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- EMDB-12087: Cryo-EM structure of mammalian RNA polymerase II in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12087
TitleCryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2
Map data
Sample
  • Complex: RNA polymerase II -RPAP2 complex
    • Complex: DNA-directed RNA polymerase II
      • Protein or peptide: x 10 types
    • Complex: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
      • Protein or peptide: x 2 types
  • Ligand: x 1 types
KeywordsRPAP2 / RNA polymerase II / Nuclear import / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat phosphatase activity / snRNA transcription / RNA polymerase core enzyme binding / PERK-mediated unfolded protein response / 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 CTD heptapeptide repeat phosphatase activity / snRNA transcription / RNA polymerase core enzyme binding / PERK-mediated unfolded protein response / 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 / transcription preinitiation complex / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II transcribes snRNA genes / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / core promoter sequence-specific DNA binding / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / DNA-directed RNA polymerase complex / transcription initiation at RNA polymerase II promoter / euchromatin / ribonucleoside binding / fibrillar center / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / nucleic acid binding / transcription by RNA polymerase II / protein dimerization activity / cilium / DNA-templated transcription / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rtr1/RPAP2 domain / Rtr1/RPAP2 domain superfamily / Rtr1/RPAP2 / Rtr1/RPAP2 family / RTR1-type zinc finger. / 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 ...Rtr1/RPAP2 domain / Rtr1/RPAP2 domain superfamily / Rtr1/RPAP2 / Rtr1/RPAP2 family / RTR1-type zinc finger. / 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 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 / Zinc finger TFIIS-type signature. / 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, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta / 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 RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB9 / Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsFianu I / Dienemann C
Funding support Germany, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)693023 Germany
German Research Foundation (DFG)SFB860, SPP2191, EXC 2067/1-390729940 Germany
Marie Sklodowska-Curie Actions, FragNET ITN894862 Germany
CitationJournal: Commun Biol / Year: 2021
Title: Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2.
Authors: Isaac Fianu / Christian Dienemann / Shintaro Aibara / Sandra Schilbach / Patrick Cramer /
Abstract: Nuclear import of RNA polymerase II (Pol II) involves the conserved factor RPAP2. Here we report the cryo-electron microscopy (cryo-EM) structure of mammalian Pol II in complex with human RPAP2 at 2. ...Nuclear import of RNA polymerase II (Pol II) involves the conserved factor RPAP2. Here we report the cryo-electron microscopy (cryo-EM) structure of mammalian Pol II in complex with human RPAP2 at 2.8 Å resolution. The structure shows that RPAP2 binds between the jaw domains of the polymerase subunits RPB1 and RPB5. RPAP2 is incompatible with binding of downstream DNA during transcription and is displaced upon formation of a transcription pre-initiation complex.
History
DepositionDec 11, 2020-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b7u
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12087.png

Downloads & links

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Map

FileDownload / File: emd_12087.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.05476526 - 0.1502014
Average (Standard dev.)-0.00045896997 (±0.0037967553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 377.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0550.150-0.000

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Supplemental data

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Mask #1

Fileemd_12087_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_12087_additional_1.map
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Half map: #1

Fileemd_12087_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_12087_half_map_2.map
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Sample components

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Entire : RNA polymerase II -RPAP2 complex

EntireName: RNA polymerase II -RPAP2 complex
Components
  • Complex: RNA polymerase II -RPAP2 complex
    • Complex: DNA-directed 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 polymerases I, II, and III subunit RPABC3
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9
      • Protein or peptide: Uncharacterized Protein
      • Protein or peptide: RNA_pol_L_2 domain-containing protein
      • Protein or peptide: RNA polymerase II subunit K
    • Complex: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
      • Protein or peptide: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
      • Protein or peptide: Unknown
  • Ligand: ZINC ION

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Supramolecule #1: RNA polymerase II -RPAP2 complex

SupramoleculeName: RNA polymerase II -RPAP2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12

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Supramolecule #2: DNA-directed RNA polymerase II

SupramoleculeName: DNA-directed RNA polymerase II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#10
Source (natural)Organism: Sus scrofa domesticus (domestic pig)

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Supramolecule #3: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2

SupramoleculeName: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #11-#12
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA-directed RNA polymerase subunit

MacromoleculeName: 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 domesticus (domestic pig) / Tissue: Thymus
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 subunit

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Macromolecule #2: DNA-directed RNA polymerase subunit beta

MacromoleculeName: 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 domesticus (domestic pig) / Tissue: Thymus
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 #3: DNA-directed RNA polymerase II subunit RPB3

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Tissue: Thymus
Molecular weightTheoretical: 30.997557 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 QSDV

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

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

MacromoleculeName: DNA-directed RNA polymerase II subunit E / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Tissue: Thymus
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 polymerases I, II, and III subunit RPABC1

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

MacromoleculeName: DNA-directed RNA polymerase II subunit F / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Tissue: Thymus
Molecular weightTheoretical: 14.477001 KDa
SequenceString:
MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIISD

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

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Macromolecule #6: 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: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Tissue: Thymus
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 #7: DNA-directed RNA polymerase II subunit RPB9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Tissue: Thymus
Molecular weightTheoretical: 14.541221 KDa
SequenceString:
MEPDGTYEPG FVGIRFCQEC NNMLYPKEDK ENRILLYACR NCDYQQEADN SCIYVNKITH EVDELTQIIA DVSQDPTLPR TEDHPCQKC GHKEAVFFQS HSARAEDAMR LYYVCTAPHC GHRWTE

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

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Macromolecule #8: Uncharacterized Protein

MacromoleculeName: Uncharacterized Protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Tissue: Thymus
Molecular weightTheoretical: 7.655123 KDa
SequenceString:
MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

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Macromolecule #9: RNA_pol_L_2 domain-containing protein

MacromoleculeName: RNA_pol_L_2 domain-containing protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Tissue: Thymus
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 #10: RNA polymerase II subunit K

MacromoleculeName: RNA polymerase II subunit K / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Tissue: Thymus
Molecular weightTheoretical: 7.018244 KDa
SequenceString:
MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

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

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Macromolecule #11: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2

MacromoleculeName: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.614773 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADFAGPSSA GRKAGAPRCS RKAAGTKQTS TLKQEDASKR KAELEAAVRK KIEFERKALH IVEQLLEENI TEEFLMECGR FITPAHYSD VVDERSIVKL CGYPLCQKKL GIVPKQKYKI STKTNKVYDI TERKSFCSNF CYQASKFFEA QIPKTPVWVR E EERHPDFQ ...String:
MADFAGPSSA GRKAGAPRCS RKAAGTKQTS TLKQEDASKR KAELEAAVRK KIEFERKALH IVEQLLEENI TEEFLMECGR FITPAHYSD VVDERSIVKL CGYPLCQKKL GIVPKQKYKI STKTNKVYDI TERKSFCSNF CYQASKFFEA QIPKTPVWVR E EERHPDFQ LLKEEQSGHS GEEVQLCSKA IKTSDIDNPS HFEKQYESSS SSTHSDSSSD NEQDFVSSIL PGNRPNSTNI RP QLHQKSI MKKKAGHKAN SKHKDKEQTV VDVTEQLGDC KLDSQEKDAT CELPLQKVNT QSSSNSTLPE RLKASENSES EYS RSEITL VGISKKSAEH FKRKFAKSNQ VSRSVSSSVQ VCPEVGKRNL LKVLKETLIE WKTEETLRFL YGQNYASVCL KPEA SLVKE ELDEDDIISD PDSHFPAWRE SQNSLDESLP FRGSGTAIKP LPSYENLKKE TEKLNLRIRE FYRGRYVLGE ETTKS QDSE EHDSTFPLID SSSQNQIRKR IVLEKLSKVL PGLLVPLQIT LGDIYTQLKN LVRTFRLTNR NIIHKPAEWT LIAMVL LSL LTPILGIQKH SQEGMVFTRF LDTLLEELHL KNEDLESLTI IFRTSCLPE

UniProtKB: Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2

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Macromolecule #12: Unknown

MacromoleculeName: Unknown / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.571161 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
(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)

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Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
GridModel: UltrAuFoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 2.21 sec. / Average electron dose: 42.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER

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Image processing

Particle selectionNumber selected: 1556776
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 364771
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.5)
Final 3D classificationNumber classes: 4 / Avg.num./class: 400000 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5flm


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7b7u:
Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2

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