

MacromoleculeName: DNA (52-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 16.13634 KDa
SequenceString: (DC)(DT)(DC)(DT)(DT)(DG)(DA)(DC)(DA)(DT) (DA)(DA)(DT)(DC)(DC)(DA)(DT)(DA)(DT)(DG) (DG)(DT)(DT)(DG)(DG)(DG)(DT)(DA)(DT) (DA)(DA)(DT)(DG)(DG)(DG)(DA)(DT)(DT)(DG) (DT) (DC)(DT)(DC)(DG)(DG)(DA) ...String:
(DC)(DT)(DC)(DT)(DT)(DG)(DA)(DC)(DA)(DT) (DA)(DA)(DT)(DC)(DC)(DA)(DT)(DA)(DT)(DG) (DG)(DT)(DT)(DG)(DG)(DG)(DT)(DA)(DT) (DA)(DA)(DT)(DG)(DG)(DG)(DA)(DT)(DT)(DG) (DT) (DC)(DT)(DC)(DG)(DG)(DA)(DT)(DG) (DC)(DA)(DG)(DG)

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 5 / 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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Macromolecule #10: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}pho...

MacromoleculeName: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine
type: ligand / ID: 10 / Number of copies: 2 / Formula: 2TM
Molecular weightTheoretical: 481.184 Da
Chemical component information

ChemComp-2TM:
5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine

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Macromolecule #11: BIS(ADENOSINE)-5'-TETRAPHOSPHATE

MacromoleculeName: BIS(ADENOSINE)-5'-TETRAPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: B4P
Molecular weightTheoretical: 836.387 Da
Chemical component information

ChemComp-B4P:
BIS(ADENOSINE)-5'-TETRAPHOSPHATE

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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: 7.9
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 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:

4q4z

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76802
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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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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