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- EMDB-19022: Structure of Sen1-ADP.BeF3 bound RNA Polymerase II pre-terminatio... -

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Basic information

Entry
Database: EMDB / ID: EMD-19022
TitleStructure of Sen1-ADP.BeF3 bound RNA Polymerase II pre-termination complex
Map data
Sample
  • Complex: Tertiary complex of RNA Polymerase II with elongation factors Elf1, Spt4, Spt5 and the termination factor Sen1
    • Complex: DNA-directed RNA polymerase II
      • Protein or peptide: x 12 types
    • Complex: Transcription elongation factors
      • Protein or peptide: x 4 types
    • Complex: RNA
      • DNA: x 2 types
    • Complex: DNA
      • RNA: x 1 types
  • Ligand: x 4 types
KeywordsRNA Polymerase II / Pol II / termination / Sen1 / GENE REGULATION
Function / homology
Function and homology information


negative regulation of transcription elongation by RNA polymerase I / transcription termination site sequence-specific DNA binding / negative regulation of flocculation / 5'-3' DNA/RNA helicase activity / Nrd1 complex / mating-type region heterochromatin / positive regulation of transcription elongation by RNA polymerase I / sno(s)RNA 3'-end processing / regulation of transcription-coupled nucleotide-excision repair / DNA-templated DNA replication maintenance of fidelity ...negative regulation of transcription elongation by RNA polymerase I / transcription termination site sequence-specific DNA binding / negative regulation of flocculation / 5'-3' DNA/RNA helicase activity / Nrd1 complex / mating-type region heterochromatin / positive regulation of transcription elongation by RNA polymerase I / sno(s)RNA 3'-end processing / regulation of transcription-coupled nucleotide-excision repair / DNA-templated DNA replication maintenance of fidelity / regulation of rRNA processing / snRNA processing / RNA polymerase I core binding / DSIF complex / intracellular mRNA localization / rDNA heterochromatin / rDNA binding / RNA polymerase I general transcription initiation factor binding / RPB4-RPB7 complex / snRNP binding / U4 snRNA binding / mRNA 3'-end processing / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase III Transcription Initiation From Type 2 Promoter / tRNA processing / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / spliceosomal complex assembly / RNA polymerase II complex binding / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / nuclear-transcribed mRNA catabolic process / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / 7-methylguanosine mRNA capping / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / U5 snRNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / translesion synthesis / U2 snRNA binding / RNA polymerase II, core complex / U6 snRNA binding / positive regulation of autophagy / U1 snRNA binding / translation initiation factor binding / cell redox homeostasis / negative regulation of autophagy / transcription initiation-coupled chromatin remodeling / transcription elongation factor complex / maturation of SSU-rRNA / replication fork / DNA-templated transcription initiation / small-subunit processome / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / DNA-templated transcription termination / transcription elongation by RNA polymerase II / P-body / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / heterochromatin formation / ribonucleoside binding / kinetochore / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / rRNA processing / peroxisome / ribosome biogenesis / chromatin organization / single-stranded DNA binding
Similarity search - Function
Helicase Sen1, 1B domain / Helicase Sen1, N-terminal / SEN1 N terminal / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger ...Helicase Sen1, 1B domain / Helicase Sen1, N-terminal / SEN1 N terminal / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / DNA2/NAM7 helicase, helicase domain / AAA domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / : / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / DNA2/NAM7-like helicase / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / 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 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / 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 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / 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, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / 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. / Zinc finger, TFIIS-type / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB9 ...DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription elongation factor SPT4 / DNA-directed RNA polymerase II subunit RPB7 / Transcription elongation factor 1 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Helicase SEN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Human immunodeficiency virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsRengachari S / Lidscreiber M / Cramer P
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Mechanism of polyadenylation-independent RNA polymerase II termination.
Authors: Srinivasan Rengachari / Thomas Hainthaler / Christiane Oberthuer / Michael Lidschreiber / Patrick Cramer /
Abstract: The mechanisms underlying the initiation and elongation of RNA polymerase II (Pol II) transcription are well-studied, whereas termination remains poorly understood. Here we analyze the mechanism of ...The mechanisms underlying the initiation and elongation of RNA polymerase II (Pol II) transcription are well-studied, whereas termination remains poorly understood. Here we analyze the mechanism of polyadenylation-independent Pol II termination mediated by the yeast Sen1 helicase. Cryo-electron microscopy structures of two pretermination intermediates show that Sen1 binds to Pol II and uses its adenosine triphosphatase activity to pull on exiting RNA in the 5' direction. This is predicted to push Pol II forward, induce an unstable hypertranslocated state and destabilize the transcription bubble, thereby facilitating termination. This mechanism of transcription termination may be widely used because it is conceptually conserved in the bacterial transcription system.
History
DepositionDec 1, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19022.png

Downloads & links

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Map

FileDownload / File: emd_19022.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 378. Å		1.05 Å/pix.
x 360 pix.
= 378. Å		1.05 Å/pix.
x 360 pix.
= 378. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
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Contour LevelBy AUTHOR: 0.0065
Minimum - Maximum-0.041529328 - 0.08746848
Average (Standard dev.)-0.00012362734 (±0.0030015977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 377.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19022_msk_1.map
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Half map: #2

Fileemd_19022_half_map_1.map
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Half map: #1

Fileemd_19022_half_map_2.map
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Sample components

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Entire : Tertiary complex of RNA Polymerase II with elongation factors Elf...

EntireName: Tertiary complex of RNA Polymerase II with elongation factors Elf1, Spt4, Spt5 and the termination factor Sen1
Components
  • Complex: Tertiary complex of RNA Polymerase II with elongation factors Elf1, Spt4, Spt5 and the termination factor Sen1
    • Complex: DNA-directed RNA polymerase II
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB2
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB4
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC1
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB7
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB11
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4
    • Complex: Transcription elongation factors
      • Protein or peptide: Transcription elongation factor 1
      • Protein or peptide: Helicase SEN1
      • Protein or peptide: Transcription elongation factor SPT4
      • Protein or peptide: Transcription elongation factor SPT5
    • Complex: RNA
      • DNA: Non-template strand
      • DNA: Template strand
    • Complex: DNA
      • RNA: RNA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: Tertiary complex of RNA Polymerase II with elongation factors Elf...

SupramoleculeName: Tertiary complex of RNA Polymerase II with elongation factors Elf1, Spt4, Spt5 and the termination factor Sen1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19

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Supramolecule #2: DNA-directed RNA polymerase II

SupramoleculeName: DNA-directed RNA polymerase II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#12
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: Transcription elongation factors

SupramoleculeName: Transcription elongation factors / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13, #15, #18-#19
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #4: RNA

SupramoleculeName: RNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #14, #17
Source (natural)Organism: Human immunodeficiency virus 2

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Supramolecule #5: DNA

SupramoleculeName: DNA / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #16
Source (natural)Organism: Human immunodeficiency virus 2

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Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 191.821578 KDa
SequenceString: MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKP VFHVGFIAKI KKVCECVCMH CGKLLLDEHN ELMRQALAIK DSKKRFAAIW TLCKTKMVCE TDVPSEDDPT Q LVSRGGCG ...String:
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKP VFHVGFIAKI KKVCECVCMH CGKLLLDEHN ELMRQALAIK DSKKRFAAIW TLCKTKMVCE TDVPSEDDPT Q LVSRGGCG NTQPTIRKDG LKLVGSWKKD RATGDADEPE LRVLSTEEIL NIFKHISVKD FTSLGFNEVF SRPEWMILTC LP VPPPPVR PSISFNESQR GEDDLTFKLA DILKANISLE TLEHNGAPHH AIEEAESLLQ FHVATYMDND IAGQPQALQK SGR PVKSIR ARLKGKEGRI RGNLMGKRVD FSARTVISGD PNLELDQVGV PKSIAKTLTY PEVVTPYNID RLTQLVRNGP NEHP GAKYV IRDSGDRIDL RYSKRAGDIQ LQYGWKVERH IMDNDPVLFN RQPSLHKMSM MAHRVKVIPY STFRLNLSVT SPYNA DFDG DEMNLHVPQS EETRAELSQL CAVPLQIVSP QSNKPCMGIV QDTLCGIRKL TLRDTFIELD QVLNMLYWVP DWDGVI PTP AIIKPKPLWS GKQILSVAIP NGIHLQRFDE GTTLLSPKDN GMLIIDGQII FGVVEKKTVG SSNGGLIHVV TREKGPQ VC AKLFGNIQKV VNFWLLHNGF STGIGDTIAD GPTMREITET IAEAKKKVLD VTKEAQANLL TAKHGMTLRE SFEDNVVR F LNEARDKAGR LAEVNLKDLN NVKQMVMAGS KGSFINIAQM SACVGQQSVE GKRIAFGFVD RTLPHFSKDD YSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGS DAAFEKRYRV DLLNTDHTLD PSLLESGSEI LGDLKLQVLL DEEYKQLVKD RKFLREVFVD GEANWPLPVN I RRIIQNAQ QTFHIDHTKP SDLTIKDIVL GVKDLQENLL VLRGKNEIIQ NAQRDAVTLF CCLLRSRLAT RRVLQEYRLT KQ AFDWVLS NIEAQFLRSV VHPGEMVGVL AAQSIGEPAT QMTLNTFHFA GVASKKVTSG VPRLKEILNV AKNMKTPSLT VYL EPGHAA DQEQAKLIRS AIEHTTLKSV TIASEIYYDP DPRSTVIPED EEIIQLHFSL LDEEAEQSFD QQSPWLLRLE LDRA AMNDK DLTMGQVGER IKQTFKNDLF VIWSEDNDEK LIIRCRVVRP KSLDAETEAE EDHMLKKIEN TMLENITLRG VENIE RVVM MKYDRKVPSP TGEYVKEPEW VLETDGVNLS EVMTVPGIDP TRIYTNSFID IMEVLGIEAG RAALYKEVYN VIASDG SYV NYRHMALLVD VMTTQGGLTS VTRHGFNRSN TGALMRCSFE ETVEILFEAG ASAELDDCRG VSENVILGQM APIGTGA FD VMIDEESLVK YMPEQKITEI EDGQDGGVTP YSNESGLVNA DLDVKDELMF SPLVDSGSND AMAGGFTAYG GADYGEAT S PFGAYGEAPT SPGFGVSSPG FSPTSPTYSP TSPAYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP SYSPTSPSY SPTSPNYSPT SPSYSPTSPG YSPGSPAYSP KQDEQKHNEN ENSR

UniProtKB: DNA-directed RNA polymerase II subunit RPB1

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Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 138.937297 KDa
SequenceString: MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYE ISFGKIYVTK PMVNESDGVT HALYPQEARL RNLTYSSGLF VDVKKRTYEA IDVPGRELKY ELIAEESEDD S ESGKVFIG ...String:
MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYE ISFGKIYVTK PMVNESDGVT HALYPQEARL RNLTYSSGLF VDVKKRTYEA IDVPGRELKY ELIAEESEDD S ESGKVFIG RLPIMLRSKN CYLSEATESD LYKLKECPFD MGGYFIINGS EKVLIAQERS AGNIVQVFKK AAPSPISHVA EI RSALEKG SRFISTLQVK LYGREGSSAR TIKATLPYIK QDIPIVIIFR ALGIIPDGEI LEHICYDVND WQMLEMLKPC VED GFVIQD RETALDFIGR RGTALGIKKE KRIQYAKDIL QKEFLPHITQ LEGFESRKAF FLGYMINRLL LCALDRKDQD DRDH FGKKR LDLAGPLLAQ LFKTLFKKLT KDIFRYMQRT VEEAHDFNMK LAINAKTITS GLKYALATGN WGEQKKAMSS RAGVS QVLN RYTYSSTLSH LRRTNTPIGR DGKLAKPRQL HNTHWGLVCP AETPEGQACG LVKNLSLMSC ISVGTDPMPI ITFLSE WGM EPLEDYVPHQ SPDATRVFVN GVWHGVHRNP ARLMETLRTL RRKGDINPEV SMIRDIREKE LKIFTDAGRV YRPLFIV ED DESLGHKELK VRKGHIAKLM ATEYQDIEGG FEDVEEYTWS SLLNEGLVEY IDAEEEESIL IAMQPEDLEP AEANEEND L DVDPAKRIRV SHHATTFTHC EIHPSMILGV AASIIPFPDH NQSPRNTYQS AMGKQAMGVF LTNYNVRMDT MANILYYPQ KPLGTTRAME YLKFRELPAG QNAIVAIACY SGYNQEDSMI MNQSSIDRGL FRSLFFRSYM DQEKKYGMSI TETFEKPQRT NTLRMKHGT YDKLDDDGLI APGVRVSGED VIIGKTTPIS PDEEELGQRT AYHSKRDAST PLRSTENGIV DQVLVTTNQD G LKFVKVRV RTTKIPQIGD KFASRHGQKG TIGITYRRED MPFTAEGIVP DLIINPHAIP SRMTVAHLIE CLLSKVAALS GN EGDASPF TDITVEGISK LLREHGYQSR GFEVMYNGHT GKKLMAQIFF GPTYYQRLRH MVDDKIHARA RGPMQVLTRQ PVE GRSRDG GLRFGEMERD CMIAHGAASF LKERLMEASD AFRVHICGIC GLMTVIAKLN HNQFECKGCD NKIDIYQIHI PYAA KLLFQ ELMAMNITPR LYTDRSRDF

UniProtKB: DNA-directed RNA polymerase II subunit RPB2

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Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 35.330457 KDa
SequenceString: MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCE DHCDKCSVVL TLQAFGESES TTNVYSKDLV IVSNLMGRNI GHPIIQDKEG NGVLICKLRK GQELKLTCVA K KGIAKEHA ...String:
MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCE DHCDKCSVVL TLQAFGESES TTNVYSKDLV IVSNLMGRNI GHPIIQDKEG NGVLICKLRK GQELKLTCVA K KGIAKEHA KWGPAAAIEF EYDPWNKLKH TDYWYEQDSA KEWPQSKNCE YEDPPNEGDP FDYKAQADTF YMNVESVGSI PV DQVVVRG IDTLQKKVAS ILLALTQMDQ DKVNFASGDN NTASNMLGSN EDVMMTGAEQ DPYSNASQMG NTGSGGYDNA W

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

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Macromolecule #4: DNA-directed RNA polymerase II subunit RPB4

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.451191 KDa
SequenceString: MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL NLSEARLVIK EALVERRRAF KRSQKKHKKK HLKHENAND ETTAVEDEDD DLDEDDVNAD DDDFMHSETR EKELESIDVL LEQTTGGNNK DLKNTMQYLT NFSRFRDQET V GAVIQLLK ...String:
MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL NLSEARLVIK EALVERRRAF KRSQKKHKKK HLKHENAND ETTAVEDEDD DLDEDDVNAD DDDFMHSETR EKELESIDVL LEQTTGGNNK DLKNTMQYLT NFSRFRDQET V GAVIQLLK STGLHPFEVA QLGSLACDTA DEAKTLIPSL NNKISDDELE RILKELSNLE TLY

UniProtKB: DNA-directed RNA polymerase II subunit RPB4

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Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.117094 KDa
SequenceString: MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY ...String:
MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY RLKESQLPRI QRADPVALYL GLKRGEVVKI IRKSETSGRY ASYRICM

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

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Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.931834 KDa
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTLK EKAIPKDQRA TTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR IAMKELAEKK IPLVIRRYLP DGSFEDWSVE ELIVDL

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

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Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 19.081053 KDa
SequenceString:
MFFIKDLSLN ITLHPSFFGP RMKQYLKTKL LEEVEGSCTG KFGYILCVLD YDNIDIQRGR ILPTDGSAEF NVKYRAVVFK PFKGEVVDG TVVSCSQHGF EVQVGPMKVF VTKHLMPQDL TFNAGSNPPS YQSSEDVITI KSRIRVKIEG CISQVSSIHA I GSIKEDYL GAI

UniProtKB: DNA-directed RNA polymerase II subunit RPB7

+
Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.525363 KDa
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTPA NDSSATRSWR PPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG GLLMRLEGNY RNLNNLKQEN AYLLIRR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

+
Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.308161 KDa
SequenceString:
MTTFRFCRDC NNMLYPREDK ENNRLLFECR TCSYVEEAGS PLVYRHELIT NIGETAGVVQ DIGSDPTLPR SDRECPKCHS RENVFFQSQ QRRKDTSMVL FFVCLSCSHI FTSDQKNKRT QFS

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

+
Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.290732 KDa
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKRD

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

+
Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.633493 KDa
SequenceString:
MNAPDRFELF LLGEGESKLK IDPDTKAPNA VVITFEKEDH TLGNLIRAEL LNDRKVLFAA YKVEHPFFAR FKLRIQTTEG YDPKDALKN ACNSIINKLG ALKTNFETEW NLQTLAADDA F

UniProtKB: DNA-directed RNA polymerase II subunit RPB11

+
Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.729969 KDa
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEAR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC4

+
Macromolecule #13: Transcription elongation factor 1

MacromoleculeName: Transcription elongation factor 1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.179386 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MGKRKKSTRK PTKRLVQKLD TKFNCLFCNH EKSVSCTLDK KNSIGTLSCK ICGQSFQTRI NSLSQPVDVY SDWFDAVEEV NSGRGSDTD DGDEGSDSDY ESDSEQDAKT QNDGEIDSDE EEVDSDEERI GQVKRGRGAL VDSDDE

UniProtKB: Transcription elongation factor 1

+
Macromolecule #15: Helicase SEN1

MacromoleculeName: Helicase SEN1 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 252.835922 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNSNNPDNNN SNNINNNNKD KDIAPNSDVQ LATVYTKAKS YIPQIEQVYQ GTNPNIQEAK LLGELLQVLA EVPKGTHLFC DPILEPISI FSLTIFSFNE EATATWLKNH FNPILSVCDK CILNFARGKC KMLQHFAIQR HVPHEHVAKF NDIVCQWRVE A VFPILRNI ...String:
MNSNNPDNNN SNNINNNNKD KDIAPNSDVQ LATVYTKAKS YIPQIEQVYQ GTNPNIQEAK LLGELLQVLA EVPKGTHLFC DPILEPISI FSLTIFSFNE EATATWLKNH FNPILSVCDK CILNFARGKC KMLQHFAIQR HVPHEHVAKF NDIVCQWRVE A VFPILRNI SVNDNTGINI TNEIETAMYE CLCNPHMLRL NKQLKATFEA IFKFFYDTKH RLLDVTNPLS IKTFISGVIF CW CEGSKEE NEWSRAFLKD LYSRNFHINL SNLTPDIIEE VYIHILFLQN PANWTEIVVS QFWSRLLPVF NLFDKDVFIE YFQ VPKNVE SLKKTFKFPL EPIFKMWYNH LSKSYHDKPL DFLLRGLTMF LNKFGSEFWS KIEPFTFHSI LDIIFNRDSF PIKL IKIQD NPIVEHQTEV YFQLTGSVTD LLSWTLPFYH ALSPSKRIQM VRKVSMAFLR IIANYPSLKS IPKACLMNSA TALLR AVLT IKENERAMLY KNDEFETVLL TKTDSRALLN NPLIQDIIIR SASNPNDFYP GLGAASASVA TSTMMVLAEC IDFDIL LLC HRTFKLYSGK PISEIPISTN VLENVTNKID LRSFHDGPLL AKQLLVSLKN INGLLIVPSN TAVAEAHNAL NQKFLLL ST RLMEKFADIL PGQLSKILAD EDASQGFWSC IFSSDKHLYQ AATNILYNTF DVEGRLEGIL AILNSNLTVN LKNINVML Q RLINCEFYEP CPRAVRVLMD VVSAFVDPIS GVFANFQTLK SQNTEKEFLK FWESCWLFLD TIYKFTLKWA SKYDYSELE NFTKDTLDLS RSLVDSFREF SDILHDQTKN LLLNVLETFK NMLYWLRLSD EVLLESCVRL IISTSDLAHE KHVKVDDSLV EMMAKYASK AKRFSNKLTE QQASEILQKA KIFNKALTEE VATEAENYRK EKELSRLGKV IDLTDSVPAS PSLSPSLSST I ASSSAESR ADYLQRKALS SSITGRPRVA QPKITSFGTF QSSANAKLHR TKPVKPLSKM ELARMQLLNN RVVHPPSAPA FH TKSRGLS NKNDDSSSEE SDNDIESARE LFAIAKAKGK GIQTVDINGK VVKRQTAAEL AKQELEHMRK RLNVDMNPLY EII LQWDYT RNSEYPDDEP IGNYSDVKDF FNSPADYQKV MKPLLLLESW QGLCSSRDRE DYKPFSIIVG NRTAVSDFYD VYAS VAKQV IQDCGISESD LIVMAYLPDF RPDKRLSSDD FKKAQHTCLA KVRTLKNTKG GNVDVTLRIH RNHSFSKFLT LRSEI YCVK VMQMTTIERE YSTLEGLEYY DLVGQILQAK PSPPVNVDAA EIETVKKSYK LNTSQAEAIV NSVSKEGFSL IQGPPG TGK TKTILGIIGY FLSTKNASSS NVIKVPLEKN SSNTEQLLKK QKILICAPSN AAVDEICLRL KSGVYDKQGH QFKPQLV RV GRSDVVNVAI KDLTLEELVD KRIGERNYEI RTDPELERKF NNAVTKRREL RGKLDSESGN PESPMSTEDI SKLQLKIR E LSKIINELGR DRDEMREKNS VNYRNRDLDR RNAQAHILAV SDIICSTLSG SAHDVLATMG IKFDTVIIDE ACQCTELSS IIPLRYGGKR CIMVGDPNQL PPTVLSGAAS NFKYNQSLFV RMEKNSSPYL LDVQYRMHPS ISKFPSSEFY QGRLKDGPGM DILNKRPWH QLEPLAPYKF FDIISGRQEQ NAKTMSYTNM EEIRVAIELV DYLFRKFDNK IDFTGKIGII SPYREQMQKM R KEFARYFG GMINKSIDFN TIDGFQGQEK EIILISCVRA DDTKSSVGFL KDFRRMNVAL TRAKTSIWVL GHQRSLAKSK LW RDLIEDA KDRSCLAYAC SGFLDPRNNR AQSILRKFNV PVPSEQEDDY KLPMEYITQG PDEVKSNKDT KKRRVVDEGE EAD KAVKKK KKEKKKEKKK SKADDKKKNN KKAESPSTSS GTKKKSSIFG GMSVPSAVVP KTFPDVDSNK KAAAVVGKKK NNKH VCFSD DVSFIPRNDE PEIKVTRSLS SVLKEKQLGL KETRTISPPE ISNNEDDDDE DDYTPSISDS SLMKSEANGR NNRVA SHNQ NFSASIYDDP QVSQAKQTQV PAAITKHRSS NSVLSGGSSR ILTASDYGEP NQNGQNGANR TLSQHVGNAN QYSTAP VGT GELHETLPAH PQDSYPAEAE DPYDLNPHPQ PQSSAFKGPG SGPTGTRNSS RRNASSSPFI PKKRKPRS

UniProtKB: Helicase SEN1

+
Macromolecule #18: Transcription elongation factor SPT4

MacromoleculeName: Transcription elongation factor SPT4 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 11.168772 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSSERACMLC GIVQTTNEFN RDGCPNCQGI FEEAGVSTME CTSPSFEGLV GMCKPTKSWV AKWLSVDHSI AGMYAIKVDG RLPAEVVEL LPHYKPRDGS QVE

UniProtKB: Transcription elongation factor SPT4

+
Macromolecule #19: Transcription elongation factor SPT5

MacromoleculeName: Transcription elongation factor SPT5 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 115.797969 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSDNSDTNVS MQDHDQQFAD PVVVPQSTDT KDENTSDKDT VDSGNVTTTE STERAESTSN IPPLDGEEKE AKSEPQQPED NAETAATEQ VSSSNGPATD DAQATLNTDS SEANEIVKKE EGSDERKRPR EEDTKNSDGD TKDEGDNKDE DDDEDDDDDD D DEDDDDEA ...String:
MSDNSDTNVS MQDHDQQFAD PVVVPQSTDT KDENTSDKDT VDSGNVTTTE STERAESTSN IPPLDGEEKE AKSEPQQPED NAETAATEQ VSSSNGPATD DAQATLNTDS SEANEIVKKE EGSDERKRPR EEDTKNSDGD TKDEGDNKDE DDDEDDDDDD D DEDDDDEA PTKRRRQERN RFLDIEAEVS DDEDEDEDEE DSELVREGFI THGDDEDDEA SAPGARRDDR LHRQLDQDLN KT SEEDAQR LAKELRERYG RSSSKQYRAA AQDGYVPQRF LLPSVDTATI WGVRCRPGKE KELIRKLLKK KFNLDRAMGK KKL KILSIF QRDNYTGRIY IEAPKQSVIE KFCNGVPDIY ISQKLLIPVQ ELPLLLKPNK SDDVALEEGS YVRIKRGIYK GDLA MVDQI SENNLEVMLK IVPRLDYGKF DEIDPTTQQR KSRRPTFAHR APPQLFNPTM ALRLDQANLY KRDDRHFTYK NEDYI DGYL YKSFRIQHVE TKNIQPTVEE LARFGSKEGA VDLTSVSQSI KKAQAAKVTF QPGDRIEVLN GEQRGSKGIV TRTTKD IAT IKLNGFTTPL EFPISTLRKI FEPGDHVTVI NGEHQGDAGL VLMVEQGQVT FMSTQTSREV TITANNLSKS IDTTATS SE YALHDIVELS AKNVACIIQA GHDIFKVIDE TGKVSTITKG SILSKINTAR ARVSSVDANG NEIKIGDTIV EKVGSRRE G QVLYIQTQQI FVVSKKIVEN AGVFVVNPSN VEAVASKDNM LSNKMDLSKM NPEIISKMGP PSSKTFQQPI QSRGGREVA LGKTVRIRSA GYKGQLGIVK DVNGDKATVE LHSKNKHITI DKHKLTYYNR EGGEGITYDE LVNRRGRVPQ ARMGPSYVSA PRNMATGGI AAGAAATSSG LSGGMTPGWS SFDGGKTPAV NAHGGSGGGG VSSWGGASTW GGQGNGGASA WGGAGGGASA W GGQGTGAT STWGGASAWG NKSSWGGAST WASGGESNGA MSTWGGTGDR SAYGGASTWG GNNNNKSTRD GGASAWGNQD DG NRSAWNN QGNKSNYGGN STWGGH

UniProtKB: Transcription elongation factor SPT5

+
Macromolecule #14: Non-template strand

MacromoleculeName: Non-template strand / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human immunodeficiency virus 2
Molecular weightTheoretical: 17.79341 KDa
SequenceString: (DC)(DG)(DG)(DT)(DC)(DT)(DG)(DC)(DA)(DT) (DG)(DT)(DA)(DC)(DA)(DC)(DT)(DA)(DG)(DT) (DA)(DC)(DC)(DT)(DA)(DC)(DT)(DC)(DG) (DA)(DG)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DA) (DA) (DG)(DC)(DC)(DT)(DC)(DA) ...String:
(DC)(DG)(DG)(DT)(DC)(DT)(DG)(DC)(DA)(DT) (DG)(DT)(DA)(DC)(DA)(DC)(DT)(DA)(DG)(DT) (DA)(DC)(DC)(DT)(DA)(DC)(DT)(DC)(DG) (DA)(DG)(DT)(DG)(DA)(DG)(DC)(DT)(DT)(DA) (DA) (DG)(DC)(DC)(DT)(DC)(DA)(DA)(DT) (DA)(DA)(DA)(DG)(DC)(DT)(DT)(DG)(DC)(DC)

+
Macromolecule #17: Template strand

MacromoleculeName: Template strand / type: dna / ID: 17 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human immunodeficiency virus 2
Molecular weightTheoretical: 18.009531 KDa
SequenceString: (DG)(DG)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DT) (DA)(DT)(DT)(DG)(DA)(DG)(DG)(DC)(DT)(DT) (DA)(DA)(DG)(DC)(DA)(DG)(DT)(DG)(DG) (DG)(DT)(DT)(DC)(DC)(DA)(DG)(DG)(DT)(DA) (DC) (DT)(DA)(DG)(DT)(DG)(DT) ...String:
(DG)(DG)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DT) (DA)(DT)(DT)(DG)(DA)(DG)(DG)(DC)(DT)(DT) (DA)(DA)(DG)(DC)(DA)(DG)(DT)(DG)(DG) (DG)(DT)(DT)(DC)(DC)(DA)(DG)(DG)(DT)(DA) (DC) (DT)(DA)(DG)(DT)(DG)(DT)(DA)(DC) (DA)(DT)(DG)(DC)(DA)(DG)(DA)(DC)(DC)(DG)

+
Macromolecule #16: RNA

MacromoleculeName: RNA / type: rna / ID: 16 / Number of copies: 1
Source (natural)Organism: Human immunodeficiency virus 2
Molecular weightTheoretical: 11.28279 KDa
SequenceString:
AGUCGUGCGU CUAAUAACCG GAGAGGGAAC CCACU

+
Macromolecule #20: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 20 / Number of copies: 9 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #21: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 21 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #22: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 22 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #23: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 23 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.02 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9095
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7nkx

source_name: PDB, initial_model_type: experimental model

2xzo

source_name: PDB, initial_model_type: experimental model

6i59

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementProtocol: OTHER
Output model

PDB-8rap:
Structure of Sen1-ADP.BeF3 bound RNA Polymerase II pre-termination complex

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