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- EMDB-17408: Structural insights into human co-transcriptional capping - struc... -

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Basic information

Entry
Database: EMDB / ID: EMD-17408
TitleStructural insights into human co-transcriptional capping - structure 6
Map data
Sample
  • Complex: Pol II - TPase complex
    • RNA: x 1 types
    • Protein or peptide: x 13 types
    • DNA: x 2 types
  • Protein or peptide: x 2 types
  • Ligand: x 4 types
Keywordsrna polymerase II / capping / TRANSCRIPTION
Function / homology
Function and homology information


: / negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / : / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter ...: / negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / : / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / 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 - Major Pathway / 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 / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / transcription elongation-coupled chromatin remodeling / : / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / 7-methylguanosine mRNA capping / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II activity / positive regulation of macroautophagy / organelle membrane / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / translation initiation factor binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / positive regulation of RNA splicing / DNA-directed RNA polymerase complex / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / TP53 Regulates Transcription of DNA Repair Genes / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / chromatin organization / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / transcription by RNA polymerase II / chromosome, telomeric region / nucleic acid binding / protein dimerization activity / nuclear speck / RNA-directed RNA polymerase / protein heterodimerization activity / nucleotide binding / mRNA binding / intracellular membrane-bounded organelle / DNA-templated transcription / chromatin binding / nucleolus / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II
Similarity search - Function
RrmJ-type ribose 2-O-methyltransferase domain / RrmJ-type ribose 2'-O-methyltransferase (EC 2.1.1.57) domain profile. / Spt5, KOW domain repeat 6 / G-patch domain / G-patch domain profile. / Transcription initiation Spt4 / Spt4 superfamily / G-patch domain / glycine rich nucleic binding domain / Spt4/RpoE2 zinc finger ...RrmJ-type ribose 2-O-methyltransferase domain / RrmJ-type ribose 2'-O-methyltransferase (EC 2.1.1.57) domain profile. / Spt5, KOW domain repeat 6 / G-patch domain / G-patch domain profile. / Transcription initiation Spt4 / Spt4 superfamily / G-patch domain / glycine rich nucleic binding domain / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / 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 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / WW/rsp5/WWP domain signature. / DNA-directed RNA polymerase II subunit Rpb4-like / Domain with 2 conserved Trp (W) residues / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / WW domain / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit Rpo11 / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 / 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, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit
Similarity search - Domain/homology
RNA polymerase II subunit D / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E ...RNA polymerase II subunit D / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB9 / Transcription elongation factor SPT4 / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others) / pig (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsGarg G / Dienemann C / Farnung L / Schwarz J / Linden A / Urlaub H / Cramer P
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)693023European Union
German Research Foundation (DFG)SFB 860 Germany
CitationJournal: Mol Cell / Year: 2023
Title: Structural insights into human co-transcriptional capping.
Authors: Gaurika Garg / Christian Dienemann / Lucas Farnung / Juliane Schwarz / Andreas Linden / Henning Urlaub / Patrick Cramer /
Abstract: Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights ...Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights into the three major steps of human co-transcriptional pre-mRNA capping based on six different cryoelectron microscopy (cryo-EM) structures. The human mRNA capping enzyme, RNGTT, first docks to the Pol II stalk to position its triphosphatase domain near the RNA exit site. The capping enzyme then moves onto the Pol II surface, and its guanylyltransferase receives the pre-mRNA 5'-diphosphate end. Addition of a GMP moiety can occur when the RNA is ∼22 nt long, sufficient to reach the active site of the guanylyltransferase. For subsequent cap(1) methylation, the methyltransferase CMTR1 binds the Pol II stalk and can receive RNA after it is grown to ∼29 nt in length. The observed rearrangements of capping factors on the Pol II surface may be triggered by the completion of catalytic reaction steps and are accommodated by domain movements in the elongation factor DRB sensitivity-inducing factor (DSIF).
History
DepositionMay 20, 2023-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17408.png

Downloads & links

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Map

FileDownload / File: emd_17408.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0193
Minimum - Maximum-0.021455443 - 0.074880645
Average (Standard dev.)-0.00026533235 (±0.0047302553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17408_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_17408_half_map_2.map
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Sample components

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Entire : Pol II - TPase complex

EntireName: Pol II - TPase complex
Components
  • Complex: Pol II - TPase complex
    • RNA: RNA (29-MER)
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB3Polymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit EPolymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9Polymerase
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB11-aPolymerase
    • Protein or peptide: RNA polymerase II subunit K
    • DNA: DNA (38-MER)
    • DNA: DNA (38-MER)
    • Protein or peptide: Transcription elongation factor SPT4
    • Protein or peptide: Transcription elongation factor SPT5
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB7Polymerase
  • Protein or peptide: RNA polymerase II subunit D
  • Protein or peptide: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
  • Ligand: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: S-ADENOSYLMETHIONINES-Adenosyl methionine

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Supramolecule #1: Pol II - TPase complex

SupramoleculeName: Pol II - TPase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RNA (29-MER)

MacromoleculeName: RNA (29-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.368747 KDa
SequenceString:
GAUCAAAAAG ACAUACAUAA AGACCAGGC

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Macromolecule #2: DNA-directed RNA polymerase II subunit RPB1

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 217.450078 KDa
SequenceString: MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP RQGVIERTGR CQTCAGNMTE CPGHFGHIE LAKPVFHVGF LVKTMKVLRC VCFFCSKLLV DSNNPKIKDI LAKSKGQPKK RLTHVYDLCK GKNICEGGEE M DNKFGVEQ ...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

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Macromolecule #3: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 134.041422 KDa
SequenceString: MYDADEDMQY DEDDDEITPD LWQEACWIVI SSYFDEKGLV RQQLDSFDEF IQMSVQRIVE DAPPIDLQAE AQHASGEVEE PPRYLLKFE QIYLSKPTHW ERDGAPSPMM PNEARLRNLT YSAPLYVDIT KTVIKEGEEQ LQTQHQKTFI GKIPIMLRST Y CLLNGLTD ...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

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Macromolecule #4: DNA-directed RNA polymerase II subunit RPB3

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 31.439074 KDa
SequenceString: MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD LISNSPRVIP VTSRNRDNDP SDYVEQDDIL IVKLRKGQEL R LRAYAKKG ...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

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

MacromoleculeName: DNA-directed RNA polymerase II subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 24.644318 KDa
SequenceString: MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQFGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN ...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

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

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 14.491026 KDa
SequenceString:
MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIITD

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

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Macromolecule #7: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 17.162273 KDa
SequenceString:
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

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Macromolecule #8: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 14.507205 KDa
SequenceString:
MEPDGTYEPG IVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN SCIYVNKITH EVDELTQIIA DVSQDPTLPR TEDHPCQKC GHKEAVFFQS HSARAEDAMR LYYVCTAPHC GHRWTE

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

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Macromolecule #9: DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 7.655123 KDa
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

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

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Macromolecule #10: DNA-directed RNA polymerase II subunit RPB11-a

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB11-a / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 13.310284 KDa
SequenceString:
MNAPPAFESF LLFEGEKKIT INKDTKVPNA CLFTINKEDH TLGNIIKSQL LKDPQVLFAG YKVPHPLEHK IIIRVQTTPD YSPQEAFTN AITDLISELS LLEERFRVAI KDKQEGIE

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

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Macromolecule #11: RNA polymerase II subunit K

MacromoleculeName: RNA polymerase II subunit K / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 7.018244 KDa
SequenceString:
MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

UniProtKB: RNA polymerase II, I and III subunit K

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Macromolecule #14: Transcription elongation factor SPT4

MacromoleculeName: Transcription elongation factor SPT4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.210201 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALETVPKDL RHLRACLLCS LVKTIDQFEY DGCDNCDAYL QMKGNREMVY DCTSSSFDGI IAMMSPEDSW VSKWQRVSNF KPGVYAVSV TGRLPQGIVR ELKSRGVAYK SRDTAIKT

UniProtKB: Transcription elongation factor SPT4

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Macromolecule #15: Transcription elongation factor SPT5

MacromoleculeName: Transcription elongation factor SPT5 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 121.145477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDSEDSNFS EEEDSERSSD GEEAEVDEER RSAAGSEKEE EPEDEEEEEE EEEYDEEEEE EDDDRPPKKP RHGGFILDEA DVDDEYEDE DQWEDGAEDI LEKEEIEASN IDNVVLDEDR SGARRLQNLW RDQREEELGE YYMKKYAKSS VGETVYGGSD E LSDDITQQ ...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

UniProtKB: Transcription elongation factor SPT5

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Macromolecule #16: DNA-directed RNA polymerase II subunit RPB7

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 19.314283 KDa
SequenceString:
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

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Macromolecule #17: RNA polymerase II subunit D

MacromoleculeName: RNA polymerase II subunit D / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: pig (pig)
Molecular weightTheoretical: 16.331255 KDa
SequenceString:
MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQ KKLHKFELAC LANLCPETAE ESKALIPSLE GRFEDEELQQ ILDDIQTKRS FQY

UniProtKB: RNA polymerase II subunit D

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Macromolecule #18: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1

MacromoleculeName: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO / EC number: methyltransferase cap1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.454773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRRTDPECT APIKKQKKRV AELALSLSST SDDEPPSSVS HGAKASTTSL SGSDSETEGK QHSSDSFDDA FKADSLVEGT SSRYSMYNS VSQKLMAKMG FREGEGLGKY SQGRKDIVEA SSQKGRRGLG LTLRGFDQEL NVDWRDEPEP SACEQVSWFP E CTTEIPDT ...String:
MKRRTDPECT APIKKQKKRV AELALSLSST SDDEPPSSVS HGAKASTTSL SGSDSETEGK QHSSDSFDDA FKADSLVEGT SSRYSMYNS VSQKLMAKMG FREGEGLGKY SQGRKDIVEA SSQKGRRGLG LTLRGFDQEL NVDWRDEPEP SACEQVSWFP E CTTEIPDT QEMSDWMVVG KRKMIIEDET EFCGEELLHS VLQCKSVFDV LDGEEMRRAR TRANPYEMIR GVFFLNRAAM KM ANMDFVF DRMFTNPRDS YGKPLVKDRE AELLYFADVC AGPGGFSEYV LWRKKWHAKG FGMTLKGPND FKLEDFYSAS SEL FEPYYG EGGIDGDGDI TRPENISAFR NFVLDNTDRK GVHFLMADGG FSVEGQENLQ EILSKQLLLC QFLMALSIVR TGGH FICKT FDLFTPFSVG LVYLLYCCFE RVCLFKPITS RPANSERYVV CKGLKVGIDD VRDYLFAVNI KLNQLRNTDS DVNLV VPLE VIKGDHEFTD YMIRSNESHC SLQIKALAKI HAFVQDTTLS EPRQAEIRKE CLRLWGIPDQ ARVAPSSSDP KSKFFE LIQ GTEIDIFSYK PTLLTSKTLE KIRPVFDYRC MVSGSEQKFL IGLGKSQIYT WDGRQSDRWI KLDLKTELPR DTLLSVE IV HELKGEGKAQ RKISAIHILD VLVLNGTDVR EQHFNQRIQL AEKFVKAVSK PSRPDMNPIR VKEVYRLEEM EKIFVRLE M KIIKGSSGTP KLSYTGRDDR HFVPMGLYIV RTVNEPWTMG FSKSFKKKFF YNKKTKDSTF DLPADSIAPF HICYYGRLF WEWGDGIRVH DSQKPQDQDK LSKEDVLSFI QMHRA

UniProtKB: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1

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Macromolecule #12: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.762597 KDa
SequenceString:
(DA)(DG)(DT)(DA)(DC)(DT)(DA)(DG)(DT)(DA) (DT)(DT)(DC)(DT)(DA)(DG)(DT)(DA)(DT)(DT) (DG)(DA)(DA)(DA)(DG)(DT)(DA)(DC)(DT) (DT)(DG)(DA)(DG)(DC)(DT)(DT)(DG)(DA)

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Macromolecule #13: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.628501 KDa
SequenceString:
(DT)(DC)(DA)(DA)(DG)(DC)(DT)(DC)(DA)(DA) (DG)(DT)(DA)(DC)(DT)(DT)(DA)(DA)(DG)(DC) (DC)(DT)(DG)(DG)(DT)(DC)(DT)(DA)(DT) (DA)(DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)

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Macromolecule #19: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 19 / Number of copies: 1 / Formula: MGT
Molecular weightTheoretical: 539.223 Da
Chemical component information

ChemComp-MGT:
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE

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Macromolecule #20: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 20 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #21: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #22: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 22 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE / S-Adenosyl methionine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31423

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