EMDB-19909: PolII-TCR-STK19 structure.

Basic information

Entry

Database: EMDB / ID: EMD-19909

• Title: PolII-TCR-STK19 structure.
• Map data: Main map.

Sample

• Complex: Pol II-TCR-STK19
  • RNA: x 1 types
  • Protein or peptide: x 17 types
  • DNA: x 2 types
• Protein or peptide: x 1 types
• Ligand: x 4 types

• Keywords: Complex / DNA repair / TRANSCRIPTION

Function / homology

Function:

negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / positive regulation of single strand break repair / regulation of transcription elongation by RNA polymerase II / B-WICH complex / DNA protection / single strand break repair / positive regulation by virus of viral protein levels in host cell / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / double-strand break repair via classical nonhomologous end joining / response to superoxide / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / ATP-dependent chromatin remodeler activity / photoreceptor cell maintenance / Cul4-RING E3 ubiquitin ligase complex / nuclear lumen / UV-damage excision repair / positive regulation of Ras protein signal transduction / positive regulation of DNA-templated transcription, elongation / response to UV-B / RNA polymerase binding / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / positive regulation of transcription by RNA polymerase III / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / positive regulation of transcription by RNA polymerase I / negative regulation of reproductive process / negative regulation of developmental process / RNA polymerase II complex binding / cullin family protein binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / viral release from host cell / site of DNA damage / protein tyrosine kinase activator activity / RNA Polymerase I Transcription Initiation / pyrimidine dimer repair / ATP-dependent activity, acting on DNA / response to X-ray / positive regulation of transcription initiation by RNA polymerase II / ectopic germ cell programmed cell death / transcription by RNA polymerase III / transcription by RNA polymerase I / positive regulation of double-strand break repair via homologous recombination / positive regulation of viral genome replication / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / proteasomal protein catabolic process / transcription-coupled nucleotide-excision repair / response to UV / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / protein autoubiquitination / : / JNK cascade / translation initiation factor binding / neurogenesis / positive regulation of gluconeogenesis / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / positive regulation of DNA repair / DNA damage checkpoint signaling / transcription elongation factor complex / regulation of DNA-templated transcription elongation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / response to gamma radiation / nucleotide-excision repair / helicase activity / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / base-excision repair

Domain/homology:

Serine-threonine protein kinase 19 / Inactive serine-threonine protein kinase 19 / UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / : / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / ENTH/VHS / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / 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 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 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, 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 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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 / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6

Component:

RNA polymerase II subunit D / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase subunit / RNA polymerase II subunit K / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit E / Inactive serine/threonine-protein kinase 19 / Transcription elongation factor 1 homolog / DNA-directed RNA polymerase II subunit RPB9 / DNA excision repair protein ERCC-6 / DNA excision repair protein ERCC-8 / DNA damage-binding protein 1 / UV-stimulated scaffold protein A

• Biological species: Homo sapiens (human) / Sus scrofa (pig)
• Method: single particle reconstruction / cryo EM / Resolution: 3.3 Å
• Authors: Kokic G

Funding support

Germany, European Union, 2 items

Organization	Grant number	Country
German Research Foundation (DFG)	EXC 2067/1-390729940	Germany
European Research Council (ERC)	Advanced Investigator Grant CHROMATRANS (grant agreement No. 882357)	European Union

• Citation: Journal: Cell / Year: 2024; Title: STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair.; Authors: Diana van den Heuvel / Marta Rodríguez-Martínez / Paula J van der Meer / Nicolas Nieto Moreno / Jiyoung Park / Hyun-Suk Kim / Janne J M van Schie / Annelotte P Wondergem / Areetha D'Souza / George Yakoub / Anna E Herlihy / Krushanka Kashyap / Thierry Boissière / Jane Walker / Richard Mitter / Katja Apelt / Klaas de Lint / Idil Kirdök / Mats Ljungman / Rob M F Wolthuis / Patrick Cramer / Orlando D Schärer / Goran Kokic / Jesper Q Svejstrup / Martijn S Luijsterburg / ; Abstract: Transcription-coupled DNA repair (TCR) removes bulky DNA lesions impeding RNA polymerase II (RNAPII) transcription. Recent studies have outlined the stepwise assembly of TCR factors CSB, CSA, UVSSA, and transcription factor IIH (TFIIH) around lesion-stalled RNAPII. However, the mechanism and factors required for the transition to downstream repair steps, including RNAPII removal to provide repair proteins access to the DNA lesion, remain unclear. Here, we identify STK19 as a TCR factor facilitating this transition. Loss of STK19 does not impact initial TCR complex assembly or RNAPII ubiquitylation but delays lesion-stalled RNAPII clearance, thereby interfering with the downstream repair reaction. Cryoelectron microscopy (cryo-EM) and mutational analysis reveal that STK19 associates with the TCR complex, positioning itself between RNAPII, UVSSA, and CSA. The structural insights and molecular modeling suggest that STK19 positions the ATPase subunits of TFIIH onto DNA in front of RNAPII. Together, these findings provide new insights into the factors and mechanisms required for TCR.

History

Deposition	Mar 22, 2024	-
Header (metadata) release	Dec 4, 2024	-
Map release	Dec 4, 2024	-
Update	Dec 25, 2024	-
Current status	Dec 25, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_19909.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Main map.
• Voxel size: X=Y=Z: 1.23 Å

Density

Contour Level	By AUTHOR: 0.873
Minimum - Maximum	-3.7455173 - 7.590248
Average (Standard dev.)	0.014050737 (±0.14010772)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 360 360 360 Spacing 360 360 360
Cell	A=B=C: 442.80002 Å α=β=γ: 90.0 °

Supplemental data

Half map: Half map.

• File: emd_19909_half_map_1.map
• Annotation: Half map.

Half map: Half map.

• File: emd_19909_half_map_2.map
• Annotation: Half map.

Sample components

Entire : Pol II-TCR-STK19

• Entire: Name: Pol II-TCR-STK19

Components

• Complex: Pol II-TCR-STK19
  • RNA: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')
  • Protein or peptide: Isoform 1 of Inactive serine/threonine-protein kinase 19
  • Protein or peptide: DNA-directed RNA polymerase subunit
  • Protein or peptide: DNA-directed RNA polymerase subunit beta
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
  • Protein or peptide: RNA polymerase II subunit D
  • Protein or peptide: DNA-directed RNA polymerase II subunit E
  • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
  • Protein or peptide: DNA-directed RNA polymerase subunit
  • 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-a
  • Protein or peptide: RNA polymerase II subunit K
  • DNA: NTS
  • DNA: TS
  • Protein or peptide: UV-stimulated scaffold protein A
  • Protein or peptide: DNA excision repair protein ERCC-6
  • Protein or peptide: DNA excision repair protein ERCC-8
  • Protein or peptide: DNA damage-binding protein 1
• Protein or peptide: Transcription elongation factor 1 homolog
• Ligand: ZINC ION
• Ligand: MAGNESIUM ION
• Ligand: ADENOSINE-5'-DIPHOSPHATE
• Ligand: BERYLLIUM TRIFLUORIDE ION

Supramolecule #1: Pol II-TCR-STK19

• Supramolecule: Name: Pol II-TCR-STK19 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17, #19-#21
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')

• Macromolecule: Name: RNA (5'-R(P*CP*AP*AP*AP*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3'); type: rna / ID: 1 / Number of copies: 1
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 4.556836 KDa

Sequence

String:

CAAAAUCGAG AGGA

Macromolecule #2: Isoform 1 of Inactive serine/threonine-protein kinase 19

• Macromolecule: Name: Isoform 1 of Inactive serine/threonine-protein kinase 19; type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 28.9265 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSWKRHHLIP ETFGVKRRRK RGPVESDPLR GEPGSARAAV SELMQLFPRG LFEDALPPIV LRSQVYSLVP DRTVADRQLK ELQEQGEIR IVQLGFDLDA HGIIFTEDYR TRVCDCVLKA CDGRPYAGAV QKFLASVLPA CGDLSFQQDQ MTQTFGFRDS E ITHLVNAG VLTVRDAGSW WLAVPGAGRF IKYFVKGRQA VLSMVRKAKY RELLLSELLG RRAPVVVRLG LTYHVHDLIG AQ LVDCIST TSGTLLRLPE T

UniProtKB: Inactive serine/threonine-protein kinase 19

Macromolecule #3: DNA-directed RNA polymerase subunit

• Macromolecule: Name: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 218.889547 KDa

Sequence

String:

MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK RLTHVYDLCK GKNICEGGEE M DNKFGVEQ PEGDEDLTKE KGHGGCGRYQ PRIRRSGLEL YAEWKHVNED SQEKKILLSP ERVHEIFKRI SDEECFVLGM EP RYARPEW MIVTVLPVPP LSVRPAVVMQ GSARNQDDLT HKLADIVKIN NQLRRNEQNG AAAHVIAEDV KLLQFHVATM VDN ELPGLP RAMQKSGRPL KSLKQRLKGK EGRVRGNLMG KRVDFSARTV ITPDPNLSID QVGVPRSIAA NMTFAEIVTP FNID RLQEL VRRGNSQYPG AKYIIRDNGD RIDLRFHPKP SDLHLQTGYK VERHMCDGDI VIFNRQPTLH KMSMMGHRVR ILPWS TFRL NLSVTTPYNA DFDGDEMNLH LPQSLETRAE IQELAMVPRM IVTPQSNRPV MGIVQDTLTA VRKFTKRDVF LERGEV MNL LMFLSTWDGK VPQPAILKPR PLWTGKQIFS LIIPGHINCI RTHSTHPDDE DSGPYKHISP GDTKVVVENG ELIMGIL CK KSLGTSAGSL VHISYLEMGH DITRLFYSNI QTVINNWLLI EGHTIGIGDS IADSKTYQDI QNTIKKAKQD VIEVIEKA H NNELEPTPGN TLRQTFENQV NRILNDARDK TGSSAQKSLS EYNNFKSMVV SGAKGSKINI SQVIAVVGQQ NVEGKRIPF GFKHRTLPHF IKDDYGPESR GFVENSYLAG LTPTEFFFHA MGGREGLIDT AVKTAETGYI QRRLIKSMES VMVKYDATVR NSINQVVQL RYGEDGLAGE SVEFQNLATL KPSNKAFEKK FRFDYTNERA LRRTLQEDLV KDVLSNAHIQ NELEREFERM R EDREVLRV IFPTGDSKVV LPCNLLRMIW NAQKIFHINP RLPSDLHPIK VVEGVKELSK KLVIVNGDDP LSRQAQENAT LL FNIHLRS TLCSRRMAEE FRLSGEAFDW LLGEIESKFN QAIAHPGEMV GALAAQSLGE PATQMTLNTF HYAGVSAKNV TLG VPRLKE LINISKKPKT PSLTVFLLGQ SARDAERAKD ILCRLEHTTL RKVTANTAIY YDPNPQSTVV AEDQEWVNVY YEMP DFDVA RISPWLLRVE LDRKHMTDRK LTMEQIAEKI NAGFGDDLNC IFNDDNAEKL VLRIRIMNSD ENKMQEEEEV VDKMD DDVF LRCIESNMLT DMTLQGIEQI SKVYMHLPQT DNKKKIIITE DGEFKALQEW ILETDGVSLM RVLSEKDVDP VRTTSN DIV EIFTVLGIEA VRKALERELY HVISFDGSYV NYRHLALLCD TMTCRGHLMA ITRHGVNRQD TGPLMKCSFE ETVDVLM EA AAHGESDPMK GVSENIMLGQ LAPAGTGCFD LLLDAEKCKY GMEIPTNIPG LGAAGPTGMF FGSAPSPMGG ISPAMTPW N QGATPAYGAW SPSVGSGMTP GAAGFSPSAA SDASGFSPGY SPAWSPTPGS PGSPGPSSPY IPSPGGAMSP SYSPTSPAY EPRSPGGYTP QSPSYSPTSP SYSPTSPSYS PTSPNYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS P NYSPTSPN YTPTSPSYSP TSPSYSPTSP NYTPTSPNYS PTSPSYSPTS PSYSPTSPSY SPSSPRYTPQ SPTYTPSSPS YS PSSPSYS PTSPKYTPTS PSYSPSSPEY TPTSPKYSPT SPKYSPTSPK YSPTSPTYSP TTPKYSPTSP TYSPTSPVYT PTS PKYSPT SPTYSPTSPK YSPTSPTYSP TSPKGSTYSP TSPGYSPTSP TYSLTSPAIS PDDSDEEN

UniProtKB: DNA-directed RNA polymerase subunit

Macromolecule #4: DNA-directed RNA polymerase subunit beta

• Macromolecule: Name: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 133.201625 KDa

Sequence

String:

MQYDEDDDEI TPDLWQEACW IVISSYFDEK GLVRQQLDSF DEFIQMSVQR IVEDAPPIDL QAEAQHASGE VEEPPRYLLK FEQIYLSKP THWERDGAPS PMMPNEARLR NLTYSAPLYV DITKTVIKEG EEQLQTQHQK TFIGKIPIML RSTYCLLNGL T DRDLCELN ECPLDPGGYF IINGSEKVLI AQEKMATNTV YVFAKKDSKY AYTGECRSCL ENSSRPTSTI WVSMLARGGQ GA KKSAIGQ RIVATLPYIK QEVPIIIVFR ALGFVSDRDI LEHIIYDFED PEMMEMVKPS LDEAFVIQEQ NVALNFIGSR GAK PGVTKE KRIKYAKEVL QKEMLPHVGV SDFCETKKAY FLGYMVHRLL LAALGRRELD DRDHYGNKRL DLAGPLLAFL FRGM FKNLL KEVRIYAQKF IDRGKDFNLE LAIKTRIISD GLKYSLATGN WGDQKKAHQA RAGVSQVLNR LTFASTLSHL RRLNS PIGR DGKLAKPRQL HNTLWGMVCP AETPEGHAVG LVKNLALMAY ISVGSQPSPI LEFLEEWSME NLEEISPAAI ADATKI FVN GCWVGIHKDP EQLMNTLRKL RRQMDIIVSE VSMIRDIRER EIRIYTDAGR ICRPLLIVEK QKLLLKKRHI DQLKERE YN NYSWQDLVAS GVVEYIDTLE EETVMLAMTP DDLQEKEVAY CSTYTHCEIH PSMILGVCAS IIPFPDHNQS PRNTYQSA M GKQAMGVYIT NFHVRMDTLA HVLYYPQKPL VTTRSMEYLR FRELPAGINS IVAIASYTGY NQEDSVIMNR SAVDRGFFR SVFYRSYKEQ ESKKGFDQEE VFEKPTRETC QGMRHAIYDK LDDDGLIAPG VRVSGDDVII GKTVTLPENE DELEGTNRRY TKRDCSTFL RTSETGIVDQ VMVTLNQEGY KFCKIRVRSV RIPQIGDKFA SRHGQKGTCG IQYRQEDMPF TCEGITPDII I NPHAIPSR MTIGHLIECL QGKVSANKGE IGDATPFNDA VNVQKISNLL SDYGYHLRGN EVLYNGFTGR KITSQIFIGP TY YQRLKHM VDDKIHSRAR GPIQILNRQP MEGRSRDGGL RFGEMERDCQ IAHGAAQFLR ERLFEASDPY QVHVCNLCGI MAI ANTRTH TYECRGCRNK TQISLVRMPY ACKLLFQELM SMSIAPRMMS V

UniProtKB: DNA-directed RNA polymerase subunit beta

Macromolecule #5: DNA-directed RNA polymerase II subunit RPB3

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 31.439074 KDa

Sequence

String:

MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD LISNSPRVIP VTSRNRDNDP SDYVEQDDIL IVKLRKGQEL R LRAYAKKG FGKEHAKWNP TAGVAFEYDP DNALRHTVYP KPEEWPKSEY SELDEDESQA PYDPNGKPER FYYNVESCGS LR PETIVLS ALSGLKKKLS DLQTQLSHEI QSDVLTIN

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

Macromolecule #6: RNA polymerase II subunit D

• Macromolecule: Name: RNA polymerase II subunit D / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 16.331255 KDa

Sequence

String:

MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQ KKLHKFELAC LANLCPETAE ESKALIPSLE GRFEDEELQQ ILDDIQTKRS FQY

UniProtKB: RNA polymerase II subunit D

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

• Macromolecule: Name: DNA-directed RNA polymerase II subunit E / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 24.644318 KDa

Sequence

String:

MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN QLPRIQAGDP VARYFGIKRG QVVKIIRPSE TAGRYITYRL VQ

UniProtKB: DNA-directed RNA polymerase II subunit E

Macromolecule #8: 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: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 14.477001 KDa

Sequence

String:

MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIISD

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

Macromolecule #9: DNA-directed RNA polymerase subunit

• Macromolecule: Name: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 19.314283 KDa

Sequence

String:

MFYHISLEHE ILLHPRYFGP NLLNTVKQKL FTEVEGTCTG KYGFVIAVTT IDNIGAGVIQ PGRGFVLYPV KYKAIVFRPF KGEVVDAVV TQVNKVGLFT EIGPMSCFIS RHSIPSEMEF DPNSNPPCYK TMDEDIVIQQ DDEIRLKIVG TRVDKNDIFA I GSLMDDYL GLVS

UniProtKB: DNA-directed RNA polymerase subunit

Macromolecule #10: 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: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 17.162273 KDa

Sequence

String:

MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGTL DDGEYNPTDD RPSRADQFE YVMYGKVYRI EGDETSTEAA TRLSAYVSYG GLLMRLQGDA NNLHGFEVDS RVYLLMKKLA F

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

Macromolecule #11: DNA-directed RNA polymerase II subunit RPB9

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 14.541221 KDa

Sequence

String:

MEPDGTYEPG FVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN SCIYVNKITH EVDELTQIIA DVSQDPTLPR TEDHPCQKC GHKEAVFFQS HSARAEDAMR LYYVCTAPHC GHRWTE

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

Macromolecule #12: 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: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 7.655123 KDa

Sequence

String:

MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

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

Macromolecule #13: DNA-directed RNA polymerase II subunit RPB11-a

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB11-a / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 13.310284 KDa

Sequence

String:

MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEHK IIIRVQTTPD YSPQEAFTN AITDLISELS LLEERFRVAI KDKQEGIE

UniProtKB: DNA-directed RNA polymerase II subunit RPB11-a

Macromolecule #14: RNA polymerase II subunit K

• Macromolecule: Name: RNA polymerase II subunit K / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 7.018244 KDa

Sequence

String:

MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

UniProtKB: RNA polymerase II subunit K

Macromolecule #17: UV-stimulated scaffold protein A

• Macromolecule: Name: UV-stimulated scaffold protein A / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 80.72168 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELFV RSHQFRMLVV SNFQEFLEL TLGTDPAQPL PPPREAAQRL RQATTRAVEG WNEKFGEAYK KLALGYHFLR HNKKVDFQDT NARSLAERKR E EEKQKHLD KIYQERASQA EREMQEMSGE IESCLTEVES CFRLLVPFDF DPNPETESLG MASGMSDALR SSCAGQVGPC RS GTPDPRD GEQPCCSRDL PASAGHPRAG GGAQPSQTAT GDPSDEDEDS DLEEFVRSHG LGSHKYTLDV ELCSEGLKVQ ENE DNLALI HAARDTLKLI RNKFLPAVCS WIQRFTRVGT HGGCLKRAID LKAELELVLR KYKELDIEPE GGERRRTEAL GDAE EDEDD EDFVEVPEKE GYEPHIPDHL RPEYGLEAAP EKDTVVRCLR TRTRMDEEVS DPTSAAAQLR QLRDHLPPPS SASPS RALP EPQEAQKLAA ERARAPVVPY GVDLHYWGQE LPTAGKIVKS DSQHRFWKPS EVEEEVVNAD ISEMLRSRHI TFAGKF EPV QHWCRAPRPD GRLCERQDRL KCPFHGKIVP RDDEGRPLDP EDRAREQRRQ LQKQERPEWQ DPELMRDVEA ATGQDLG SS RYSGKGRGKK RRYPSLTNLK AQADTARARI GRKVFAKAAV RRVVAAMNRM DQKKHEKFSN QFNYALN

UniProtKB: UV-stimulated scaffold protein A

Macromolecule #18: Transcription elongation factor 1 homolog

• Macromolecule: Name: Transcription elongation factor 1 homolog / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 7.272097 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

LETQFTCPFC NHEKSCDVKM DRARNTGVIS CTVCLEEFQT PITYLSEPVD VYSDWIDACE AANQ

UniProtKB: Transcription elongation factor 1 homolog

Macromolecule #19: DNA excision repair protein ERCC-6

• Macromolecule: Name: DNA excision repair protein ERCC-6 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO; EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 168.673547 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MPNEGIPHSS QTQEQDCLQS QPVSNNEEMA IKQESGGDGE VEEYLSFRSV GDGLSTSAVG CASAAPRRGP ALLHIDRHQI QAVEPSAQA LELQGLGVDV YDQDVLEQGV LQQVDNAIHE ASRASQLVDV EKEYRSVLDD LTSCTTSLRQ INKIIEQLSP Q AATSRDIN RKLDSVKRQK YNKEQQLKKI TAKQKHLQAI LGGAEVKIEL DHASLEEDAE PGPSSLGSML MPVQETAWEE LI RTGQMTP FGTQIPQKQE KKPRKIMLNE ASGFEKYLAD QAKLSFERKK QGCNKRAARK APAPVTPPAP VQNKNKPNKK ARV LSKKEE RLKKHIKKLQ KRALQFQGKV GLPKARRPWE SDMRPEAEGD SEGEESEYFP TEEEEEEEDD EVEGAEADLS GDGT DYELK PLPKGGKRQK KVPVQEIDDD FFPSSGEEAE AASVGEGGGG GRKVGRYRDD GDEDYYKQRL RRWNKLRLQD KEKRL KLED DSEESDAEFD EGFKVPGFLF KKLFKYQQTG VRWLWELHCQ QAGGILGDEM GLGKTIQIIA FLAGLSYSKI RTRGSN YRF EGLGPTVIVC PTTVMHQWVK EFHTWWPPFR VAILHETGSY THKKEKLIRD VAHCHGILIT SYSYIRLMQD DISRYDW HY VILDEGHKIR NPNAAVTLAC KQFRTPHRII LSGSPMQNNL RELWSLFDFI FPGKLGTLPV FMEQFSVPIT MGGYSNAS P VQVKTAYKCA CVLRDTINPY LLRRMKSDVK MSLSLPDKNE QVLFCRLTDE QHKVYQNFVD SKEVYRILNG EMQIFSGLI ALRKICNHPD LFSGGPKNLK GLPDDELEED QFGYWKRSGK MIVVESLLKI WHKQGQRVLL FSQSRQMLDI LEVFLRAQKY TYLKMDGTT TIASRQPLIT RYNEDTSIFV FLLTTRVGGL GVNLTGANRV VIYDPDWNPS TDTQARERAW RIGQKKQVTV Y RLLTAGTI EEKIYHRQIF KQFLTNRVLK DPKQRRFFKS NDLYELFTLT SPDASQSTET SAIFAGTGSD VQTPKCHLKR RI QPAFGAD HDVPKRKKFP ASNISVNDAT SSEEKSEAKG AEVNAVTSNR SDPLKDDPHM SSNVTSNDRL GEETNAVSGP EEL SVISGN GECSNSSGTG KTSMPSGDES IDEKLGLSYK RERPSQAQTE AFWENKQMEN NFYKHKSKTK HHSVAEEETL EKHL RPKQK PKNSKHCRDA KFEGTRIPHL VKKRRYQKQD SENKSEAKEQ SNDDYVLEKL FKKSVGVHSV MKHDAIMDGA SPDYV LVEA EANRVAQDAL KALRLSRQRC LGAVSGVPTW TGHRGISGAP AGKKSRFGKK RNSNFSVQHP SSTSPTEKCQ DGIMKK EGK DNVPEHFSGR AEDADSSSGP LASSSLLAKM RARNHLILPE RLESESGHLQ EASALLPTTE HDDLLVEMRN FIAFQAH TD GQASTREILQ EFESKLSASQ SCVFRELLRN LCTFHRTSGG EGIWKLKPEY C

UniProtKB: DNA excision repair protein ERCC-6

Macromolecule #20: DNA excision repair protein ERCC-8

• Macromolecule: Name: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 44.10716 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV QLCDLKSGSC SHILQGHRQE ILAVSWSPRY DYILATASAD SRVKLWDVRR ASGCLITLDQ HNGKKSQAVE SA NTAHNGK VNGLCFTSDG LHLLTVGTDN RMRLWNSSNG ENTLVNYGKV CNNSKKGLKF TVSCGCSSEF VFVPYGSTIA VYT VYSGEQ ITMLKGHYKT VDCCVFQSNF QELYSGSRDC NILAWVPSLY EPVPDDDETT TKSQLNPAFE DAWSSSDEEG

UniProtKB: DNA excision repair protein ERCC-8

Macromolecule #21: DNA damage-binding protein 1

• Macromolecule: Name: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 127.097469 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNG VVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSGAFKEGS LRIIRNGIGI HEHA SIDLP GIKGLWPLRS DPNRETDDTL VLSFVGQTRV LMLNGEEVEE TELMGFVDDQ QTFFCGNVAH QQLIQITSAS VRLVS QEPK ALVSEWKEPQ AKNISVASCN SSQVVVAVGR ALYYLQIHPQ ELRQISHTEM EHEVACLDIT PLGDSNGLSP LCAIGL WTD ISARILKLPS FELLHKEMLG GEIIPRSILM TTFESSHYLL CALGDGALFY FGLNIETGLL SDRKKVTLGT QPTVLRT FR SLSTTNVFAC SDRPTVIYSS NHKLVFSNVN LKEVNYMCPL NSDGYPDSLA LANNSTLTIG TIDEIQKLHI RTVPLYES P RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSASTQAL SSSVSSSKLF SSSTAPHETS FGEEVEVHNL LIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKTKGD FILVGDLMRS VLLLAYKPME GNFEEIARDF NPNWMSAVEI L DDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVGLF HLGEFVNVFC HGSLVMQNLG ETSTPTQGSV LFGTVNGMIG LV TSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDISRPKMQE VVANLQYDDG SGM KREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1

Macromolecule #15: NTS

• Macromolecule: Name: NTS / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 16.027309 KDa

Sequence

String:

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

Macromolecule #16: TS

• Macromolecule: Name: TS / type: dna / ID: 16 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.824121 KDa

Sequence

String:

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

Macromolecule #22: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 22 / Number of copies: 11 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #23: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 23 / Number of copies: 2 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #24: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 24 / Number of copies: 1 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

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

Macromolecule #25: BERYLLIUM TRIFLUORIDE ION

• Macromolecule: Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 25 / Number of copies: 1 / Formula: BEF
• Molecular weight: Theoretical: 66.007 Da

Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS GLACIOS
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.6 e/Ų
• Electron beam: Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

Image processing

• Startup model: Type of model: OTHER
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113958
• Initial angle assignment: Type: PROJECTION MATCHING
• Final angle assignment: Type: PROJECTION MATCHING