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- EMDB-18683: RNAPII elongation complex bound to RECQ5_R502E -

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Basic information

Entry
Database: EMDB / ID: EMD-18683
TitleRNAPII elongation complex bound to RECQ5_R502E
Map data
Sample
  • Complex: RNAP II EC -- RECQ5_R502E(1-650)
    • Complex: DNA-directed RNA polymerase
      • Protein or peptide: x 12 types
    • Complex: DNA-RNA ELONGATION SCAFFOLD
      • RNA: x 1 types
      • DNA: x 2 types
    • Complex: ATP-dependent DNA helicase Q5
    • Protein or peptide: x 1 types
  • Ligand: x 2 types
KeywordsRNA polymerase II / transcription inhibition / electron cryomicroscopy / electron cryotomography / TRANSCRIPTION
Function / homology
Function and homology information


Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape ...Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase I Transcription Termination / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / 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 / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Processing of Capped Intron-Containing Pre-mRNA / B-WICH complex positively regulates rRNA expression / mitotic DNA-templated DNA replication / mRNA Splicing - Major Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome separation / cellular response to camptothecin / DNA/RNA hybrid binding / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / DNA 3'-5' helicase / DNA metabolic process / 3'-5' DNA helicase activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / positive regulation of translational initiation / negative regulation of transcription elongation by RNA polymerase II / negative regulation of double-strand break repair via homologous recombination / 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 / translation initiation factor binding / transcription-coupled nucleotide-excision repair / DNA helicase activity / replication fork / double-strand break repair via homologous recombination / transcription initiation at RNA polymerase II promoter / P-body / helicase activity / euchromatin / protein-DNA complex / ribonucleoside binding / cellular response to xenobiotic stimulus / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / mitotic cell cycle / single-stranded DNA binding / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding / transcription by RNA polymerase II / chromosome, telomeric region / DNA replication / hydrolase activity / single-stranded RNA binding / protein dimerization activity / cell division / RNA-directed RNA polymerase / DNA repair / nucleotide binding / RNA-directed RNA polymerase activity / chromatin binding / nucleolus / magnesium ion binding / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DNA-directed RNA polymerase II subunit Rpb4-like ...RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb4/RPC9, core / Eukaryotic RNA polymerase II heptapeptide repeat. / DNA-directed RNA-polymerase II subunit / 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 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / 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. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Helicase conserved C-terminal domain / 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
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB1 / ATP-dependent DNA helicase Q5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 ...DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB1 / ATP-dependent DNA helicase Q5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB7
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsSkubnik K / Sebesta M / Stefl R
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Czech Science Foundation Czech Republic
CitationJournal: To Be Published
Title: Spatial organization of RNA polymerase II-RECQ5 transcriptional condensate
Authors: Sebesta M / Skubnik K / Stefl R
History
DepositionOct 19, 2023-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_18683.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8336 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.42167154 - 0.75609255
Average (Standard dev.)0.00094922027 (±0.02445976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 333.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : RNAP II EC -- RECQ5_R502E(1-650)

EntireName: RNAP II EC -- RECQ5_R502E(1-650)
Components
  • Complex: RNAP II EC -- RECQ5_R502E(1-650)
    • Complex: DNA-directed RNA polymerase
      • 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 polymerases I, II, and III subunit RPABC1
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB11
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4
      • Protein or peptide: Polymerase (RNA) II (DNA directed) polypeptide D
      • Protein or peptide: DNA-directed RNA polymerase II subunit RPB7
    • Complex: DNA-RNA ELONGATION SCAFFOLD
      • RNA: RNA, DNA-RNA ELONGATION SCAFFOLD
      • DNA: DNA, DNA-RNA ELONGATION SCAFFOLD
      • DNA: DNA, DNA-RNA ELONGATION SCAFFOLD
    • Complex: ATP-dependent DNA helicase Q5
    • Protein or peptide: ATP-dependent DNA helicase Q5
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RNAP II EC -- RECQ5_R502E(1-650)

SupramoleculeName: RNAP II EC -- RECQ5_R502E(1-650) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Molecular weightTheoretical: 500 KDa

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Supramolecule #2: DNA-directed RNA polymerase

SupramoleculeName: DNA-directed RNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#12
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #3: DNA-RNA ELONGATION SCAFFOLD

SupramoleculeName: DNA-RNA ELONGATION SCAFFOLD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13-#15
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: ATP-dependent DNA helicase Q5

SupramoleculeName: ATP-dependent DNA helicase Q5 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #15
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
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 217.436062 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 DDEN

UniProtKB: DNA-directed RNA polymerase II subunit RPB1

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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
Source (natural)Organism: Bos taurus (domestic cattle)
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 II subunit RPB2

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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: Bos taurus (domestic cattle)
Molecular weightTheoretical: 31.466098 KDa
SequenceString: MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD LISNSPRVIP VTSRNRDNDP NDYVEQDDIL IVKLRKGQEL R LRAYAKKG ...String:
MPYANQPTVR ITELTDENVK FIIENTDLAV ANSIRRVFIA EVPIIAIDWV QIDANSSVLH DEFIAHRLGL IPLTSDDIVD KLQYSRDCT CEEFCPECSV EFTLDVRCNE DQTRHVTSRD LISNSPRVIP VTSRNRDNDP NDYVEQDDIL 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 #4: DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 24.514219 KDa
SequenceString: MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DGLDQTLEEF KAQFGGKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN ...String:
MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DGLDQTLEEF KAQFGGKPSE 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 polymerases I, II, and III subunit RPABC2

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
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 #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: Bos taurus (domestic cattle)
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: Bos taurus (domestic cattle)
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 #8: 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: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
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 #9: DNA-directed RNA polymerase II subunit RPB11

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB11 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
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

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Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
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: Polymerase (RNA) II (DNA directed) polypeptide D

MacromoleculeName: Polymerase (RNA) II (DNA directed) polypeptide D / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 16.347255 KDa
SequenceString:
MAAGGSDPRS GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQ KKLHKFELAC LANLCPETAE ESKALIPSLE GRFEDEELQQ ILDDIQTKRS FQY

UniProtKB: DNA-directed RNA polymerase II subunit RPB4

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Macromolecule #12: DNA-directed RNA polymerase II subunit RPB7

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
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 II subunit RPB7

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Macromolecule #16: ATP-dependent DNA helicase Q5

MacromoleculeName: ATP-dependent DNA helicase Q5 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.471594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSHHTTFPF DPERRVRSTL KKVFGFDSFK TPLQESATMA VVKGNKDVFV CMPTGAGKSL CYQLPALLAK GITIVVSPLI ALIQDQVDH LLTLKVRVSS LNSKLSAQER KELLADLERE KPQTKILYIT PEMAASSSFQ PTLNSLVSRH LLSYLVVDEA H CVSQWGHD ...String:
MSSHHTTFPF DPERRVRSTL KKVFGFDSFK TPLQESATMA VVKGNKDVFV CMPTGAGKSL CYQLPALLAK GITIVVSPLI ALIQDQVDH LLTLKVRVSS LNSKLSAQER KELLADLERE KPQTKILYIT PEMAASSSFQ PTLNSLVSRH LLSYLVVDEA H CVSQWGHD FRPDYLRLGA LRSRLGHAPC VALTATATPQ VQEDVFAALH LKKPVAIFKT PCFRANLFYD VQFKELISDP YG NLKDFCL KALGQEADKG LSGCGIVYCR TREACEQLAI ELSCRGVNAK AYHAGLKASE RTLVQNDWME EKVPVIVATI SFG MGVDKA NVRFVAHWNI AKSMAGYYQE SGRAGRDGKP SWCRLYYSRN DRDQVSFLIR KEVAKLQEKR GNKASDKATI MAFD ALVTF CEELGCRHAA IAKYFGDALP ACAKGCDHCQ NPTAVRRRLE ALERSSSWSK TCIGPSQGNG FDPELYEGGR KGYGD FSRY DEGSGGSGDE GRDEAHKEEW NLFYQKQMQL RKGKDPKIEE FVPPDENCPL KEASSRRIPR LTVKAREHCL RLLEEA LSS NRQSTRTADE ADLRAKAVEL EHETFRNAKV ANLYKASVLK KVADIHRASK DGQPYDMGGS AKSCSAQAEP PEPNEYD IP PASHVYSL

UniProtKB: ATP-dependent DNA helicase Q5

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Macromolecule #13: RNA, DNA-RNA ELONGATION SCAFFOLD

MacromoleculeName: RNA, DNA-RNA ELONGATION SCAFFOLD / type: rna / ID: 13 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.320109 KDa
SequenceString:
UUUUUUGGCA UAGUUCC

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Macromolecule #14: DNA, DNA-RNA ELONGATION SCAFFOLD

MacromoleculeName: DNA, DNA-RNA ELONGATION SCAFFOLD / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.780168 KDa
SequenceString:
(DC)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DA)(DG) (DA)(DA)(DC)(DA)(DG)(DA)(DA)(DA)(DC)(DA) (DA)(DC)(DG)(DG)(DG)(DC)(DG)(DG)(DA) (DA)(DC)(DT)(DA)(DT)(DG)(DC)(DC)(DG)(DG) (DA) (DC)(DG)(DT)(DA)(DC)(DT)(DG)(DA) (DC)(DC)(DA)

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Macromolecule #15: DNA, DNA-RNA ELONGATION SCAFFOLD

MacromoleculeName: DNA, DNA-RNA ELONGATION SCAFFOLD / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 16.86173 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DG)(DG)(DT)(DC)(DA) (DG)(DT)(DA)(DC)(DG)(DT)(DC)(DC)(DG)(DG) (DC)(DA)(DT)(DA)(DG)(DT)(DT)(DC)(DC) (DG)(DC)(DC)(DC)(DG)(DT)(DT)(DG)(DT)(DT) (DT) (DC)(DT)(DG)(DT)(DT)(DC) ...String:
(DT)(DT)(DT)(DT)(DT)(DG)(DG)(DT)(DC)(DA) (DG)(DT)(DA)(DC)(DG)(DT)(DC)(DC)(DG)(DG) (DC)(DA)(DT)(DA)(DG)(DT)(DT)(DC)(DC) (DG)(DC)(DC)(DC)(DG)(DT)(DT)(DG)(DT)(DT) (DT) (DC)(DT)(DG)(DT)(DT)(DC)(DT)(DT) (DC)(DC)(DT)(DG)(DT)(DG)(DG)

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Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.7
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9046 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 787289
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 19142
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Ab initio model was generated in CryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Avg.num./class: 22000 / Software - Name: cryoSPARC

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