EMDB-13016: Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5)

Basic information

• Entry: Database: EMDB / ID: EMD-13016
• Title: Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5)
• Map data: The main map.

Sample

• Complex: Transcribing Pol II bound to TRC factors, SPT6 and PAF.
  • Complex: DNA-directed RNA polymerase with RNA_pol_L_2 and RNA polymerase
    • Protein or peptide: x 12 types
  • Complex: Supplementary proteins
    • Protein or peptide: x 12 types
  • Complex: NTS, RNA, TS
    • DNA: x 2 types
    • RNA: x 1 types
  • Complex: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: x 1 types
• Ligand: x 2 types

• Keywords: transcription / DNA repair / ubiquitin

Function / homology

Function:

Prolactin receptor signaling / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / negative regulation of double-strand break repair via nonhomologous end joining / Gap-filling DNA repair synthesis and ligation in TC-NER / blastocyst growth / regulation of transcription-coupled nucleotide-excision repair / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / positive regulation of mRNA 3'-end processing / Degradation of DVL / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / nucleotide-excision repair complex / mRNA decay by 3' to 5' exoribonuclease / Degradation of beta-catenin by the destruction complex / Cdc73/Paf1 complex / regulation of isotype switching / inner cell mass cell differentiation / negative regulation of granulocyte differentiation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of muscle cell differentiation / eukaryotic initiation factor 4E binding / regulation of mRNA export from nucleus / endodermal cell fate commitment / Interleukin-1 signaling / : / negative regulation of myeloid cell differentiation / anaphase-promoting complex / GLI3 is processed to GLI3R by the proteasome / positive regulation of cell cycle G1/S phase transition / trophectodermal cell differentiation / blastocyst hatching / Neddylation / regulation of transcription elongation by RNA polymerase II / regulation of mRNA processing / cullin-RING-type E3 NEDD8 transferase / DNA protection / B-WICH complex / cullin-RING ubiquitin ligase complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / regulation of DNA damage checkpoint / nucleosome organization / Cul7-RING ubiquitin ligase complex / 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 / KEAP1-NFE2L2 pathway / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of nucleotide-excision repair / 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 / blastocyst formation / photoreceptor cell maintenance / Cul4-RING E3 ubiquitin ligase complex / positive regulation of protein autoubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / UV-damage excision repair / mRNA 3'-end processing / protein neddylation / positive regulation of DNA-templated transcription, elongation / response to UV-B / RNA polymerase binding / NEDD8 ligase activity / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / biological process involved in interaction with symbiont

Domain/homology:

UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / Paf1 complex subunit Cdc73, N-terminal domain / Paf1 complex subunit CDC73 N-terminal / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / : / HHH domain 9 / HHH domain / Leo1-like protein / Leo1-like protein / RNA polymerase II associated factor Paf1 / Paf1 / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / RNA pol II accessory factor, Cdc73 family, C-terminal / : / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / : / Tex central region-like / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / Tetratricopeptide repeat / RNA-binding domain, S1 / ENTH/VHS / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Tetratricopeptide repeat / Cullin protein neddylation domain / RuvA domain 2-like / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / 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 / Tetratricopeptide repeat / 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 / S1 domain profile. / 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

Component:

RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB9 / E3 ubiquitin-protein ligase RBX1 / DNA excision repair protein ERCC-6 / DNA excision repair protein ERCC-8 / Cullin-4A / DNA damage-binding protein 1 / UV-stimulated scaffold protein A / Parafibromin / RNA polymerase-associated protein CTR9 homolog / Transcription elongation factor SPT6 / RNA polymerase II-associated factor 1 homolog / RNA polymerase-associated protein LEO1 / Superkiller complex protein 8

• Biological species: Sus scrofa (pig) / Homo sapiens (human) / Mus musculus (house mouse)
• Method: single particle reconstruction / cryo EM / Resolution: 3.0 Å
• Authors: Kokic G / Cramer P

Funding support

Germany, 2 items

Organization	Grant number	Country
German Research Foundation (DFG)	EXC 2067/1 39072994, SFB860, SPP2191	Germany
European Research Council (ERC)	882357	Germany

• Citation: Journal: Nature / Year: 2021; Title: Structural basis of human transcription-DNA repair coupling.; Authors: Goran Kokic / Felix R Wagner / Aleksandar Chernev / Henning Urlaub / Patrick Cramer / ; Abstract: Transcription-coupled DNA repair removes bulky DNA lesions from the genome and protects cells against ultraviolet (UV) irradiation. Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4 and UV-stimulated scaffold protein A (UVSSA). Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published data, the structures provide a model for transcription-repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, EC, uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4 spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4 lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired DNA.

History

Deposition	May 31, 2021	-
Header (metadata) release	Oct 6, 2021	-
Map release	Oct 6, 2021	-
Update	Jul 17, 2024	-
Current status	Jul 17, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_13016.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: The main map.
• Voxel size: X=Y=Z: 1.05 Å

Density

Contour Level	By AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum	-0.116809994 - 0.16665676
Average (Standard dev.)	0.00007193676 (±0.002828977)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 420 420 420 Spacing 420 420 420
Cell	A=B=C: 440.99997 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.05	1.05	1.05
M x/y/z	420	420	420
origin x/y/z	0.000	0.000	0.000
length x/y/z	441.000	441.000	441.000
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	29	29	0
NX/NY/NZ	140	137	200
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	420	420	420
D min/max/mean	-0.117	0.167	0.000

Supplemental data

Mask #1

• File: emd_13016_msk_1.map

Mask #2

• File: emd_13016_msk_2.map

Mask #3

• File: emd_13016_msk_3.map

Mask #4

• File: emd_13016_msk_4.map

Mask #5

• File: emd_13016_msk_5.map

Mask #6

• File: emd_13016_msk_6.map

Additional map: Half map corresponding to the map focused refined...

• File: emd_13016_additional_1.map
• Annotation: Half map corresponding to the map focused refined on CRL4CSA-CSB. This map was resampled while making the main map.

Additional map: Half map corresponding to the map focused refined on PAF.

• File: emd_13016_additional_10.map
• Annotation: Half map corresponding to the map focused refined on PAF.

Additional map: Half map corresponding to the map focused refined on SPT6.

• File: emd_13016_additional_11.map
• Annotation: Half map corresponding to the map focused refined on SPT6.

Additional map: Half map corresponding to the map focused refined on SPT6.

• File: emd_13016_additional_12.map
• Annotation: Half map corresponding to the map focused refined on SPT6.

Additional map: Half map corresponding to the map focused refined...

• File: emd_13016_additional_2.map
• Annotation: Half map corresponding to the map focused refined on CRL4CSA-CSB. This map was resampled while making the main map.

Additional map: Half map corresponding to the map focused refined...

• File: emd_13016_additional_3.map
• Annotation: Half map corresponding to the map focused refined on CRL4CSA-CSB. This map was not resampled.

Additional map: Half map corresponding to the map focused refined...

• File: emd_13016_additional_4.map
• Annotation: Half map corresponding to the map focused refined on CRL4CSA-CSB. This map was not resampled.

Additional map: Half map corresponding to the map focused refined on PAF.

• File: emd_13016_additional_5.map
• Annotation: Half map corresponding to the map focused refined on PAF.

Additional map: Half map corresponding to the map focused refined on Pol II.

• File: emd_13016_additional_6.map
• Annotation: Half map corresponding to the map focused refined on Pol II.

Additional map: Half map corresponding to the map focused refined on CSA-DDB1-CSB.

• File: emd_13016_additional_7.map
• Annotation: Half map corresponding to the map focused refined on CSA-DDB1-CSB.

Additional map: Half map corresponding to the map focused refined on Pol II.

• File: emd_13016_additional_8.map
• Annotation: Half map corresponding to the map focused refined on Pol II.

Additional map: Half map corresponding to the map focused refined on CSA-DDB1-CSB.

• File: emd_13016_additional_9.map
• Annotation: Half map corresponding to the map focused refined on CSA-DDB1-CSB.

Half map: Half map corresponding to the main map.

• File: emd_13016_half_map_1.map
• Annotation: Half map corresponding to the main map.

Half map: Half map corresponding to the main map.

• File: emd_13016_half_map_2.map
• Annotation: Half map corresponding to the main map.

Sample components

Entire : Transcribing Pol II bound to TRC factors, SPT6 and PAF.

• Entire: Name: Transcribing Pol II bound to TRC factors, SPT6 and PAF.

Components

• Complex: Transcribing Pol II bound to TRC factors, SPT6 and PAF.
  • Complex: DNA-directed RNA polymerase with RNA_pol_L_2 and RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3
    • Protein or peptide: RPOL4c domain-containing protein
    • Protein or peptide: DNA-directed RNA polymerase II subunit E
    • Protein or peptide: DNA-directed RNA polymerase II subunit F
    • 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: RNA_pol_L_2 domain-containing protein
    • Protein or peptide: RNA polymerase II subunit K
  • Complex: Supplementary proteins
    • Protein or peptide: Transcription elongation factor SPT6
    • Protein or peptide: LEO1 helix
    • Protein or peptide: RNA polymerase-associated protein CTR9 homolog
    • Protein or peptide: RNA polymerase-associated protein LEO1
    • Protein or peptide: RNA polymerase II-associated factor 1 homolog
    • Protein or peptide: WD repeat-containing protein 61
    • Protein or peptide: Parafibromin
    • Protein or peptide: DNA excision repair protein ERCC-8
    • Protein or peptide: DNA excision repair protein ERCC-6
    • Protein or peptide: UV-stimulated scaffold protein A
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Cullin-4A
  • Complex: NTS, RNA, TS
    • DNA: NTS
    • RNA: RNA
    • DNA: TS
  • Complex: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
• Ligand: ZINC ION
• Ligand: MAGNESIUM ION

Supramolecule #1: Transcribing Pol II bound to TRC factors, SPT6 and PAF.

• Supramolecule: Name: Transcribing Pol II bound to TRC factors, SPT6 and PAF.; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#28

Supramolecule #2: DNA-directed RNA polymerase with RNA_pol_L_2 and RNA polymerase

• Supramolecule: Name: DNA-directed RNA polymerase with RNA_pol_L_2 and RNA polymerase; type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#12
• Source (natural): Organism: Sus scrofa (pig)

Supramolecule #3: Supplementary proteins

• Supramolecule: Name: Supplementary proteins / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13, #16-#17, #19-#27
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #4: NTS, RNA, TS

• Supramolecule: Name: NTS, RNA, TS / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #14-#15, #18
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #5: E3 ubiquitin-protein ligase RBX1

• Supramolecule: Name: E3 ubiquitin-protein ligase RBX1 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #28
• Source (natural): Organism: Mus musculus (house mouse)

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
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 217.450078 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 SYSPTSPNYS PTSPNYTPTS P SYSPTSPS YSPTSPNYTP TSPNYSPTSP SYSPTSPSYS PTSPSYSPSS PRYTPQSPTY TPSSPSYSPS SPSYSPTSPK YT PTSPSYS PSSPEYTPTS PKYSPTSPKY SPTSPKYSPT SPTYSPTTPK YSPTSPTYSP TSPVYTPTSP KYSPTSPTYS PTS PKYSPT SPTYSPTSPK GSTYSPTSPG YSPTSPTYSL TSPAISPDDS DEEN

UniProtKB: DNA-directed RNA polymerase II subunit RPB1

Macromolecule #2: DNA-directed RNA polymerase subunit beta

• Macromolecule: Name: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
• Source (natural): Organism: Sus scrofa (pig)
• Molecular weight: Theoretical: 134.041422 KDa

Sequence

String:

MYDADEDMQY DEDDDEITPD LWQEACWIVI SSYFDEKGLV RQQLDSFDEF IQMSVQRIVE DAPPIDLQAE AQHASGEVEE PPRYLLKFE QIYLSKPTHW ERDGAPSPMM PNEARLRNLT YSAPLYVDIT KTVIKEGEEQ LQTQHQKTFI GKIPIMLRST Y CLLNGLTD RDLCELNECP LDPGGYFIIN GSEKVLIAQE KMATNTVYVF AKKDSKYAYT GECRSCLENS SRPTSTIWVS ML ARGGQGA KKSAIGQRIV ATLPYIKQEV PIIIVFRALG FVSDRDILEH IIYDFEDPEM MEMVKPSLDE AFVIQEQNVA LNF IGSRGA KPGVTKEKRI KYAKEVLQKE MLPHVGVSDF CETKKAYFLG YMVHRLLLAA LGRRELDDRD HYGNKRLDLA GPLL AFLFR GMFKNLLKEV RIYAQKFIDR GKDFNLELAI KTRIISDGLK YSLATGNWGD QKKAHQARAG VSQVLNRLTF ASTLS HLRR LNSPIGRDGK LAKPRQLHNT LWGMVCPAET PEGHAVGLVK NLALMAYISV GSQPSPILEF LEEWSMENLE EISPAA IAD ATKIFVNGCW VGIHKDPEQL MNTLRKLRRQ MDIIVSEVSM IRDIREREIR IYTDAGRICR PLLIVEKQKL LLKKRHI DQ LKEREYNNYS WQDLVASGVV EYIDTLEEET VMLAMTPDDL QEKEVAYCST YTHCEIHPSM ILGVCASIIP FPDHNQSP R NTYQSAMGKQ AMGVYITNFH VRMDTLAHVL YYPQKPLVTT RSMEYLRFRE LPAGINSIVA IASYTGYNQE DSVIMNRSA VDRGFFRSVF YRSYKEQESK KGFDQEEVFE KPTRETCQGM RHAIYDKLDD DGLIAPGVRV SGDDVIIGKT VTLPENEDEL EGTNRRYTK RDCSTFLRTS ETGIVDQVMV TLNQEGYKFC KIRVRSVRIP QIGDKFASRH GQKGTCGIQY RQEDMPFTCE G ITPDIIIN PHAIPSRMTI GHLIECLQGK VSANKGEIGD ATPFNDAVNV QKISNLLSDY GYHLRGNEVL YNGFTGRKIT SQ IFIGPTY YQRLKHMVDD KIHSRARGPI QILNRQPMEG RSRDGGLRFG EMERDCQIAH GAAQFLRERL FEASDPYQVH VCN LCGIMA IANTRTHTYE CRGCRNKTQI SLVRMPYACK LLFQELMSMS IAPRMMSV

UniProtKB: DNA-directed RNA polymerase subunit beta

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: 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 #4: RPOL4c domain-containing protein

• Macromolecule: Name: RPOL4c domain-containing protein / type: protein_or_peptide / ID: 4 / 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 #5: DNA-directed RNA polymerase II subunit E

• Macromolecule: Name: DNA-directed RNA polymerase II subunit E / type: protein_or_peptide / ID: 5 / 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 #6: DNA-directed RNA polymerase II subunit F

• Macromolecule: Name: DNA-directed RNA polymerase II subunit F / type: protein_or_peptide / ID: 6 / 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 #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: 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 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: 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 #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: 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 #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: 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 #11: RNA_pol_L_2 domain-containing protein

• Macromolecule: Name: RNA_pol_L_2 domain-containing protein / type: protein_or_peptide / ID: 11 / 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 #12: RNA polymerase II subunit K

• Macromolecule: Name: RNA polymerase II subunit K / type: protein_or_peptide / ID: 12 / 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, I and III subunit K

Macromolecule #13: Transcription elongation factor SPT6

• Macromolecule: Name: Transcription elongation factor SPT6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 199.602969 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

SNAMSDFVES EAEESEEEYN DEGEVVPRVT KKFVEEEDDD EEEEEENLDD QDEQGNLKGF INDDDDEDEG EEDEGSDSGD SEDDVGHKK RKRTSFDDRL EDDDFDLIEE NLGVKVKRGQ KYRRVKKMSD DEDDDEEEYG KEEHEKEAIA EEIFQDGEGE E GQEAMEAP MAPPEEEEED DEESDIDDFI VDDDGQPLKK PKWRKKLPGY TDAALQEAQE IFGVDFDYDE FEKYNEYDEE LE EEYEYED DEAEGEIRVR PKKTTKKRVS RRSIFEMYEP SELESSHLTD QDNEIRATDL PERFQLRSIP VKGAEDDELE EEA DWIYRN AFATPTISLQ ESCDYLDRGQ PASSFSRKGP STIQKIKEAL GFMRNQHFEV PFIAFYRKEY VEPELHINDL WRVW QWDEK WTQLRIRKEN LTRLFEKMQA YQYEQISADP DKPLADGIRA LDTTDMERLK DVQSMDELKD VYNHFLLYYG RDIPK MQNA AKASRKKLKR VREEGDEEGE GDEAEDEEQR GPELKQASRR DMYTICQSAG LDGLAKKFGL TPEQFGENLR DSYQRH ETE QFPAEPLELA KDYVCSQFPT PEAVLEGARY MVALQIAREP LVRQVLRQTF QERAKLNITP TKKGRKDVDE AHYAYSF KY LKNKPVKELR DDQFLKICLA EDEGLLTTDI SIDLKGVEGY GNDQTYFEEI KQFYYRDEFS HQVQEWNRQR TMAIERAL Q QFLYVQMAKE LKNKLLAEAK EYVIKACSRK LYNWLRVAPY RPDQQVEEDD DFMDENQGKG IRVLGIAFSS ARDHPVFCA LVNGEGEVTD FLRLPHFTKR RTAWREEERE KKAQDIETLK KFLLNKKPHV VTVAGENRDA QMLIEDVKRI VHELDQGQQL SSIGVELVD NELAILYMNS KKSEAEFRDY PPVLRQAVSL ARRIQDPLIE FAQVCSSDED ILCLKFHPLQ EHVVKEELLN A LYCEFINR VNEVGVDVNR AIAHPYSQAL IQYVCGLGPR KGTHLLKILK QNNTRLESRT QLVTMCHMGP KVFMNCAGFL KI DTASLGD STDSYIEVLD GSRVHPETYE WARKMAVDAL EYDESAEDAN PAGALEEILE NPERLKDLDL DAFAEELERQ GYG DKHITL YDIRAELSCR YKDLRTAYRS PNTEEIFNML TKETPETFYI GKLIICNVTG IAHRRPQGES YDQAIRNDET GLWQ CPFCQ QDNFPELSEV WNHFDSGSCP GQAIGVKTRL DNGVTGFIPT KFLSDKVVKR PEERVKVGMT VHCRIMKIDI EKFSA DLTC RTSDLMDRNN EWKLPKDTYY DFDAEAADHK QEEDMKRKQQ RTTYIKRVIA HPSFHNINFK QAEKMMETMD QGDVII RPS SKGENHLTVT WKVSDGIYQH VDVREEGKEN AFSLGATLWI NSEEFEDLDE IVARYVQPMA SFARDLLNHK YYQDCSG GD RKKLEELLIK TKKEKPTFIP YFICACKELP GKFLLGYQPR GKPRIEYVTV TPEGFRYRGQ IFPTVNGLFR WFKDHYQD P VPGITPSSSS RTRTPASINA TPANINLADL TRAVNALPQN MTSQMFSAIA AVTGQGQNPN ATPAQWASSQ YGYGGSGGG SSAYHVFPTP AQQPVATPLM TPSYSYTTPS QPITTPQYHQ LQASTTPQSA QAQPQPSSSS RQRQQQPKSN SHAAIDWGKM AEQWLQEKE AERRKQKQRL TPRPSPSPMI ESTPMSIAGD ATPLLDEMDR

UniProtKB: Transcription elongation factor SPT6

Macromolecule #16: LEO1 helix

• Macromolecule: Name: LEO1 helix / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 3.422209 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

Macromolecule #17: RNA polymerase-associated protein CTR9 homolog

• Macromolecule: Name: RNA polymerase-associated protein CTR9 homolog / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 134.510203 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MSRGSIEIPL RDTDEVIELD FDQLPEGDEV ISILKQEHTQ LHIWIALALE YYKQGKTEEF VKLLEAARID GNLDYRDHEK DQMTCLDTL AAYYVQQARK EKNKDNKKDL ITQATLLYTM ADKIIMYDQN HLLGRACFCL LEGDKMDQAD AQFHFVLNQS P NNIPALLG KACISFNKKD YRGALAYYKK ALRTNPGCPA EVRLGMGHCF VKLNKLEKAR LAFSRALELN SKCVGALVGL AV LELNNKE ADSIKNGVQL LSRAYTIDPS NPMVLNHLAN HFFFKKDYSK VQHLALHAFH NTEVEAMQAE SCYQLARSFH VQE DYDQAF QYYYQATQFA SSSFVLPFFG LGQMYIYRGD KENASQCFEK VLKAYPNNYE TMKILGSLYA ASEDQEKRDI AKGH LKKVT EQYPDDVEAW IELAQILEQT DIQGALSAYG TATRILQEKV QADVPPEILN NVGALHFRLG NLGEAKKYFL ASLDR AKAE AEHDEHYYNA ISVTTSYNLA RLYEAMCEFH EAEKLYKNIL REHPNYVDCY LRLGAMARDK GNFYEASDWF KEALQI NQD HPDAWSLIGN LHLAKQEWGP GQKKFERILK QPSTQSDTYS MLALGNVWLQ TLHQPTRDRE KEKRHQDRAL AIYKQVL RN DAKNLYAANG IGAVLAHKGY FREARDVFAQ VREATADISD VWLNLAHIYV EQKQYISAVQ MYENCLRKFY KHQNTEVV L YLARALFKCG KLQECKQTLL KARHVAPSDT VLMFNVALVL QRLATSVLKD EKSNLKEVLN AVKELELAHR YFSYLSKVG DKMRFDLALA ATEARQCSDL LSQAQYHVAR ARKQDEEERE LRAKQEQEKE LLRQKLLKEQ EEKRLREKEE QKKLLEQRAQ YVEKTKNIL MFTGETEATK EKKRGGGGGR RSKKGGEFDE FVNDDTDDDL PISKKKKRRK GSGSEQEGED EEGGERKKKK R RRHPKGEE GSDDDETENG PKPKKRRPPK AEKKKAPKPE RLPPSMKGKI KSKAIISSSD DSSDEDKLKI ADEGHPRNSN SN SDSDEDE QRKKCASSES DSDENQNKSG SEAGSPRRPR RQRSDQDSDS DQPSRKRRPS GSEQSDNESV QSGRSHSGVS END SRPASP SAESDHESER GSDNEGSGQG SGNESEPEGS NNEASDRGSE HGSDDSDENL YFQ

UniProtKB: RNA polymerase-associated protein CTR9 homolog

Macromolecule #19: RNA polymerase-associated protein LEO1

• Macromolecule: Name: RNA polymerase-associated protein LEO1 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 75.514172 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MADMEDLFGS DADSEAERKD SDSGSDSDSD QENAASGSNA SGSESDQDER GDSGQPSNKE LFGDDSEDEG ASHHSGSDNH SERSDNRSE ASERSDHEDN DPSDVDQHSG SEAPNDDEDE GHRSDGGSHH SEAEGSEKAH SDDEKWGRED KSDQSDDEKI Q NSDDEERA QGSDEDKLQN SDDDEKMQNT DDEERPQLSD DERQQLSEEE KANSDDERPV ASDNDDEKQN SDDEEQPQLS DE EKMQNSD DERPQASDEE HRHSDDEEEQ DHKSESARGS DSEDEVLRMK RKNAIASDSE ADSDTEVPKD NSGTMDLFGG ADD ISSGSD GEDKPPTPGQ PVDENGLPQD QQEEEPIPET RIEVEIPKVN TDLGNDLYFV KLPNFLSVEP RPFDPQYYED EFED EEMLD EEGRTRLKLK VENTIRWRIR RDEEGNEIKE SNARIVKWSD GSMSLHLGNE VFDVYKAPLQ GDHNHLFIRQ GTGLQ GQAV FKTKLTFRPH STDSATHRKM TLSLADRCSK TQKIRILPMA GRDPECQRTE MIKKEEERLR ASIRRESQQR RMREKQ HQR GLSASYLEPD RYDEEEEGEE SISLAAIKNR YKGGIREERA RIYSSDSDEG SEEDKAQRLL KAKKLTSDEE GEPSGKR KA EDDDKANKKH KKYVISDEEE EDDD

UniProtKB: RNA polymerase-associated protein LEO1

Macromolecule #20: RNA polymerase II-associated factor 1 homolog

• Macromolecule: Name: RNA polymerase II-associated factor 1 homolog / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 60.052672 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MAPTIQTQAQ REDGHRPNSH RTLPERSGVV CRVKYCNSLP DIPFDPKFIT YPFDQNRFVQ YKATSLEKQH KHDLLTEPDL GVTIDLINP DTYRIDPNVL LDPADEKLLE EEIQAPTSSK RSQQHAKVVP WMRKTEYIST EFNRYGISNE KPEVKIGVSV K QQFTEEEI YKDRDSQITA IEKTFEDAQK SISQHYSKPR VTPVEVMPVF PDFKMWINPC AQVIFDSDPA PKDTSGAAAL EM MSQAMIR GMMDEEGNQF VAYFLPVEET LKKRKRDQEE EMDYAPDDVY DYKIAREYNW NVKNKASKGY EENYFFIFRE GDG VYYNEL ETRVRLSKRR AKAGVQSGTN ALLVVKHRDM NEKELEAQEA RKAQLENHEP EEEEEEEMET EEKEAGGSDE EQEK GSSSE KEGSEDEHSG SESEREEGDR DEASDKSGSG EDESSEDEAR AARDKEEIFG SDADSEDDAD SDDEDRGQAQ GGSDN DSDS GSNGGGQRSR SHSRSASPFP SGSEHSAQED GSEAAASDSS EADSDSD

UniProtKB: RNA polymerase II-associated factor 1 homolog

Macromolecule #21: WD repeat-containing protein 61

• Macromolecule: Name: WD repeat-containing protein 61 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 33.617465 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MTNQYGILFK QEQAHDDAIW SVAWGTNKKE NSETVVTGSL DDLVKVWKWR DERLDLQWSL EGHQLGVVSV DISHTLPIAA SSSLDAHIR LWDLENGKQI KSIDAGPVDA WTLAFSPDSQ YLATGTHVGK VNIFGVESGK KEYSLDTRGK FILSIAYSPD G KYLASGAI DGIINIFDIA TGKLLHTLEG HAMPIRSLTF SPDSQLLVTA SDDGYIKIYD VQHANLAGTL SGHASWVLNV AF CPDDTHF VSSSSDKSVK VWDVGTRTCV HTFFDHQDQV WGVKYNGNGS KIVSVGDDQE IHIYDCPI

UniProtKB: Superkiller complex protein 8

Macromolecule #22: Parafibromin

• Macromolecule: Name: Parafibromin / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 60.673539 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MADVLSVLRQ YNIQKKEIVV KGDEVIFGEF SWPKNVKTNY VVWGTGKEGQ PREYYTLDSI LFLLNNVHLS HPVYVRRAAT ENIPVVRRP DRKDLLGYLN GEASTSASID RSAPLEIGLQ RSTQVKRAAD EVLAEAKKPR IEDEECVRLD KERLAARLEG H KEGIVQTE QIRSLSEAMS VEKIAAIKAK IMAKKRSTIK TDLDDDITAL KQRSFVDAEV DVTRDIVSRE RVWRTRTTIL QS TGKNFSK NIFAILQSVK AREEGRAPEQ RPAPNAAPVD PTLRTKQPIP AAYNRYDQER FKGKEETEGF KIDTMGTYHG MTL KSVTEG ASARKTQTPA AQPVPRPVSQ ARPPPNQKKG SRTPIIIIPA ATTSLITMLN AKDLLQDLKF VPSDEKKKQG CQRE NETLI QRRKDQMQPG GTAISVTVPY RVVDQPLKLM PQDWDRVVAV FVQGPAWQFK GWPWLLPDGS PVDIFAKIKA FHLKY DEVR LDPNVQKWDV TVLELSYHKR HLDRPVFLRF WETLDRYMVK HKSHLRF

UniProtKB: Parafibromin

Macromolecule #23: DNA excision repair protein ERCC-8

• Macromolecule: Name: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 23 / 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 #24: DNA excision repair protein ERCC-6

• Macromolecule: Name: DNA excision repair protein ERCC-6 / type: protein_or_peptide / ID: 24 / 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: 168.973812 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

SNAMPNEGIP HSSQTQEQDC LQSQPVSNNE EMAIKQESGG DGEVEEYLSF RSVGDGLSTS AVGCASAAPR RGPALLHIDR HQIQAVEPS AQALELQGLG VDVYDQDVLE QGVLQQVDNA IHEASRASQL VDVEKEYRSV LDDLTSCTTS LRQINKIIEQ L SPQAATSR DINRKLDSVK RQKYNKEQQL KKITAKQKHL QAILGGAEVK IELDHASLEE DAEPGPSSLG SMLMPVQETA WE ELIRTGQ MTPFGTQIPQ KQEKKPRKIM LNEASGFEKY LADQAKLSFE RKKQGCNKRA ARKAPAPVTP PAPVQNKNKP NKK ARVLSK KEERLKKHIK KLQKRALQFQ GKVGLPKARR PWESDMRPEA EGDSEGEESE YFPTEEEEEE EDDEVEGAEA DLSG DGTDY ELKPLPKGGK RQKKVPVQEI DDDFFPSSGE EAEAASVGEG GGGGRKVGRY RDDGDEDYYK QRLRRWNKLR LQDKE KRLK LEDDSEESDA EFDEGFKVPG FLFKKLFKYQ QTGVRWLWEL HCQQAGGILG DEMGLGRTIQ IIAFLAGLSY SKIRTR GSN YRFEGLGPTV IVCPTTVMHQ WVKEFHTWWP PFRVAILHET GSYTHKKEKL IRDVAHCHGI LITSYSYIRL MQDDISR YD WHYVILDEGH KIRNPNAAVT LACKQFRTPH RIILSGSPMQ NNLRELWSLF DFIFPGKLGT LPVFMEQFSV PITMGGYS N ASPVQVKTAY KCACVLRDTI NPYLLRRMKS DVKMSLSLPD KNEQVLFCRL TDEQHKVYQN FVDSKEVYRI LNGEMQIFS GLIALRKICN HPDLFSGGPK NLKGLPDDEL EEDQFGYWKR SGKMIVVESL LKIWHKQGQR VLLFSQSRQM LDILEVFLRA QKYTYLKMD GTTTIASRQP LITRYNEDTS IFVFLLTTRV GGLGVNLTGA NRVVIYDPDW NPSTDTQARE RAWRIGQKKQ V TVYRLLTA GTIEEKIYHR QIFKQFLTNR VLKDPKQRRF FKSNDLYELF TLTSPDASQS TETSAIFAGT GSDVQTPKCH LK RRIQPAF GADHDVPKRK KFPASNISVN DATSSEEKSE AKGAEVNAVT SNRSDPLKDD PHMSSNVTSN DRLGEETNAV SGP EELSVI SGNGECSNSS GTGKTSMPSG DESIDEKLGL SYKRERPSQA QTEAFWENKQ MENNFYKHKS KTKHHSVAEE ETLE KHLRP KQKPKNSKHC RDAKFEGTRI PHLVKKRRYQ KQDSENKSEA KEQSNDDYVL EKLFKKSVGV HSVMKHDAIM DGASP DYVL VEAEANRVAQ DALKALRLSR QRCLGAVSGV PTWTGHRGIS GAPAGKKSRF GKKRNSNFSV QHPSSTSPTE KCQDGI MKK EGKDNVPEHF SGRAEDADSS SGPLASSSLL AKMRARNHLI LPERLESESG HLQEASALLP TTEHDDLLVE MRNFIAF QA HTDGQASTRE ILQEFESKLS ASQSCVFREL LRNLCTFHRT SGGEGIWKLK PEYC

UniProtKB: DNA excision repair protein ERCC-6

Macromolecule #25: UV-stimulated scaffold protein A

• Macromolecule: Name: UV-stimulated scaffold protein A / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 80.993945 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

SNAMDQKLSK LVEELTTSGE PRLNPEKMKE LKKICKSSEE QLSRAYRLLI AQLTQEHAEI RLSAFQIVEE LFVRSHQFRM LVVSNFQEF LELTLGTDPA QPLPPPREAA QRLRQATTRA VEGWNEKFGE AYKKLALGYH FLRHNKKVDF QDTNARSLAE R KREEEKQK HLDKIYQERA SQAEREMQEM SGEIESCLTE VESCFRLLVP FDFDPNPETE SLGMASGMSD ALRSSCAGQV GP CRSGTPD PRDGEQPCCS RDLPASAGHP RAGGGAQPSQ TATGDPSDED EDSDLEEFVR SHGLGSHKYT LDVELCSEGL KVQ ENEDNL ALIHAARDTL KLIRNKFLPA VCSWIQRFTR VGTHGGCLKR AIDLKAELEL VLRKYKELDI EPEGGERRRT EALG DAEED EDDEDFVEVP EKEGYEPHIP DHLRPEYGLE AAPEKDTVVR CLRTRTRMDE EVSDPTSAAA QLRQLRDHLP PPSSA SPSR ALPEPQEAQK LAAERARAPV VPYGVDLHYW GQELPTAGKI VKSDSQHRFW KPSEVEEEVV NADISEMLRS RHITFA GKF EPVQHWCRAP RPDGRLCERQ DRLKCPFHGK IVPRDDEGRP LDPEDRAREQ RRQLQKQERP EWQDPELMRD VEAATGQ DL GSSRYSGKGR GKKRRYPSLT NLKAQADTAR ARIGRKVFAK AAVRRVVAAM NRMDQKKHEK FSNQFNYALN

UniProtKB: UV-stimulated scaffold protein A

Macromolecule #26: DNA damage-binding protein 1

• Macromolecule: Name: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 127.369719 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

SNAMSYNYVV TAQKPTAVNG CVTGHFTSAE DLNLLIAKNT RLEIYVVTAE GLRPVKEVGM YGKIAVMELF RPKGESKDLL FILTAKYNA CILEYKQSGE SIDIITRAHG NVQDRIGRPS ETGIIGIIDP ECRMIGLRLY DGLFKVIPLD RDNKELKAFN I RLEELHVI DVKFLYGCQA PTICFVYQDP QGRHVKTYEV SLREKEFNKG PWKQENVEAE ASMVIAVPEP FGGAIIIGQE SI TYHNGDK YLAIAPPIIK QSTIVCHNRV DPNGSRYLLG DMEGRLFMLL LEKEEQMDGT VTLKDLRVEL LGETSIAECL TYL DNGVVF VGSRLGDSQL VKLNVDSNEQ GSYVVAMETF TNLGPIVDMC VVDLERQGQG QLVTCSGAFK EGSLRIIRNG IGIH EHASI DLPGIKGLWP LRSDPNRETD DTLVLSFVGQ TRVLMLNGEE VEETELMGFV DDQQTFFCGN VAHQQLIQIT SASVR LVSQ EPKALVSEWK EPQAKNISVA SCNSSQVVVA VGRALYYLQI HPQELRQISH TEMEHEVACL DITPLGDSNG LSPLCA IGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH YLLCALGDGA LFYFGLNIET GLLSDRKKVT LGTQPTV LR TFRSLSTTNV FACSDRPTVI YSSNHKLVFS NVNLKEVNYM CPLNSDGYPD SLALANNSTL TIGTIDEIQK LHIRTVPL Y ESPRKICYQE VSQCFGVLSS RIEVQDTSGG TTALRPSAST QALSSSVSSS KLFSSSTAPH ETSFGEEVEV HNLLIIDQH TFEVLHAHQF LQNEYALSLV SCKLGKDPNT YFIVGTAMVY PEEAEPKQGR IVVFQYSDGK LQTVAEKEVK GAVYSMVEFN GKLLASINS TVRLYEWTTE KELRTECNHY NNIMALYLKT KGDFILVGDL MRSVLLLAYK PMEGNFEEIA RDFNPNWMSA V EILDDDNF LGAENAFNLF VCQKDSAATT DEERQHLQEV GLFHLGEFVN VFCHGSLVMQ NLGETSTPTQ GSVLFGTVNG MI GLVTSLS ESWYNLLLDM QNRLNKVIKS VGKIEHSFWR SFHTERKTEP ATGFIDGDLI ESFLDISRPK MQEVVANLQY DDG SGMKRE ATADDLIKVV EELTRIH

UniProtKB: DNA damage-binding protein 1

Macromolecule #27: Cullin-4A

• Macromolecule: Name: Cullin-4A / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 88.086562 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

SNAMADEAPR KGSFSALVGR TNGLTKPAAL AAAPAKPGGA GGSKKLVIKN FRDRPRLPDN YTQDTWRKLH EAVRAVQSST SIRYNLEEL YQAVENLCSH KVSPMLYKQL RQACEDHVQA QILPFREDSL DSVLFLKKIN TCWQDHCRQM IMIRSIFLFL D RTYVLQNS TLPSIWDMGL ELFRTHIISD KMVQSKTIDG ILLLIERERS GEAVDRSLLR SLLGMLSDLQ VYKDSFELKF LE ETNCLYA AEGQRLMQER EVPEYLNHVS KRLEEEGDRV ITYLDHSTQK PLIACVEKQL LGEHLTAILQ KGLDHLLDEN RVP DLAQMY QLFSRVRGGQ QALLQHWSEY IKTFGTAIVI NPEKDKDMVQ DLLDFKDKVD HVIEVCFQKN ERFVNLMKES FETF INKRP NKPAELIAKH VDSKLRAGNK EATDEELERT LDKIMILFRF IHGKDVFEAF YKKDLAKRLL VGKSASVDAE KSMLS KLKH ECGAAFTSKL EGMFKDMELS KDIMVHFKQH MQNQSDSGPI DLTVNILTMG YWPTYTPMEV HLTPEMIKLQ EVFKAF YLG KHSGRKLQWQ TTLGHAVLKA EFKEGKKEFQ VSLFQTLVLL MFNEGDGFSF EEIKMATGIE DSELRRTLQS LACGKAR VL IKSPKGKEVE DGDKFIFNGE FKHKLFRIKI NQIQMKETVE EQVSTTERVF QDRQYQIDAA IVRIMKMRKT LGHNLLVS E LYNQLKFPVK PGDLKKRIES LIDRDYMERD KDNPNQYHYV A

UniProtKB: Cullin-4A

Macromolecule #28: E3 ubiquitin-protein ligase RBX1

• Macromolecule: Name: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 12.289977 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

Macromolecule #14: NTS

• Macromolecule: Name: NTS / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 14.494314 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)

Macromolecule #18: TS

• Macromolecule: Name: TS / type: dna / ID: 18 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 14.269129 KDa

Sequence

String:

(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 #15: RNA

• Macromolecule: Name: RNA / type: rna / ID: 15 / Number of copies: 1
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 14.490756 KDa

Sequence

String:

ACAUCAUAAC AUUUGAACAA GAAUAUAUAU ACAAAAUCGA GAGGA

Macromolecule #29: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 29 / Number of copies: 8 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #30: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 30 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Experimental details

Structure determination

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

Sample preparation

• Concentration: 0.3 mg/mL
• Buffer: pH: 7.5
• Grid: Model: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.4 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 81000
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: EMDB MAP
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION; Details: Different number of particles was used for different focused refined maps.; Number images used: 100000
• Initial angle assignment: Type: PROJECTION MATCHING
• Final angle assignment: Type: PROJECTION MATCHING