EMDB-61058: Paused elongation complex of mammalian RNA polymerase II with nuc...

Basic information

Entry

Database: EMDB / ID: EMD-61058

• Title: Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)

Sample

• Complex: RNA polymerase II in complex with DSIF, NELF, and nucleosome
  • Complex: RNA polymerase II
    • Protein or peptide: x 12 types
  • Complex: Spt4 and Spt5
    • Protein or peptide: x 2 types
  • Complex: Negative elongation factor (NELF)
    • Protein or peptide: x 4 types
  • Complex: Histone proteins
    • Protein or peptide: x 4 types
  • DNA: x 2 types
  • RNA: x 1 types
  • Protein or peptide: x 1 types
• Ligand: x 2 types

• Keywords: RNA polymerase / NELF / nucleosome / DNA / RNA / TFIIS / TRANSCRIPTION

Function / homology

Function:

NELF complex / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / regulation of transcription elongation by RNA polymerase II / pericentric heterochromatin formation / inner kinetochore / 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 / negative regulation of stem cell differentiation / muscle cell differentiation / nuclear lumen / positive regulation of DNA-templated transcription, elongation / oocyte maturation / Abortive elongation of HIV-1 transcript in the absence of Tat / nucleosomal DNA binding / transcription elongation-coupled chromatin remodeling / transcription factor TFIID complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / nucleus organization / spermatid development / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / single fertilization / negative regulation of tumor necrosis factor-mediated signaling pathway / Tat-mediated elongation of the HIV-1 transcript / transcription by RNA polymerase III / transcription by RNA polymerase I / Formation of HIV-1 elongation complex containing HIV-1 Tat / subtelomeric heterochromatin formation / negative regulation of megakaryocyte differentiation / RNA polymerase I complex / RNA polymerase III complex / protein localization to CENP-A containing chromatin / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II core promoter sequence-specific DNA binding / transcription-coupled nucleotide-excision repair / Replacement of protamines by nucleosomes in the male pronucleus / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / CENP-A containing nucleosome / RNA Polymerase II Transcription Elongation / Packaging Of Telomere Ends / Formation of RNA Pol II elongation complex / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase II Pre-transcription Events / embryo implantation / telomere organization / DNA-directed RNA polymerase activity / Inhibition of DNA recombination at telomere / DNA-directed RNA polymerase complex / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression

Domain/homology:

Negative elongation factor E / Negative elongation factor E, RNA recognition motif / Cofactor of BRCA1 / Cofactor of BRCA1 (COBRA1) / : / NELF-A N-terminal domain / TH1 protein / TH1 protein / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile. / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Transcription initiation Spt4 / Spt4 superfamily / TFIIS N-terminal domain profile. / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / TFIIS/LEDGF domain superfamily / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase 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

Component:

DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / Transcription elongation factor SPT5 / Histone H2A type 1-B/E / Histone H2B type 1-J / Negative elongation factor E / Transcription elongation factor A protein 1 / DNA-directed RNA polymerase II subunit RPB9 / Histone H4 / Transcription elongation factor SPT4 / Histone H3.3 / Negative elongation factor C/D / Negative elongation factor B / Negative elongation factor A

• Biological species: Sus scrofa (pig) / Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.4 Å
• Authors: Naganuma M / Kujirai T / Ehara H / Uejima T / Ito T / Goto M / Aoki M / Henmi M / Miyamoto-Kohno S / Shirouzu M / Kurumizaka H / Sekine S

Funding support

Japan, 9 items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	JP20H05690	Japan
Japan Society for the Promotion of Science (JSPS)	JP20H03201	Japan
Japan Society for the Promotion of Science (JSPS)	JP23H05475	Japan
Japan Society for the Promotion of Science (JSPS)	JPMJER1901	Japan
Japan Agency for Medical Research and Development (AMED)	JP23ama121009	Japan
Japan Society for the Promotion of Science (JSPS)	JP24H00062	Japan
Other private		Japan
Japan Society for the Promotion of Science (JSPS)	JP22K15033	Japan
Japan Society for the Promotion of Science (JSPS)	JP23K17392	Japan

• Citation: Journal: Sci Adv / Year: 2025; Title: Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome.; Authors: Masahiro Naganuma / Tomoya Kujirai / Haruhiko Ehara / Tamami Uejima / Tomoko Ito / Mie Goto / Mari Aoki / Masami Henmi / Sayako Miyamoto-Kohno / Mikako Shirouzu / Hitoshi Kurumizaka / Shun-Ichi Sekine / ; Abstract: The metazoan transcription elongation complex (EC) of RNA polymerase II (RNAPII) generally stalls between the transcription start site and the first (+1) nucleosome. This promoter-proximal pausing involves negative elongation factor (NELF), 5,6-dichloro-1-β-d-ribobenzimidazole sensitivity-inducing factor (DSIF), and transcription elongation factor IIS (TFIIS) and is critical for subsequent productive transcription elongation. However, the detailed pausing mechanism and the involvement of the +1 nucleosome remain enigmatic. Here, we report cryo-electron microscopy structures of ECs stalled on nucleosomal DNA. In the absence of TFIIS, the EC is backtracked/arrested due to conflicts between NELF and the nucleosome. We identified two alternative binding modes of NELF, one of which reveals a critical contact with the downstream DNA through the conserved NELF-E basic helix. Upon binding with TFIIS, the EC progressed to the nucleosome to establish a paused EC with a partially unwrapped nucleosome. This paused EC strongly restricts EC progression further downstream. These structures illuminate the mechanism of RNAPII pausing/stalling at the +1 nucleosome.

History

Deposition	Aug 2, 2024	-
Header (metadata) release	Feb 5, 2025	-
Map release	Feb 5, 2025	-
Update	Mar 19, 2025	-
Current status	Mar 19, 2025	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_61058.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.484 Å

Density

Contour Level	By AUTHOR: 0.013
Minimum - Maximum	-0.056044593 - 0.14907002
Average (Standard dev.)	0.00046130497 (±0.0053197066)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 240 240 240 Spacing 240 240 240
Cell	A=B=C: 356.16 Å α=β=γ: 90.0 °

Supplemental data

Additional map: NELF-focused map

• File: emd_61058_additional_1.map
• Annotation: NELF-focused map

Additional map: RNAPII-focused map

• File: emd_61058_additional_2.map
• Annotation: RNAPII-focused map

Additional map: Nucleosome-focused map

• File: emd_61058_additional_3.map
• Annotation: Nucleosome-focused map

Half map: #2

• File: emd_61058_half_map_1.map

Half map: #1

• File: emd_61058_half_map_2.map

Sample components

Entire : RNA polymerase II in complex with DSIF, NELF, and nucleosome

• Entire: Name: RNA polymerase II in complex with DSIF, NELF, and nucleosome

Components

• Complex: RNA polymerase II in complex with DSIF, NELF, and nucleosome
  • Complex: RNA polymerase II
    • 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: 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 polymerase II subunit RPB4
    • 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: RPB12
  • Complex: Spt4 and Spt5
    • Protein or peptide: Transcription elongation factor SPT4
    • Protein or peptide: Transcription elongation factor SPT5
  • Complex: Negative elongation factor (NELF)
    • Protein or peptide: Negative elongation factor A
    • Protein or peptide: Negative elongation factor B
    • Protein or peptide: Negative elongation factor C/D
    • Protein or peptide: Negative elongation factor E
  • Complex: Histone proteins
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
  • DNA: Non-template DNA (157-MER)
  • RNA: RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*CP*C)-3')
  • DNA: Template DNA (168-MER)
  • Protein or peptide: Transcription elongation factor A protein 1
• Ligand: ZINC ION
• Ligand: MAGNESIUM ION

Supramolecule #1: RNA polymerase II in complex with DSIF, NELF, and nucleosome

• Supramolecule: Name: RNA polymerase II in complex with DSIF, NELF, and nucleosome; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#26

Supramolecule #2: RNA polymerase II

• Supramolecule: Name: RNA polymerase II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#8, #14-#17
• Source (natural): Organism: Sus scrofa (pig)

Supramolecule #3: Spt4 and Spt5

• Supramolecule: Name: Spt4 and Spt5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #9-#10
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #4: Negative elongation factor (NELF)

• Supramolecule: Name: Negative elongation factor (NELF) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #23-#26
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #5: Histone proteins

• Supramolecule: Name: Histone proteins / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #19-#22
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: DNA-directed RNA polymerase subunit

• Macromolecule: Name: DNA-directed RNA polymerase subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
• 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 subunit

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: 30.997557 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 QSDV

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

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

• Macromolecule: Name: DNA-directed RNA polymerase II subunit E / type: protein_or_peptide / ID: 4 / 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 #5: DNA-directed RNA polymerase II subunit F

• Macromolecule: Name: DNA-directed RNA polymerase II subunit F / type: protein_or_peptide / ID: 5 / 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 #6: DNA-directed RNA polymerase II subunit RPB7

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 6 / 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 #7: 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: 7 / 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 #8: DNA-directed RNA polymerase II subunit RPB9

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 8 / 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 #9: Transcription elongation factor SPT4

• Macromolecule: Name: Transcription elongation factor SPT4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.297278 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SMALETVPKD LRHLRACLLC SLVKTIDQFE YDGCDNCDAY LQMKGNREMV YDCTSSSFDG IIAMMSPEDS WVSKWQRVSN FKPGVYAVS VTGRLPQGIV RELKSRGVAY KSRDTAIKT

UniProtKB: Transcription elongation factor SPT4

Macromolecule #10: Transcription elongation factor SPT5

• Macromolecule: Name: Transcription elongation factor SPT5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 123.297812 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSDSEDSNFS EEEDSERSSD GEEAEVDEER RSAAGSEKEE EPEDEEEEEE EEEYDEEEEE EDDDRPPKKP RHGGFILDEA DVDDEYEDE DQWEDGAEDI LEKEEIEASN IDNVVLDEDR SGARRLQNLW RDQREEELGE YYMKKYAKSS VGETVYGGSD E LSDDITQQ QLLPGVKDPN LWTVKCKIGE ERATAISLMR KFIAYQFTDT PLQIKSVVAP EHVKGYIYVE AYKQTHVKQA IE GVGNLRL GYWNQQMVPI KEMTDVLKVV KEVANLKPKS WVRLKRGIYK DDIAQVDYVE PSQNTISLKM IPRIDYDRIK ARM SLKDWF AKRKKFKRPP QRLFDAEKIR SLGGDVASDG DFLIFEGNRY SRKGFLFKSF AMSAVITEGV KPTLSELEKF EDQP EGIDL EVVTESTGKE REHNFQPGDN VEVCEGELIN LQGKILSVDG NKITIMPKHE DLKDMLEFPA QELRKYFKMG DHVKV IAGR FEGDTGLIVR VEENFVILFS DLTMHELKVL PRDLQLCSET ASGVDVGGQH EWGELVQLDP QTVGVIVRLE RETFQV LNM YGKVVTVRHQ AVTRKKDNRF AVALDSEQNN IHVKDIVKVI DGPHSGREGE IRHLFRSFAF LHCKKLVENG GMFVCKT RH LVLAGGSKPR DVTNFTVGGF APMSPRISSP MHPSAGGQRG GFGSPGGGSG GMSRGRGRRD NELIGQTVRI SQGPYKGY I GVVKDATEST ARVELHSTCQ TISVDRQRLT TVGSRRPGGM TSTYGRTPMY GSQTPMYGSG SRTPMYGSQT PLQDGSRTP HYGSQTPLHD GSRTPAQSGA WDPNNPNTPS RAEEEYEYAF DDEPTPSPQA YGGTPNPQTP GYPDPSSPQV NPQYNPQTPG TPAMYNTDQ FSPYAAPSPQ GSYQPSPSPQ SYHQVAPSPA GYQNTHSPAS YHPTPSPMAY QASPSPSPVG YSPMTPGAPS P GGYNPHTP GSGIEQNSSD WVTTDIQVKV RDTYLDTQVV GQTGVIRSVT GGMCSVYLKD SEKVVSISSE HLEPITPTKN NK VKVILGE DREATGVLLS IDGEDGIVRM DLDEQLKILN LRFLGKLLEA KETAAAKFER QHMDSSTSAA

UniProtKB: Transcription elongation factor SPT5

Macromolecule #14: DNA-directed RNA polymerase II subunit RPB4

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB4 / type: protein_or_peptide / ID: 14 / 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: DNA-directed RNA polymerase II subunit RPB4

Macromolecule #15: 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: 15 / 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 #16: DNA-directed RNA polymerase II subunit RPB11-a

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB11-a / type: protein_or_peptide / ID: 16 / 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 #17: RPB12

• Macromolecule: Name: RPB12 / type: protein_or_peptide / ID: 17 / 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 #18: Transcription elongation factor A protein 1

• Macromolecule: Name: Transcription elongation factor A protein 1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 34.022723 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MEDEVVRFAK KMDKMVQKKN AAGALDLLKE LKNIPMTLEL LQSTRIGMSV NAIRKQSTDE EVTSLAKSLI KSWKKLLDGP STEKDLDEK KKEPAITSQN SPEAREESTS SGNVSNRKDE TNARDTYVSS FPRAPSTSDS VRLKCREMLA AALRTGDDYI A IGADEEEL GSQIEEAIYQ EIRNTDMKYK NRVRSRISNL KDAKNPNLRK NVLCGNIPPD LFARMTAEEM ASDELKEMRK NL TKEAIRE HQMAKTGGTQ TDLFTCGKCK KKNCTYTQVQ TRSADEPMTT FVVCNECGNR WKFC

UniProtKB: Transcription elongation factor A protein 1

Macromolecule #19: Histone H3.3

• Macromolecule: Name: Histone H3.3 / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.360983 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAA IGALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.3

Macromolecule #20: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.394426 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

Macromolecule #21: Histone H2A type 1-B/E

• Macromolecule: Name: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 14.165551 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 1-B/E

Macromolecule #22: Histone H2B type 1-J

• Macromolecule: Name: Histone H2B type 1-J / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.935239 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-J

Macromolecule #23: Negative elongation factor A

• Macromolecule: Name: Negative elongation factor A / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 57.343598 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MASMRESDTG LWLHNKLGAT DELWAPPSIA SLLTAAVIDN IRLCFHGLSS AVKLKLLLGT LHLPRRTVDE MKGALMEIIQ LASLDSDPW VLMVADILKS FPDTGSLNLE LEEQNPNVQD ILGELREKVG ECEASAMLPL ECQYLNKNAL TTLAGPLTPP V KHFQLKRK PKSATLRAEL LQKSTETAQQ LKRSAGVPFH AKGRGLLRKM DTTTPLKGIP KQAPFRSPTA PSVFSPTGNR TP IPPSRTL LRKERGVKLL DISELDMVGA GREAKRRRKT LDAEVVEKPA KEETVVENAT PDYAAGLVST QKLGSLNNEP ALP STSYLP STPSVVPASS YIPSSETPPA PSSREASRPP EEPSAPSPTL PAQFKQRAPM YNSGLSPATP TPAAPTSPLT PTTP PAVAP TTQTPPVAMV APQTQAPAQQ QPKKNLSLTR EQMFAAQEMF KTANKVTRPE KALILGFMAG SRENPCQEQG DVIQI KLSE HTEDLPKADG QGSTTMLVDT VFEMNYATGQ WTRFKKYKPM TNVS

UniProtKB: Negative elongation factor A

Macromolecule #24: Negative elongation factor B

• Macromolecule: Name: Negative elongation factor B / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 65.779227 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MFAGLQDLGV ANGEDLKETL TNCTEPLKAI EQFQTENGVL LPSLQSALPF LDLHGTPRLE FHQSVFDELR DKLLERVSAI ASEGKAEER YKKLEDLLEK SFSLVKMPSL QPVVMCVMKH LPKVPEKKLK LVMADKELYR ACAVEVKRQI WQDNQALFGD E VSPLLKQY ILEKESALFS TELSVLHNFF SPSPKTRRQG EVVQRLTRMV GKNVKLYDMV LQFLRTLFLR TRNVHYCTLR AE LLMSLHD LDVGEICTVD PCHKFTWCLD ACIRERFVDS KRARELQGFL DGVKKGQEQV LGDLSMILCD PFAINTLALS TVR HLQELV GQETLPRDSP DLLLLLRLLA LGQGAWDMID SQVFKEPKME VELITRFLPM LMSFLVDDYT FNVDQKLPAE EKAP VSYPN TLPESFTKFL QEQRMACEVG LYYVLHITKQ RNKNALLRLL PGLVETFGDL AFGDIFLHLL TGNLALLADE FALED FCSS LFDGFFLTAS PRKENVHRHA LRLLIHLHPR VAPSKLEALQ KALEPTGQSG EAVKELYSQL GEKLEQLDHR KPSPAQ AAE TPALELPLPS VPAPAPL

UniProtKB: Negative elongation factor B

Macromolecule #25: Negative elongation factor C/D

• Macromolecule: Name: Negative elongation factor C/D / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 68.547758 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MAGAVPGAIM DEDYYGSAAE WGDEADGGQQ EDDSGEGEDD AEVQQECLHK FSTRDYIMEP SIFNTLKRYF QAGGSPENVI QLLSENYTA VAQTVNLLAE WLIQTGVEPV QVQETVENHL KSLLIKHFDP RKADSIFTEE GETPAWLEQM IAHTTWRDLF Y KLAEAHPD CLMLNFTVKL ISDAGYQGEI TSVSTACQQL EVFSRVLRTS LATILDGGEE NLEKNLPEFA KMVCHGEHTY LF AQAMMSV LAQEEQGGSA VRRIAQEVQR FAQEKGHDAS QITLALGTAA SYPRACQALG AMLSKGALNP ADITVLFKMF TSM DPPPVE LIRVPAFLDL FMQSLFKPGA RINQDHKHKY IHILAYAASV VETWKKNKRV SINKDELKST SKAVETVHNL CCNE NKGAS ELVAELSTLY QCIRFPVVAM GVLKWVDWTV SEPRYFQLQT DHTPVHLALL DEISTCHQLL HPQVLQLLVK LFETE HSQL DVMEQLELKK TLLDRMVHLL SRGYVLPVVS YIRKCLEKLD TDISLIRYFV TEVLDVIAPP YTSDFVQLFL PILEND SIA GTIKTEGEHD PVTEFIAHCK SNFIMVNGSS GSSGLEVLFQ GPHHHHHH

UniProtKB: Negative elongation factor C/D

Macromolecule #26: Negative elongation factor E

• Macromolecule: Name: Negative elongation factor E / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 45.852602 KDa
• Recombinant expression: Organism: Spodoptera frugiperda (fall armyworm)

Sequence

String:

MDYKDDDDKL EVLFQGPGSS GSSGMLVIPP GLSEEEEALQ KKFNKLKKKK KALLALKKQS SSSTTSQGGV KRSLSEQPVM DTATATEQA KQLVKSGAIS AIKAETKNSG FKRSRTLEGK LKDPEKGPVP TFQPFQRSIS ADDDLQESSR RPQRKSLYES F VSSSDRLR ELGPDGEEAE GPGAGDGPPR SFDWGYEERS GAHSSASPPR SRSRDRSHER NRDRDRDRER DRDRDRDRDR ER DRDRDRD RDRDRERDRD RERDRDRDRE GPFRRSDSFP ERRAPRKGNT LYVYGEDMTP TLLRGAFSPF GNIIDLSMDP PRN CAFVTY EKMESADQAV AELNGTQVES VQLKVNIARK QPMLDAATGK SVWGSLAVQN SPKGCHRDKR TQIVYSDDVY KENL VDGF

UniProtKB: Negative elongation factor E

Macromolecule #11: Non-template DNA (157-MER)

• Macromolecule: Name: Non-template DNA (157-MER) / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 61.381906 KDa

Sequence

String:

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

Macromolecule #13: Template DNA (168-MER)

• Macromolecule: Name: Template DNA (168-MER) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 60.869977 KDa

Sequence

String:

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

Macromolecule #12: RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*CP*C)-3')

• Macromolecule: Name: RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*CP*C)-3') / type: rna / ID: 12 / Number of copies: 1
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.503828 KDa

Sequence

String:

AAUUAGCUCU UGUGUUGUGU UUGGUGUGUU UGGGUGGUGG CC

Macromolecule #27: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 27 / Number of copies: 9 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #28: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 28 / 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

• Buffer: pH: 7.9
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.0 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: 2.5 µm / Nominal defocus min: 1.0 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Startup model: Type of model: OTHER
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47563
• Initial angle assignment: Type: NOT APPLICABLE
• Final angle assignment: Type: MAXIMUM LIKELIHOOD

Atomic model buiding 1

• Refinement: Protocol: AB INITIO MODEL

Output model

PDB-9j0n:
Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)