EMDB-14927: Yeast RNA polymerase II transcription pre-initiation complex with...

Basic information

Entry

Database: EMDB / ID: EMD-14927

• Title: Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A)
• Map data: cryo-EM map of yeast PIC in complex with the 1 nucleosome

Sample

• Complex: Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome
  • Protein or peptide: x 32 types
  • DNA: x 2 types
• Ligand: x 3 types

• Keywords: PIC / nucleosome / TF / TRANSCRIPTION

Function / homology

Function:

regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / phosphatidylinositol-5-phosphate binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / regulation of transcription by RNA polymerase III / transcription factor TFIIK complex / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / transcription factor TFIIF complex / DNA 5'-3' helicase / phosphatidylinositol-3-phosphate binding / RNA polymerase I preinitiation complex assembly / transcription factor TFIIA complex / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / : / DNA binding, bending / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / transcription preinitiation complex / 3'-5' DNA helicase activity / Processing of Capped Intron-Containing Pre-mRNA / DNA 3'-5' helicase / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / poly(A)+ mRNA export from nucleus / 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 Polymerase II Pre-transcription Events / RNA-templated transcription / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase III transcription / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II complex binding / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / ATPase activator activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase I / nuclear-transcribed mRNA catabolic process / protein phosphatase activator activity / positive regulation of translational initiation / transcription by RNA polymerase III / Dual incision in TC-NER / ATP-dependent activity, acting on DNA / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase I complex / tRNA transcription by RNA polymerase III / translesion synthesis / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II core promoter sequence-specific DNA binding / transcription-coupled nucleotide-excision repair / DNA helicase activity / RNA polymerase II, core complex / : / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA-directed RNA polymerase activity / isomerase activity / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / : / : / : / : / :

Domain/homology:

: / Tfa2 E-tether / Bacterial type XPD DNA helicase, FeS cluster domain / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Helical and beta-bridge domain / Helical and beta-bridge domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIH subunit TTDA/Tfb5 / Transcription initiation factor TFIIE, beta subunit / TFB5-like superfamily / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / Transcription factor TFIIH complex subunit Tfb5 / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription factor TFIIH complex subunit Tfb5 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / ATP-dependent helicase Rad3/Chl1-like / : / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Helicase/UvrB, N-terminal / Zinc finger, TFIIB-type / Type III restriction enzyme, res subunit / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / TBP domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic

Component:

Histone H2B 1.1 / DNA-directed RNA polymerase II subunit RPB1 / General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 / DNA-directed RNA polymerase II subunit RPB2 / TATA-box-binding protein / 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 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Transcription initiation factor IIA subunit 2 / General transcription and DNA repair factor IIH subunit TFB1 / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIE subunit alpha / Transcription initiation factor IIE subunit beta / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit alpha / Transcription initiation factor IIF subunit beta / Histone H4 / Histone H3.2 / General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 / General transcription and DNA repair factor IIH subunit TFB2 / RNA polymerase II transcription factor B subunit 3 / General transcription and DNA repair factor IIH subunit SSL1 / General transcription and DNA repair factor IIH subunit TFB4 / General transcription and DNA repair factor IIH subunit TFB5 / Histone H2A

• Biological species: Saccharomyces killer virus M2-4 / Saccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 3.1 Å
• Authors: Wang H / Cramer P

Funding support

European Union, Germany, 2 items

Organization	Grant number	Country
European Research Council (ERC)	882357	European Union
German Research Foundation (DFG)	SFB860, EXC 2067/1-390729940	Germany

• Citation: Journal: Nat Struct Mol Biol / Year: 2023; Title: Structures of transcription preinitiation complex engaged with the +1 nucleosome.; Authors: Haibo Wang / Sandra Schilbach / Momchil Ninov / Henning Urlaub / Patrick Cramer / ; Abstract: The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles within chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is located downstream of the core promoter. Here we present cryo-EM structures of the yeast PIC bound to promoter DNA and the +1 nucleosome located at three different positions. The general transcription factor TFIIH engages with the incoming downstream nucleosome and its translocase subunit Ssl2 (XPB in human TFIIH) drives the rotation of the +1 nucleosome leading to partial detachment of nucleosomal DNA and intimate interactions between TFIIH and the nucleosome. The structures provide insights into how transcription initiation can be influenced by the +1 nucleosome and may explain why the transcription start site is often located roughly 60 base pairs upstream of the dyad of the +1 nucleosome in yeast.

History

Deposition	May 6, 2022	-
Header (metadata) release	Nov 16, 2022	-
Map release	Nov 16, 2022	-
Update	Jul 24, 2024	-
Current status	Jul 24, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_14927.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: cryo-EM map of yeast PIC in complex with the 1 nucleosome
• Voxel size: X=Y=Z: 1.05 Å

Density

Contour Level	By AUTHOR: 0.012
Minimum - Maximum	-0.055393033 - 0.11425798
Average (Standard dev.)	0.00017959825 (±0.0025784732)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 400 400 400 Spacing 400 400 400
Cell	A=B=C: 419.99997 Å α=β=γ: 90.0 °

Supplemental data

Additional map: focused-refinement map of the upstream complex.

• File: emd_14927_additional_1.map
• Annotation: focused-refinement map of the upstream complex.

Additional map: cryo-EM map of core PIC without post-processing shows...

• File: emd_14927_additional_2.map
• Annotation: cryo-EM map of core PIC without post-processing shows better density of Rpb6 NTT.

Additional map: focused-refinement map of TFIIE.

• File: emd_14927_additional_3.map
• Annotation: focused-refinement map of TFIIE.

Additional map: focused-refinement map of ATPase domain of TFIIH.

• File: emd_14927_additional_4.map
• Annotation: focused-refinement map of ATPase domain of TFIIH.

Half map: half map 2

• File: emd_14927_half_map_1.map
• Annotation: half map 2

Half map: half map 1

• File: emd_14927_half_map_2.map
• Annotation: half map 1

Sample components

Entire : Yeast RNA polymerase II transcription pre-initiation complex with...

• Entire: Name: Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome

Components

• Complex: Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome
  • 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
  • Protein or peptide: Transcription initiation factor IIB
  • DNA: Non-template DNA (209-MER)
  • Protein or peptide: TATA-box-binding protein
  • Protein or peptide: Transcription initiation factor IIF subunit alpha
  • Protein or peptide: Transcription initiation factor IIF subunit beta
  • DNA: Template DNA (209-MER)
  • Protein or peptide: Transcription initiation factor IIA large subunit
  • Protein or peptide: Transcription initiation factor IIA subunit 2
  • Protein or peptide: Transcription initiation factor IIE subunit alpha
  • Protein or peptide: Transcription initiation factor IIE subunit beta
  • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPD
  • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB1
  • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB2
  • Protein or peptide: RNA polymerase II transcription factor B subunit 3
  • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB4
  • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB5
  • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPB
  • Protein or peptide: Histone H3.2
  • Protein or peptide: Histone H4
  • Protein or peptide: Histone H2A
  • Protein or peptide: Histone H2B 1.1
  • Protein or peptide: General transcription and DNA repair factor IIH subunit SSL1
• Ligand: ZINC ION
• Ligand: MAGNESIUM ION
• Ligand: IRON/SULFUR CLUSTER

Supramolecule #1: Yeast RNA polymerase II transcription pre-initiation complex with...

• Supramolecule: Name: Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#28, #30-#34, #29
• Source (natural): Organism: Saccharomyces killer virus M2-4
• Molecular weight: Theoretical: 1.2 MDa

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

• Macromolecule: Name: 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 weight: Theoretical: 191.821578 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

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

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

• Macromolecule: Name: 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 weight: Theoretical: 138.937297 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

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

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

• Macromolecule: Name: 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 weight: Theoretical: 38.635883 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

String:

MGSHHHHHHS NSGLNDIFEA QKIEWHEDTG SSEGPQVKIR EASKDNVDFI LSNVDLAMAN SLRRVMIAEI PTLAIDSVEV ETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCED HCDKCSVVLT LQAFGESEST TNVYSKDLVI VSNLMGRNIG H PIIQDKEG NGVLICKLRK GQELKLTCVA KKGIAKEHAK WGPAAAIEFE YDPWNKLKHT DYWYEQDSAK EWPQSKNCEY ED PPNEGDP FDYKAQADTF YMNVESVGSI PVDQVVVRGI DTLQKKVASI LLALTQMDQD KVNFASGDNN TASNMLGSNE DVM MTGAEQ DPYSNASQMG NTGSGGYDNA W

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

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

• Macromolecule: Name: 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 weight: Theoretical: 25.451191 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

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

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

• Macromolecule: Name: 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 weight: Theoretical: 25.117094 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

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

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

• Macromolecule: Name: 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 weight: Theoretical: 17.931834 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

String:

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

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

• Macromolecule: Name: 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 weight: Theoretical: 19.909934 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

String:

MFFIKDLSLN ITLHPSFFGP RMKQYLKTKL LEEVEGSCTG KFGYILCVLD YDNIDIQRGR ILPTDGSAEF NVKYRAVVFK PFKGEVVDG TVVSCSQHGF EVQVGPMKVF VTKHLMPQDL TFNAGSNPPS YQSSEDVITI KSRIRVKIEG CISQVSSIHA I GSIKEDYL GAIHHHHHH

UniProtKB: DNA-directed RNA polymerase II subunit RPB7

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

• Macromolecule: Name: 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 weight: Theoretical: 16.525363 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

String:

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

• Macromolecule: Name: 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 weight: Theoretical: 14.308161 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

String:

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

• Macromolecule: Name: 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 weight: Theoretical: 8.290732 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

String:

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

• Macromolecule: Name: 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 weight: Theoretical: 13.633493 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

String:

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

• Macromolecule: Name: 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 weight: Theoretical: 7.729969 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae (brewer's yeast)

Sequence

String:

MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEAR

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

Macromolecule #13: Transcription initiation factor IIB

• Macromolecule: Name: Transcription initiation factor IIB / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 39.215391 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MMTRESIDKR AGRRGPNLNI VLTCPECKVY PPKIVERFSE GDVVCALCGL VLSDKLVDTR SEWRTFSNDD HNGDDPSRVG EASNPLLDG NNLSTRIGKG ETTDMRFTKE LNKAQGKNVM DKKDNEVQAA FAKITMLCDA AELPKIVKDC AKEAYKLCHD E KTLKGKSM ESIMAASILI GCRRAEVART FKEIQSLIHV KTKEFGKTLN IMKNILRGKS EDGFLKIDTD NMSGAQNLTY IP RFCSHLG LPMQVTTSAE YTAKKCKEIK EIAGKSPITI AVVSIYLNIL LFQIPITAAK VGQTLQVTEG TIKSGYKILY EHR DKLVDP QLIANGVVSL DNLPGVEKKK HHHHHH

UniProtKB: Transcription initiation factor IIB

Macromolecule #15: TATA-box-binding protein

• Macromolecule: Name: TATA-box-binding protein / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 28.000338 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MADEERLKEF KEANKIVFDP NTRQVWENQN RDGTKPATTF QSEEDIKRAA PESEKDTSAT SGIVPTLQNI VATVTLGCRL DLKTVALHA RNAEYNPKRF AAVIMRIREP KTTALIFASG KMVVTGAKSE DDSKLASRKY ARIIQKIGFA AKFTDFKIQN I VGSCDVKF PIRLEGLAFS HGTFSSYEPE LFPGLIYRMV KPKIVLLIFV SGKIVLTGAK QREEIYQAFE AIYPVLSEFR KM KHHHHHH

UniProtKB: TATA-box-binding protein

Macromolecule #16: Transcription initiation factor IIF subunit alpha

• Macromolecule: Name: Transcription initiation factor IIF subunit alpha / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 82.531789 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GPGMSRRNPP GSRNGGGPTN ASPFIKRDRM RRNFLRMRMG QNGSNSSSPG VPNGDNSRGS LVKKDDPEYA EEREKMLLQI GVEADAGRS NVKVKDEDPN EYNEFPLRAI PKEDLENMRT HLLKFQSKKK INPVTDFHLP VRLHRKDTRN LQFQLTRAEI V QRQKEISE YKKKAEQERS TPNSGGMNKS GTVSLNNTVK DGSQTPTVDS VTKDNTANGV NSSIPTVTGS SVPPASPTTV SA VESNGLS NGSTSAANGL DGNASTANLA NGRPLVTKLE DAGPAEDPTK VGMVKYDGKE VTNEPEFEEG TMDPLADVAP DGG GRAKRG NLRRKTRQLK VLDENAKKLR FEEFYPWVME DFDGYNTWVG SYEAGNSDSY VLLSVEDDGS FTMIPADKVY KFTA RNKYA TLTIDEAEKR MDKKSGEVPR WLMKHLDNIG TTTTRYDRTR RKLKAVADQQ AMDEDDRDDN SEVELDYDEE FADDE EAPI IDGNEQENKE SEQRIKKEML QANAMGLRDE EAPSENEEDE LFGEKKIDED GERIKKALQK TELAALYSSD ENEINP YLS ESDIENKENE SPVKKEEDSD TLSKSKRSSP KKQQKKATNA HVHKEPTLRV KSIKNCVIIL KGDKKILKSF PEGEWNP QT TKAVDSSNNA SNTVPSPIKQ EEGLNSTVAE REETPAPTIT EKDIIEAIGD GKVNIKEFGK FIRRKYPGAE NKKLMFAI V KKLCRKVGND HMELKKE

UniProtKB: Transcription initiation factor IIF subunit alpha

Macromolecule #17: Transcription initiation factor IIF subunit beta

• Macromolecule: Name: Transcription initiation factor IIF subunit beta / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 46.684492 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSSGSAGAPA LSNNSTNSVA KEKSGNISGD EYLSQEEEVF DGNDIENNET KVYEESLDLD LERSNRQVWL VRLPMFLAEK WRDRNNLHG QELGKIRINK DGSKITLLLN ENDNDSIPHE YDLELTKKVV ENEYVFTEQN LKKYQQRKKE LEADPEKQRQ A YLKKQERE EELKKKQQQQ KRRNNRKKFN HRVMTDRDGR DRYIPYVKTI PKKTAIVGTV CHECQVMPSM NDPNYHKIVE QR RNIVKLN NKERITTLDE TVGVTMSHTG MSMRSDNSNF LKVGREKAKS NIKSIRMPKK EILDYLFKLF DEYDYWSLKG LKE RTRQPE AHLKECLDKV ATLVKKGPYA FKYTLRPEYK KLKEEERKAT LGELADEQTG SAGDNAQGDA EADLEDEIEM EDVV

UniProtKB: Transcription initiation factor IIF subunit beta

Macromolecule #19: Transcription initiation factor IIA large subunit

• Macromolecule: Name: Transcription initiation factor IIA large subunit / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)
• Molecular weight: Theoretical: 19.432029 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSNAEASRVY EIIVESVVNE VREDFENAGI DEQTLQDLKN IWQKKLTETK VTTFSWDNQF NEGNINGVQN DLNFNLATPG VNSSEFNIK EENTGSALLD TDEVGSELDD SDDDYLISEG EEDGPDENLM LCLYDKVTRT KARWKCSLKD GVVTINRNDY T FQKAQVEA EWV

Macromolecule #20: Transcription initiation factor IIA subunit 2

• Macromolecule: Name: Transcription initiation factor IIA subunit 2 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 14.431131 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MAVPGYYELY RRSTIGNSLV DALDTLISDG RIEASLAMRV LETFDKVVAE TLKDNTQSKL TVKGNLDTYG FCDDVWTFIV KNCQVTVED SHRDASQNGS GDSQSVISVD KLRIVACNSK KSEKHHHHHH

UniProtKB: Transcription initiation factor IIA subunit 2

Macromolecule #21: Transcription initiation factor IIE subunit alpha

• Macromolecule: Name: Transcription initiation factor IIE subunit alpha / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 55.951039 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MDRPIDDIVK NLLKFVVRGF YGGSFVLVLD AILFHSVLAE DDLKQLLSIN KTELGPLIAR LRSDRLISIH KQREYPPNSK SVERVYYYV KYPHAIDAIK WKVHQVVQRL KDDLDKNSEP NGYMCPICLT KYTQLEAVQL LNFDRTEFLC SLCDEPLVED D SGKKNKEK QDKLNRLMDQ IQPIIDSLKK IDDSRIEENT FEIALARLIP PQNQSHAAYT YNPKKGSTMF RPGDSAPLPN LM GTALGND SSRRAGANSQ ATLHINITTA SDEVAQRELQ ERQAEEKRKQ NAVPEWHKQS TIGKTALGRL DNEEEFDPVV TAS AMDSIN PDNEPAQETS YQNNRTLTEQ EMEERENEKT LNDYYAALAK KQAKLNKEEE EEEEEEEDEE EEEEEEMEDV MDDN DETAR ENALEDEFED VTDTAGTAKT ESNTSNDVKQ ESINDKTEDA VNATATASGP SANAKPNDGD DDDDDDDDEM DIEFE DVAA ALEHHHHH

UniProtKB: Transcription initiation factor IIE subunit alpha

Macromolecule #22: Transcription initiation factor IIE subunit beta

• Macromolecule: Name: Transcription initiation factor IIE subunit beta / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 37.050434 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSKNRDPLLA NLNAFKSKVK SAPVIAPAKV GQKKTNDTVI TIDGNTRKRT ASERAQENTL NSAKNPVLVD IKKEAGSNSS NAISLDDDD DDEDFGSSPS KKVRPGSIAA AALQANQTDI SKSHDSSKLL WATEYIQKKG KPVLVNELLD YLSMKKDDKV I ELLKKLDR IEFDPKKGTF KYLSTYDVHS PSELLKLLRS QVTFKGISCK DLKDGWPQCD ETINQLEEDS KILVLRTKKD KT PRYVWYN SGGNLKCIDE EFVKMWENVQ LPQFAELPRK LQDLGLKPAS VDPATIKRQT KRVEVKKKRQ RKGKITNTHM TGI LKDYSH RV

UniProtKB: Transcription initiation factor IIE subunit beta

Macromolecule #23: General transcription and DNA repair factor IIH helicase subunit XPD

• Macromolecule: Name: General transcription and DNA repair factor IIH helicase subunit XPD; type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 89.899047 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MKFYIDDLPV LFPYPKIYPE QYNYMCDIKK TLDVGGNSIL EMPSGTGKTV SLLSLTIAYQ MHYPEHRKII YCSRTMSEIE KALVELENL MDYRTKELGY QEDFRGLGLT SRKNLCLHPE VSKERKGTVV DEKCRRMTNG QAKRKLEEDP EANVELCEYH E NLYNIEVE DYLPKGVFSF EKLLKYCEEK TLCPYFIVRR MISLCNIIIY SYHYLLDPKI AERVSNEVSK DSIVIFDEAH NI DNVCIES LSLDLTTDAL RRATRGANAL DERISEVRKV DSQKLQDEYE KLVQGLHSAD ILTDQEEPFV ETPVLPQDLL TEA IPGNIR RAEHFVSFLK RLIEYLKTRM KVLHVISETP KSFLQHLKQL TFIERKPLRF CSERLSLLVR TLEVTEVEDF TALK DIATF ATLISTYEEG FLLIIEPYEI ENAAVPNPIM RFTCLDASIA IKPVFERFSS VIITSGTISP LDMYPRMLNF KTVLQ KSYA MTLAKKSFLP MIITKGSDQV AISSRFEIRN DPSIVRNYGS MLVEFAKITP DGMVVFFPSY LYMESIVSMW QTMGIL DEV WKHKLILVET PDAQETSLAL ETYRKACSNG RGAILLSVAR GKVSEGIDFD HQYGRTVLMI GIPFQYTESR ILKARLE FM RENYRIREND FLSFDAMRHA AQCLGRVLRG KDDYGVMVLA DRRFSRKRSQ LPKWIAQGLS DADLNLSTDM AISNTKQF L RTMAQPTDPK DQEGVSVWSY EDLIKHQNSR KDQGGFIENE NKEGEQDEDE DEDIEMQ

UniProtKB: General transcription and DNA repair factor IIH helicase subunit XPD/RAD3

Macromolecule #24: General transcription and DNA repair factor IIH subunit TFB1

• Macromolecule: Name: General transcription and DNA repair factor IIH subunit TFB1; type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 73.194516 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GGSMSHSGAA IFEKVSGIIA INEDVSPAEL TWRSTDGDKV HTVVLSTIDK LQATPASSEK MMLRLIGKVD ESKKRKDNEG NEVVPKPQR HMFSFNNRTV MDNIKMTLQQ IISRYKDADI YEEKRRREES AQHTETPMSS SSVTAGTPTP HLDTPQLNNG A PLINTAKL DDSLSKEKLL TNLKLQQSLL KGNKVLMKVF QETVINAGLP PSEFWSTRIP LLRAFALSTS QKVGPYNVLS TI KPVASSE NKVNVNLSRE KILNIFENYP IVKKAYTDNV PKNFKEPEFW ARFFSSKLFR KLRGEKIMQN DRGDVIIDRY LTL DQEFDR KDDDMLLHPV KKIIDLDGNI QDDPVVRGNR PDFTMQPGVD INGNSDGTVD ILKGMNRLSE KMIMALKNEY SRTN LQNKS NITNDEEDED NDERNELKID DLNESYKTNY AIIHLKRNAH EKTTDNDAKS SADSIKNADL KVSNQQMLQQ LSLVM DNLI NKLDLNQVVP NNEVSNKINK RVITAIKINA KQAKHNNVNS ALGSFVDNTS QANELEVKST LPIDLLESCR MLHTTC CEF LKHFYIHFQS GEQKQASTVK KLYNHLKDCI EKLNELFQDV LNGDGESMSN TCTAYLKPVL NSITLATHKY DEYFNEY NN NSN

UniProtKB: General transcription and DNA repair factor IIH subunit TFB1

Macromolecule #25: General transcription and DNA repair factor IIH subunit TFB2

• Macromolecule: Name: General transcription and DNA repair factor IIH subunit TFB2; type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 58.900602 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GPGSMSDYSL KHSVTQYLEE IPQQVQNRLY TSPATCLAIY RILPPLAKFF IMAMVFNENE VPLLDLDKWV NSNGKLQFQN AIKSMKSLH LLIPNKSSGT LMINLNPTFK ISLRNALTGG EVQNSFGVVV EENVVSLDLL DEYSANKWET ILHFMVGTPL A KIPSEKVL NLLKHSKLME EVNSTGEFKI TNEGFQFLLQ EINSQLWTLL LQYLKMIETS KMDLVDVLHF IFMLGALEVG KA YKIDALS ETQRIMLQDM RDYGLVFQKH SNDSIFYPTK LALMLTSDTK TIRSASNAMD SVLRQNREEP SVNEDGANGK STT DITTSD DLNKAGLKNQ DIPDGSLIVE TNFKIYSYSN SPLQIAVLSL FVHLKARFVN MVLGQITRES IRRALTNGIT ADQI IAYLE THAHPQMRRL AEEKLEKKLE LDPNCKEPLQ VLPPTVVDQI RLWQLELDRV ITYEGSLYSD FETSQEYNLL SKYAQ DIGV LLWKDDKKKK FFISKEGNSQ VLDFAKRKLK KKQ

UniProtKB: General transcription and DNA repair factor IIH subunit TFB2

Macromolecule #26: RNA polymerase II transcription factor B subunit 3

• Macromolecule: Name: RNA polymerase II transcription factor B subunit 3 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 38.480746 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GPHMLMDEYE ENKDMCPICK TDRYLSPDVK FLVNPECYHR ICESCVDRIF SLGPAQCPYK GCDKILRKNK FKTQIFDDVE VEKEVDIRK RVFNVFNKTI DDFNGDLVEY NKYLEEVEDI IYKLDHGIDV AKTEEKLRTY EELNKQLIMN NLERSRTEIE S FEQRQKFE KEMKLKKRLL ERQIEEEERM NKEWTKKEIV NRLSTTTQDI NETIEGVKNT VKLKKSSARR KLEELNRVLK NN PYFNSNV NVQNSRLKDA VPFTPFNGDR EAHPRFTLKG SVYNDPFIKD LEHRKEFIAS GFNTNYAYER VLTEAFMGLG CVI SEEL

UniProtKB: RNA polymerase II transcription factor B subunit 3

Macromolecule #27: General transcription and DNA repair factor IIH subunit TFB4

• Macromolecule: Name: General transcription and DNA repair factor IIH subunit TFB4; type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 37.778676 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

SNAMDAISDP TFKHARSRKQ VTEESPSLLT VIIEIAPKLW TTFDEEGNEK GSIIKVLEAL IVFLNAHLAF NSANKVAVIA AYSQGIKYL YPESTSALKA SESENKTRSD LKIINSDMYR RFRNVDETLV EEIYKLFELE KKQIEQNSQR STLAGAMSAG L TYVNRISK ESVTTSLKSR LLVLTCGSGS SKDEIFQYIP IMNCIFSATK MKCPIDVVKI GGSKESTFLQ QTTDATNGVY LH VESTEGL IQYLATAMFI DPSLRPIIVK PNHGSVDFRT SCYLTGRVVA VGFICSVCLC VLSIIPPGNK CPACDSQFDE HVI AKLKRK PVVPRLKAKK KVTKP

UniProtKB: General transcription and DNA repair factor IIH subunit TFB4

Macromolecule #28: General transcription and DNA repair factor IIH subunit TFB5

• Macromolecule: Name: General transcription and DNA repair factor IIH subunit TFB5; type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 8.541787 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GPGSMARARK GALVQCDPSI KALILQIDAK MSDIVLEELD DTHLLVNPSK VEFVKHELNR LLSKNIYNPM DEEENQ

UniProtKB: General transcription and DNA repair factor IIH subunit TFB5

Macromolecule #29: General transcription and DNA repair factor IIH subunit SSL1

• Macromolecule: Name: General transcription and DNA repair factor IIH subunit SSL1; type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 52.571215 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GGSMAPVVIS ESEEDEDRVA ITRRTKRQVH FDGEGDDRVD QQQQQHSSSH RDRDKHVQRK KKKRLSNRNL QGSNGGYAWE DEIKRSWDL VKVDDEGDMA SLVASIVEAR KKRTAKKNIT PYQRGIIRSL ILTLDCSEAM LEKDLRPNRH AMIIQYAIDF V HEFFDQNP ISQMGIIIMR NGLAQLVSQV SGNPQDHIDA LKSIRKQEPK GNPSLQNALE MARGLLLPVP AHCTREVLIV FG SLSTTDP GDIHQTIDSL VSEKIRVKVL GLSAQVAICK ELCKATNYGD ESFYKILLDE THLKELFNEA VTPLPVNKIN KGF TLVKMG FPTRIFEDTP TFCSCHSKLV YGGYFCPNCH SKVCSLPTVC PCCDLMLILS THLARSYHHL MPLKTFAEVP TTEK FRSED CFSCQSRFPI LKNHKNGKLL TSSRYRCEDC KQEFCVDCDV FIHEILHNCP GCESKPVIT

UniProtKB: General transcription and DNA repair factor IIH subunit SSL1

Macromolecule #30: General transcription and DNA repair factor IIH helicase subunit XPB

• Macromolecule: Name: General transcription and DNA repair factor IIH helicase subunit XPB; type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 95.461664 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKD KALLQDTNSD IPADFVPDSV SGMFRSHDFS YLRLRPDHAS RPLWISPSDG RIILESFSPL AEQAQDFLVT I AEPISRPS HIHEYKITAY SLYAAVSVGL ETDDIISVLD RLSKVPVAES IINFIKGATI SYGKVKLVIK HNRYFVETTQ AD ILQMLLN DSVIGPLRID SDHQVQPPED VLQQQLQQTA GKPATNVNPN DVEAVFSAVI GGDNEREEED DDIDAVHSFE IAN ESVEVV KKRCQEIDYP VLEEYDFRND HRNPDLDIDL KPSTQIRPYQ EKSLSKMFGN GRARSGIIVL PCGAGKTLVG ITAA CTIKK SVIVLCTSSV SVMQWRQQFL QWCTLQPENC AVFTSDNKEM FQTESGLVVS TYSMVANTRN RSHDSQKVMD FLTGR EWGF IILDEVHVVP AAMFRRVVST IAAHAKLGLT ATLVREDDKI GDLNFLIGPK LYEANWMELS QKGHIANVQC AEVWCP MTA EFYQEYLRET ARKRMLLYIM NPTKFQACQF LIQYHERRGD KIIVFSDNVY ALQEYALKMG KPFIYGSTPQ QERMNIL QN FQYNDQINTI FLSKVGDTSI DLPEATCLIQ ISSHYGSRRQ EAQRLGRILR AKRRNDEGFN AFFYSLVSKD TQEMYYST K RQAFLVDQGY AFKVITHLHG MENIPNLAYA SPRERRELLQ EVLLKNEEAA GIEVGDDADN SVGRGSNGHK RFKSKAVRG EGSLSGLAGG EDMAYMEYST NKNKELKEHH PLIRKMYYKN LKK

UniProtKB: General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2

Macromolecule #31: Histone H3.2

• Macromolecule: Name: Histone H3.2 / type: protein_or_peptide / ID: 31 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 15.271863 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL AAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

Macromolecule #32: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 32 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 11.263231 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

Macromolecule #33: Histone H2A

• Macromolecule: Name: Histone H2A / type: protein_or_peptide / ID: 33 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 13.978241 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

Macromolecule #34: Histone H2B 1.1

• Macromolecule: Name: Histone H2B 1.1 / type: protein_or_peptide / ID: 34 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 13.848097 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

Macromolecule #14: Non-template DNA (209-MER)

• Macromolecule: Name: Non-template DNA (209-MER) / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 64.290992 KDa

Sequence

String:

(DA)(DG)(DC)(DA)(DC)(DG)(DC)(DT)(DG)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DA)(DT)(DA) (DG)(DC)(DT)(DA)(DT)(DG)(DG)(DA)(DA) (DC)(DG)(DT)(DT)(DC)(DG)(DA)(DT)(DT)(DC) (DA) (DC)(DC)(DT)(DC)(DC)(DG)(DA)(DT) (DG)(DT)(DG)(DT)(DG)(DT)(DT)(DG)(DT)(DA) (DC)(DA) (DT)(DA)(DC)(DA)(DT)(DA)(DA) (DA)(DA)(DA)(DT)(DA)(DT)(DC)(DA)(DT)(DA) (DG)(DC)(DT) (DC)(DT)(DT)(DC)(DT)(DG) (DC)(DG)(DC)(DT)(DG)(DT)(DG)(DT)(DT)(DG) (DG)(DT)(DC)(DG) (DT)(DA)(DG)(DA)(DC) (DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA) (DC)(DC)(DG)(DC)(DT) (DT)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG) (DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG) (DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC) (DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT) (DC) (DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG) (DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DC)(DA)(DT)(DC)(DG)(DA)(DT)

Macromolecule #18: Template DNA (209-MER)

• Macromolecule: Name: Template DNA (209-MER) / type: dna / ID: 18 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 64.754344 KDa

Sequence

String:

(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DC)(DA)(DC)(DA) (DG)(DC)(DG)(DC) (DA)(DG)(DA)(DA)(DG)(DA)(DG)(DC)(DT)(DA) (DT)(DG)(DA)(DT)(DA)(DT) (DT)(DT)(DT) (DT)(DA)(DT)(DG)(DT)(DA)(DT)(DG)(DT)(DA) (DC)(DA)(DA)(DC)(DA)(DC)(DA) (DC)(DA) (DT)(DC)(DG)(DG)(DA)(DG)(DG)(DT)(DG)(DA) (DA)(DT)(DC)(DG)(DA)(DA)(DC)(DG) (DT) (DT)(DC)(DC)(DA)(DT)(DA)(DG)(DC)(DT)(DA) (DT)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA) (DC)(DA)(DG)(DC)(DG)(DT)(DG)(DC)(DT)

Macromolecule #35: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 35 / Number of copies: 17 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #36: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 36 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #37: IRON/SULFUR CLUSTER

• Macromolecule: Name: IRON/SULFUR CLUSTER / type: ligand / ID: 37 / Number of copies: 1 / Formula: SF4
• Molecular weight: Theoretical: 351.64 Da

Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.5
• Grid: Model: UltrAuFoil R2/2 / Material: GOLD
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: INSILICO MODEL
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55851
• Initial angle assignment: Type: ANGULAR RECONSTITUTION
• Final angle assignment: Type: ANGULAR RECONSTITUTION