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- EMDB-44438: Cryo-EM structure of Thermococcus kodakarensis FttA-dependent tra... -

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Basic information

Entry
Database: EMDB / ID: EMD-44438
TitleCryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA
Map datacomposite map
Sample
  • Complex: FttA-dependent transcription termination complex
    • Protein or peptide: x 14 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 2 types
KeywordsRNA polymerase / pre-termination complex / FttA / archaea / TRANSCRIPTION
Function / homology
Function and homology information


exonuclease activity / transcription elongation-coupled chromatin remodeling / translation elongation factor activity / DNA-directed RNA polymerase complex / RNA endonuclease activity / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity ...exonuclease activity / transcription elongation-coupled chromatin remodeling / translation elongation factor activity / DNA-directed RNA polymerase complex / RNA endonuclease activity / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / Hydrolases; Acting on ester bonds / protein dimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Transcription termination factor CPSF1, archaea / KH domain, archaeal / KH domain / Archaeal transcription elongation factor Spt4 / Transcription elongation factor Spt5, archaeal / Archaeal transcription elongation factor Spt4 superfamily / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 ...Transcription termination factor CPSF1, archaea / KH domain, archaeal / KH domain / Archaeal transcription elongation factor Spt4 / Transcription elongation factor Spt5, archaeal / Archaeal transcription elongation factor Spt4 superfamily / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo7 / Metallo-beta-lactamase superfamily domain / : / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / DNA-directed RNA polymerase, subunit E/RPC8 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / S1 domain profile. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / 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 / 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 / K Homology domain / K homology RNA-binding domain / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo11 / Transcription termination factor FttA / Transcription elongation factor Spt5 / DNA-directed RNA polymerase subunit Rpo7 / Transcription elongation factor Spt4 / DNA-directed RNA polymerase subunit Rpo10
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsYou L / Ebright RH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nature / Year: 2024
Title: Structural basis of archaeal FttA-dependent transcription termination.
Authors: Linlin You / Chengyuan Wang / Vadim Molodtsov / Konstantin Kuznedelov / Xinyi Miao / Breanna R Wenck / Paul Ulisse / Travis J Sanders / Craig J Marshall / Emre Firlar / Jason T Kaelber / ...Authors: Linlin You / Chengyuan Wang / Vadim Molodtsov / Konstantin Kuznedelov / Xinyi Miao / Breanna R Wenck / Paul Ulisse / Travis J Sanders / Craig J Marshall / Emre Firlar / Jason T Kaelber / Thomas J Santangelo / Richard H Ebright /
Abstract: The ribonuclease FttA (also known as aCPSF and aCPSF1) mediates factor-dependent transcription termination in archaea. Here we report the structure of a Thermococcus kodakarensis transcription pre- ...The ribonuclease FttA (also known as aCPSF and aCPSF1) mediates factor-dependent transcription termination in archaea. Here we report the structure of a Thermococcus kodakarensis transcription pre-termination complex comprising FttA, Spt4, Spt5 and a transcription elongation complex (TEC). The structure shows that FttA interacts with the TEC in a manner that enables RNA to proceed directly from the TEC RNA-exit channel to the FttA catalytic centre and that enables endonucleolytic cleavage of RNA by FttA, followed by 5'→3' exonucleolytic cleavage of RNA by FttA and concomitant 5'→3' translocation of FttA on RNA, to apply mechanical force to the TEC and trigger termination. The structure further reveals that Spt5 bridges FttA and the TEC, explaining how Spt5 stimulates FttA-dependent termination. The results reveal functional analogy between bacterial and archaeal factor-dependent termination, functional homology between archaeal and eukaryotic factor-dependent termination, and fundamental mechanistic similarities in factor-dependent termination in bacteria, archaea, and eukaryotes.
History
DepositionApr 9, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44438.png

Downloads & links

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Map

FileDownload / File: emd_44438.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.088
Minimum - Maximum-0.13506201 - 0.65739036
Average (Standard dev.)0.0039956286 (±0.020103984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : FttA-dependent transcription termination complex

EntireName: FttA-dependent transcription termination complex
Components
  • Complex: FttA-dependent transcription termination complex
    • Protein or peptide: DNA-directed RNA polymerase subunit A'
    • Protein or peptide: DNA-directed RNA polymerase subunit B
    • Protein or peptide: DNA-directed RNA polymerase subunit A"
    • Protein or peptide: DNA-directed RNA polymerase subunit D
    • Protein or peptide: DNA-directed RNA polymerase subunit E
    • Protein or peptide: DNA-directed RNA polymerase subunit F
    • Protein or peptide: DNA-directed RNA polymerase subunit H
    • Protein or peptide: DNA-directed RNA polymerase subunit K
    • Protein or peptide: DNA-directed RNA polymerase subunit L
    • Protein or peptide: DNA-directed RNA polymerase subunit N
    • Protein or peptide: DNA-directed RNA polymerase subunit P
    • Protein or peptide: Transcription elongation factor Spt5
    • Protein or peptide: Transcription elongation factor Spt4
    • Protein or peptide: Transcription termination factor FttA
    • DNA: non-template strand DNA
    • DNA: template strand DNA
    • RNA: RNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: FttA-dependent transcription termination complex

SupramoleculeName: FttA-dependent transcription termination complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 556 KDa

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Macromolecule #1: DNA-directed RNA polymerase subunit A'

MacromoleculeName: DNA-directed RNA polymerase subunit A' / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 103.038633 KDa
SequenceString: MQSMKKVIGS IEFGILSPQE IRKMSAAEIT VPDTYDDDGY PIEGGLMDKR LGVIDPGLRC ETCGARAGEC PGHFGHIELA RPVIHVGFA KTIHRVLEST CRECGRIKLT DEEIEEYMQK FEVMGDRKGA VDKLIKEIHK KAKERMVCPH CGAPQFPIKF E RPTIYWEL ...String:
MQSMKKVIGS IEFGILSPQE IRKMSAAEIT VPDTYDDDGY PIEGGLMDKR LGVIDPGLRC ETCGARAGEC PGHFGHIELA RPVIHVGFA KTIHRVLEST CRECGRIKLT DEEIEEYMQK FEVMGDRKGA VDKLIKEIHK KAKERMVCPH CGAPQFPIKF E RPTIYWEL RKDEEGNEYK HRMMPSEVRD RLEKIPDKDL PLLGLHPEKS RPEWMVLTVL PVPPVTMRPS ITLESGIRAE DD LTHKLVD IIRINNRLKS NIEAGAPQLI IEDLWDLLQY HVTTYINNET SGVPPAKHKS GRPLKTLAQR LKGKEGRFRG NLS GKRVNF SARTVISPDP MISINEVGVP LAVAMELTVP EKVTEFNYEK LKQRVLNGPE KYPGANYVID PEGRRIRLME SNRE LIAEK LDIGWTVERH LEDGDVVLFN RQPSLHRMSI MAHRVRVMPY RTFRLNLPVC PPYNADFDGD EMNLHVPQTE EAQAE AKIL MEVQNHIISP RYGGPLIAGI QDHISGGYLL TREGAYFTRY EVEQMLMFAG MDVNELPEPD KYENGEPLWS GKTIFS LLL PDDLTIWYRN KLCDEPERCE ALEKLIEEKL IPDPEEVRKL AYDGFVYIQN GKLLSGAVDK KAYGREDGKL LDIIVRE YG VERARQFLDQ VTKLTIWVIT HKGFTTAIDD EDLPQEAIDR IHEIIREAEE KVQRLIEAYK RGELEPLPGK TLEETLES K IMAVLAEARD NAGKVAERYL GMNNHAVIMA KTGARGKILN ITQMAAMLGQ QSIRGKRLYR GYRGRVLTHF KPGDLGARA RGFVTNSYKS GLTPQEYFFH AMGGREGLVD TAVRTAQSGY MQRRLINALQ DLKVDYDGTV RDPTGIIVQF KYGEDGVDPM KSWQGKTVD VDRVIVRTLL KMRGGGE

UniProtKB: DNA-directed RNA polymerase subunit Rpo1N

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Macromolecule #2: DNA-directed RNA polymerase subunit B

MacromoleculeName: DNA-directed RNA polymerase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 127.468039 KDa
SequenceString: MSRGVTVTEP TLTPDELWLV MESYWKEKGF VRQHLDSYNA FIDHGLQDVV NEFGEVVPDI PNFKVKFGKI RIGQPEFQEA QGQRRPLYP MDARIRNLTY SAPLYLEMIP VVNGIEQEPV EVRIGELPIM LKSKACRLYG LSDEELIKLG EDPKDPGGYF I INGSERVI ...String:
MSRGVTVTEP TLTPDELWLV MESYWKEKGF VRQHLDSYNA FIDHGLQDVV NEFGEVVPDI PNFKVKFGKI RIGQPEFQEA QGQRRPLYP MDARIRNLTY SAPLYLEMIP VVNGIEQEPV EVRIGELPIM LKSKACRLYG LSDEELIKLG EDPKDPGGYF I INGSERVI VSIEDLAPNK TLVERDERQN KVVAKVFSYR HGYRALITVE RKKDGILYVT IPNVPKPVKF VYVMRALGLL TD KEIVEAV SDDPRIQQVL FDNLEDASDI STQEEALDYI GRLALPGQPK EYRLRRAEHI IDNNLLPHMG VDPENRRAKA YYL GMMALK VLELSLGLRG EDDKDHYANK RLKLAGDLLK DLFRVAFGQL VKDMQYQMTK TYQRKGERYT FENIQRFVRN SIRP DVLSE RIEHALATGS WPGGRTGVSQ LLDRTNYMST LSHLRRVTSP LSRDQPHFEA RDLHGTHWGR ICPTETPEGP NCGLV KNLA LMSQITTGIP EREVREYLMK MGVVPIEERR PAPGLYRVYL NGVLIGTVED GRKLVERIRA DRRAGKISDV INVALY EDE EVKEVYINSD DGRVRRPLIV VENGKPKLTR EHVEGIKNGT LTWSDLIRMG VIEYLDAEEE ENAYVATWPW EVTEEHT HL ELMPAAILGI PASLVPYPEH NAAPRNTYGA GMAKQSLGLG WANFRIRVDT RGHLMHYPQV PLVNSRIMKA VGFEDRPA G QNFVVAVLSY HGYNMEDAVI INKASIERGL ARSTFFRTYE AEEKRYLGGQ KDNFEVPSPN IQGYLGEKYY RHLDEDGLI FPESKVEGKD VLVGRTSPPR FIEEQSSLGS MVLQGRRETS VTVRPSEKGV VDKVIVTETG DGTKLVKVTV RDLRIPELGD KFASRHGQK GVIGLIVPQE DMPWTESGIV PDLIVNPHGI PSRMTVGQLI EAIGGKVASL TGRRVDGTAF IGEPEEKLRK E LEELGFKH SGREIMYDGI TGRRLEADIF IGVIYYQRLH HMVADKMHAR SRGPVQVLTK QPTEGRAREG GLRFGEMERD VL IGHGAAM LLIERLLEES DKTEVWVCES CGHLALEDKR RGKVYCPVCG EDERISKVEM SYAFKLLLDE LKAMVIRPSL RLK DRV

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase subunit A"

MacromoleculeName: DNA-directed RNA polymerase subunit A" / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 43.72741 KDa
SequenceString: MVAEKTIKSM VSKAELPDNI KEELYAKLIE YNEKYKLKKD EIQAIIDETV REYQKALIEP GEAVGTVAAQ SIGEPSTQMT LNTFHYAGV AEINVTLGLP RIIEIVDARK NPSTPIMTVY LDEEHRYDRD KALEVARRIE GTTLENLARE ETIDILNMEY V VEIDPERL ...String:
MVAEKTIKSM VSKAELPDNI KEELYAKLIE YNEKYKLKKD EIQAIIDETV REYQKALIEP GEAVGTVAAQ SIGEPSTQMT LNTFHYAGV AEINVTLGLP RIIEIVDARK NPSTPIMTVY LDEEHRYDRD KALEVARRIE GTTLENLARE ETIDILNMEY V VEIDPERL EKAGLDMEKV VRKLTGSFKS AEFEAEGYTL VVRPKKVTKL SDLRKIAEKV KKHRLKGLSG VGKTIIRKEG DE YVIYTEG SNFKQVLKVP GVDPTRTRTN NIWEIAEVLG IEAARNAIID EIVSTMREQG LEVDVRHIML VADMMTLDGV IRP IGRHGI VGEKASVLAR AAFEITTQHL FAAAERGEVD PLNGVVENVL IGQPVPVGTG IVKLAMSLPL RPKRE

UniProtKB: DNA-directed RNA polymerase subunit Rpo1C

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Macromolecule #4: DNA-directed RNA polymerase subunit D

MacromoleculeName: DNA-directed RNA polymerase subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 29.657955 KDa
SequenceString: MPMVEFKILE KRPDSIKFIV SGVDVPFANA LRRTILSEVP TFAVDEVEFL ENDSALFDEI IAHRLAMIPL TTPHERFSLD ALELDDYTV TLSLEAEGPG MVYSGDLKSS DGDVKPANPN IPIVKLAEGQ RLTFNAYARL GRGKDHAKWQ PGFVYYKYLT K IHVSKDVP ...String:
MPMVEFKILE KRPDSIKFIV SGVDVPFANA LRRTILSEVP TFAVDEVEFL ENDSALFDEI IAHRLAMIPL TTPHERFSLD ALELDDYTV TLSLEAEGPG MVYSGDLKSS DGDVKPANPN IPIVKLAEGQ RLTFNAYARL GRGKDHAKWQ PGFVYYKYLT K IHVSKDVP DWEELKELAE RRGLPVEESD EEIVITTIKA FYLPRKFEEH MGKGIREEIV PGSFVFTVET NGELPVEEIV SI ALKILMR KSDRFINELH KLAD

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Macromolecule #5: DNA-directed RNA polymerase subunit E

MacromoleculeName: DNA-directed RNA polymerase subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea) / Strain: TS559
Molecular weightTheoretical: 21.893438 KDa
SequenceString:
MYKLLKVKDV VRIPPRMFTM DPKEAAKIVL RETYEGIYDR DEGVVLAILD VEEISEGVIV PGDGATYHEA IFNVLVWEPR NQEVVEGEV VEMMPYGAFI RIGPMDGLVH ISQLMDDYVV FDEKNRQFIG KETNRVLKLG DYVRARIIGV SVKSRVIREN K INMTMRQP GLGKFEWIEK EKKKAKEESK GE

UniProtKB: DNA-directed RNA polymerase subunit Rpo7

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Macromolecule #6: DNA-directed RNA polymerase subunit F

MacromoleculeName: DNA-directed RNA polymerase subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 14.519659 KDa
SequenceString:
MIGRKKLEEH YITIAEAKEL LERRHAEGLA ENPEEPMFYE ARVSLEHAER FAKLKPEQAR ELKEKLMGLF DWINERIAAK LVDILPEDY LDIRVIFAKE EYMPTPEEAE EIIKVIDEYR PLE

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Macromolecule #7: DNA-directed RNA polymerase subunit H

MacromoleculeName: DNA-directed RNA polymerase subunit H / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 9.522031 KDa
SequenceString:
MAAKKEFNIF DHVLVPEHRI LSEEEKEELL KKYRIRISQL PQIKASDPAV VALGAKPGDV IEIKRKSPTA GYYYYYRLVV ED

UniProtKB: DNA-directed RNA polymerase subunit Rpo5

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Macromolecule #8: DNA-directed RNA polymerase subunit K

MacromoleculeName: DNA-directed RNA polymerase subunit K / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 6.583911 KDa
SequenceString:
MVVVFRYTRF EKARIIGARA LQIAMGAPVL IDVPEGITPL QAALLEFEKG VIPITVIRPS

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Macromolecule #9: DNA-directed RNA polymerase subunit L

MacromoleculeName: DNA-directed RNA polymerase subunit L / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 11.013504 KDa
SequenceString:
MRIEVIRREE NLLEFYLEGE DHTFANLLTE TLHENEHVTF AGYTIEHPIT MARKPRFKVV TDGKITPEKA LEEAAQKIFD RAREVLEAW KAAIE

UniProtKB: DNA-directed RNA polymerase subunit Rpo11

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Macromolecule #10: DNA-directed RNA polymerase subunit N

MacromoleculeName: DNA-directed RNA polymerase subunit N / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 7.601975 KDa
SequenceString:
MIVPVRCFTC GKVLADKYYE FKKRVEAGED PGKVLDDLGV ERYCCRRTLL SHVELIDQVM VYKVY

UniProtKB: DNA-directed RNA polymerase subunit Rpo10

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Macromolecule #11: DNA-directed RNA polymerase subunit P

MacromoleculeName: DNA-directed RNA polymerase subunit P / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 5.553708 KDa
SequenceString:
MATAVYRCAK CGKEVELDLA TAREVRCPYC GSKILYKPRP RVARRVKAI

UniProtKB: DNA-directed RNA polymerase subunit Rpo12

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Macromolecule #12: Transcription elongation factor Spt5

MacromoleculeName: Transcription elongation factor Spt5 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 16.776396 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAEGKIFTVS VTVGQETTTA NLIYSKAKTY NLPLYAILSP SKVKGYIFIE APNKSAVEEA IRGIRHAKRV LPGEIPFSEI EHFLEEKPA VSGFEPGDIV ELIAGPFKGE KAKVVRVDES KDEIVVELVS SVVPIPVTVR GEYVRLISKR QKE

UniProtKB: Transcription elongation factor Spt5

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Macromolecule #13: Transcription elongation factor Spt4

MacromoleculeName: Transcription elongation factor Spt4 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 8.56187 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HHHHHHMAKE RACRHCHYIT TEDRCPVCGS RDLSDDWFDL VIVLDVESRI AKKLRESIPE AAKVPGKYAI RVR

UniProtKB: Transcription elongation factor Spt4

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Macromolecule #14: Transcription termination factor FttA

MacromoleculeName: Transcription termination factor FttA / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 73.473719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIRRETFVDD ILKEIREIIV QMVPREAGIT DVEFEGPELV IYVKNPEAMM KDGELIKNLA KVLKKRISVR PDPDILLPPE KAEELIKQL VPPEAEITNI SFDPSVGEVL IEARKPGLVI GKNGETLRLI TQKVHWAPRV VRTPPIQSQT IYSIRSILQT E SKDRRKFL ...String:
MIRRETFVDD ILKEIREIIV QMVPREAGIT DVEFEGPELV IYVKNPEAMM KDGELIKNLA KVLKKRISVR PDPDILLPPE KAEELIKQL VPPEAEITNI SFDPSVGEVL IEARKPGLVI GKNGETLRLI TQKVHWAPRV VRTPPIQSQT IYSIRSILQT E SKDRRKFL RQVGRNIYRK SEYKSRWIRI TGLGGFREVG RSALLVQTDE SYVLVDFGVN IAALKDPTKA YPHFDAPEFR YV LDEGLLD AIIITHAALD HSGMLPYLFR YKLFDGPIYT TPPTRDLMTL LQQDFIEIQH MNGVEPLYRP KDIKEVIKHT ITL DYGEVR DIAPDIRLTL HNAGHILGSS IVHLHIGNGL HNIAITGDFK FIPTRLFEPA VSRFPRLETL VMESTYGGSN DYQM PREEA EKRLIEVIHQ TLKRGGKVLI PAMAVGRAQE IMMVLEEYAR VGGIEVPIYL DGMIWEATAI HTAYPEYLSK HIREQ IFHE GYNPFLNPIF KSVANSRERQ DIIDSGEPAI IIATSGMLVG GPSVEYFKQL APDPKNSIIF VSYQAEGTLG RQVQRG LRE IPIVGEDGRT EVINVNMEVH TIDGFSGAAD RRELMSYVAR VRPRPERIIT VHGEAHKCLD LSSSIHKKFG ISTRAPN NL DAIRLK

UniProtKB: Transcription termination factor FttA

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Macromolecule #15: non-template strand DNA

MacromoleculeName: non-template strand DNA / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.096158 KDa
SequenceString:
(DG)(DA)(DG)(DT)(DC)(DA)(DT)(DG)(DA)(DT) (DC)(DA)(DT)(DA)(DT)(DT)(DA)(DT)(DT)(DT) (DT)(DT)(DT)(DA)(DG)(DT)(DC)(DC)(DA) (DG)(DA)(DC)(DA)(DG)(DT)(DG)

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Macromolecule #16: template strand DNA

MacromoleculeName: template strand DNA / type: dna / ID: 16 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.060087 KDa
SequenceString:
(DC)(DA)(DC)(DT)(DG)(DT)(DC)(DT)(DG)(DG) (DA)(DC)(DT)(DG)(DG)(DT)(DC)(DG)(DG)(DC) (DG)(DC)(DT)(DA)(DT)(DG)(DA)(DT)(DC) (DA)(DT)(DG)(DA)(DC)(DT)(DC)

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Macromolecule #17: RNA

MacromoleculeName: RNA / type: rna / ID: 17 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.649801 KDa
SequenceString:
UUCUUUUAUC UUAUUUUUUU UCUAUUUUUU CAUUUGCGCC GACC

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Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #19: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 19 / Number of copies: 8 / 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

Concentration4.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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 / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 171269
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9bct:
Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA

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