[English] 日本語
Yorodumi
- EMDB-18643: Structure of s. pombe RNA polymerase II in complex with DSIF and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18643
TitleStructure of s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1
Map data
Sample
  • Complex: s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1
    • Protein or peptide: x 13 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 1 types
KeywordsRNA polymerase II / Rai1 / Rat1 / Spt5 / DSIF / Termination / exoribonuclease / RNA BINDING PROTEIN
Function / homology
Function and homology information


rapid tRNA decay / RNA Polymerase I Transcription Initiation / RNA polymerase II, holoenzyme / RNA polymerase II transcribes snRNA genes / 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 Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 1 Promoter ...rapid tRNA decay / RNA Polymerase I Transcription Initiation / RNA polymerase II, holoenzyme / RNA polymerase II transcribes snRNA genes / 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 Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of the Early Elongation Complex / RNA Polymerase I Promoter Escape / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / Transcriptional regulation by small RNAs / positive regulation of chromosome segregation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Las1 complex / tRNA surveillance / regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / DNA-templated transcription elongation / 5'-3' RNA exonuclease activity / DSIF complex / nuclear mRNA surveillance / intracellular phosphate ion homeostasis / chromatin-protein adaptor activity / transcription elongation factor activity / termination of RNA polymerase II transcription / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / transcription elongation-coupled chromatin remodeling / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / nuclear-transcribed mRNA catabolic process / positive regulation of translational initiation / 7-methylguanosine mRNA capping / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / pericentric heterochromatin / transcription-coupled nucleotide-excision repair / translation initiation factor binding / : / : / : / regulation of DNA-templated transcription elongation / : / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / : / : / DNA-templated transcription termination / DNA-directed RNA polymerase activity / ribonucleoside binding / DNA-directed RNA polymerase / mRNA processing / single-stranded DNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / mRNA binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol
Similarity search - Function
5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 ...5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical 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 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / 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 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / 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. / S1 RNA binding domain / S1 domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain
Similarity search - Domain/homology
DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor spt5 / DNA-directed RNA polymerase II subunit rpb7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit rpb1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / 5'-3' exoribonuclease 2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 ...DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor spt5 / DNA-directed RNA polymerase II subunit rpb7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit rpb1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / 5'-3' exoribonuclease 2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsCarrique L / Kus K / Vasiljeva L / Grimes JM
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
Wellcome Trust222510/Z/21/Z United Kingdom
Wellcome TrustWT106994/Z/15/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts.
Authors: Krzysztof Kuś / Loic Carrique / Tea Kecman / Marjorie Fournier / Sarah Sayed Hassanein / Ebru Aydin / Cornelia Kilchert / Jonathan M Grimes / Lidia Vasiljeva /
Abstract: Precursor messenger RNA (pre-mRNA) is processed into its functional form during RNA polymerase II (Pol II) transcription. Although functional coupling between transcription and pre-mRNA processing is ...Precursor messenger RNA (pre-mRNA) is processed into its functional form during RNA polymerase II (Pol II) transcription. Although functional coupling between transcription and pre-mRNA processing is established, the underlying mechanisms are not fully understood. We show that the key transcription termination factor, RNA exonuclease Xrn2 engages with Pol II forming a stable complex. Xrn2 activity is stimulated by Spt5 to ensure efficient degradation of nascent RNA leading to Pol II dislodgement from DNA. Our results support a model where Xrn2 first forms a stable complex with the elongating Pol II to achieve its full activity in degrading nascent RNA revising the current 'torpedo' model of termination, which posits that RNA degradation precedes Xrn2 engagement with Pol II. Spt5 is also a key factor that attenuates the expression of non-coding transcripts, coordinates pre-mRNA splicing and 3'-end processing. Our findings indicate that engagement with the transcribing Pol II is an essential regulatory step modulating the activity of RNA enzymes such as Xrn2, thus advancing our understanding of how RNA maturation is controlled during transcription.
History
DepositionOct 12, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18643.png

Downloads & links

-
Map

FileDownload / File: emd_18643.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 352 pix.
= 369.6 Å		1.05 Å/pix.
x 352 pix.
= 369.6 Å		1.05 Å/pix.
x 352 pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.336
Minimum - Maximum-1.6122082 - 2.5733562
Average (Standard dev.)-0.00017748088 (±0.056189895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 369.59998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18643_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18643_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18643_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1

EntireName: s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1
Components
  • Complex: s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1
    • Protein or peptide: DNA-directed RNA polymerase II subunit rpb1
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB2
    • 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 polymerase II subunit rpb7
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB9,RBP9
    • 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: Transcription elongation factor spt5
    • DNA: DNA none template (34-MER)
    • RNA: RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3')
    • DNA: DNA template (40-MER)
    • Protein or peptide: 5'-3' exoribonuclease 2
  • Ligand: ZINC ION

+
Supramolecule #1: s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1

SupramoleculeName: s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

+
Macromolecule #1: DNA-directed RNA polymerase II subunit rpb1

MacromoleculeName: DNA-directed RNA polymerase II subunit rpb1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 194.372625 KDa
SequenceString: MSGIQFSPSS VPLRRVEEVQ FGILSPEEIR SMSVAKIEFP ETMDESGQRP RVGGLLDPRL GTIDRQFKCQ TCGETMADCP GHFGHIELA KPVFHIGFLS KIKKILECVC WNCGKLKIDS SNPKFNDTQR YRDPKNRLNA VWNVCKTKMV CDTGLSAGSD N FDLSNPSA ...String:
MSGIQFSPSS VPLRRVEEVQ FGILSPEEIR SMSVAKIEFP ETMDESGQRP RVGGLLDPRL GTIDRQFKCQ TCGETMADCP GHFGHIELA KPVFHIGFLS KIKKILECVC WNCGKLKIDS SNPKFNDTQR YRDPKNRLNA VWNVCKTKMV CDTGLSAGSD N FDLSNPSA NMGHGGCGAA QPTIRKDGLR LWGSWKRGKD ESDLPEKRLL SPLEVHTIFT HISSEDLAHL GLNEQYARPD WM IITVLPV PPPSVRPSIS VDGTSRGEDD LTHKLSDIIK ANANVRRCEQ EGAPAHIVSE YEQLLQFHVA TYMDNEIAGQ PQA LQKSGR PLKSIRARLK GKEGRLRGNL MGKRVDFSAR TVITGDPNLS LDELGVPRSI AKTLTYPETV TPYNIYQLQE LVRN GPDEH PGAKYIIRDT GERIDLRYHK RAGDIPLRYG WRVERHIRDG DVVIFNRQPS LHKMSMMGHR IRVMPYSTFR LNLSV TSPY NADFDGDEMN MHVPQSEETR AEIQEITMVP KQIVSPQSNK PVMGIVQDTL AGVRKFSLRD NFLTRNAVMN IMLWVP DWD GILPPPVILK PKVLWTGKQI LSLIIPKGIN LIRDDDKQSL SNPTDSGMLI ENGEIIYGVV DKKTVGASQG GLVHTIW KE KGPEICKGFF NGIQRVVNYW LLHNGFSIGI GDTIADADTM KEVTRTVKEA RRQVAECIQD AQHNRLKPEP GMTLRESF E AKVSRILNQA RDNAGRSAEH SLKDSNNVKQ MVAAGSKGSF INISQMSACV GQQIVEGKRI PFGFKYRTLP HFPKDDDSP ESRGFIENSY LRGLTPQEFF FHAMAGREGL IDTAVKTAET GYIQRRLVKA MEDVMVRYDG TVRNAMGDII QFAYGEDGLD ATLVEYQVF DSLRLSTKQF EKKYRIDLME DRSLSLYMEN SIENDSSVQD LLDEEYTQLV ADRELLCKFI FPKGDARWPL P VNVQRIIQ NALQIFHLEA KKPTDLLPSD IINGLNELIA KLTIFRGSDR ITRDVQNNAT LLFQILLRSK FAVKRVIMEY RL NKVAFEW IMGEVEARFQ QAVVSPGEMV GTLAAQSIGE PATQMTLNTF HYAGVSSKNV TLGVPRLKEI LNVAKNIKTP SLT IYLMPW IAANMDLAKN VQTQIEHTTL STVTSATEIH YDPDPQDTVI EEDKDFVEAF FAIPDEEVEE NLYKQSPWLL RLEL DRAKM LDKKLSMSDV AGKIAESFER DLFTIWSEDN ADKLIIRCRI IRDDDRKAED DDNMIEEDVF LKTIEGHMLE SISLR GVPN ITRVYMMEHK IVRQIEDGTF ERADEWVLET DGINLTEAMT VEGVDATRTY SNSFVEILQI LGIEATRSAL LKELRN VIE FDGSYVNYRH LALLCDVMTS RGHLMAITRH GINRAETGAL MRCSFEETVE ILMDAAASGE KDDCKGISEN IMLGQLA PM GTGAFDIYLD QDMLMNYSLG TAVPTLAGSG MGTSQLPEGA GTPYERSPMV DSGFVGSPDA AAFSPLVQGG SEGREGFG D YGLLGAASPY KGVQSPGYTS PFSSAMSPGY GLTSPSYSPS SPGYSTSPAY MPSSPSYSPT SPSYSPTSPS YSPTSPSYS PTSPSYSATS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPS

UniProtKB: DNA-directed RNA polymerase II subunit rpb1

+
Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 138.027188 KDa
SequenceString: MSYEDYQYNE TLTQEDCWTV ISSFFEETSL ARQQLFSFDE FVQNTMQEIV DDDSTLTLDQ YAQHTGAQGD VTRRYEINFG QIYLSRPTM TEADGSTTTM FPQEARLRNL TYSSPLYVDM RKKVMVAADS NVPIGEEEWL VEEEDEEPSK VFIGKIPIML R STFCILNG ...String:
MSYEDYQYNE TLTQEDCWTV ISSFFEETSL ARQQLFSFDE FVQNTMQEIV DDDSTLTLDQ YAQHTGAQGD VTRRYEINFG QIYLSRPTM TEADGSTTTM FPQEARLRNL TYSSPLYVDM RKKVMVAADS NVPIGEEEWL VEEEDEEPSK VFIGKIPIML R STFCILNG VSDSELYDLN ECPYDQGGYF IINGSEKVII AQERSAANIV QVFKKAAPSP IAYVAEIRSA LERGSRLISS MQ IKLMARN TENSGQTIRA TLPYIRSDIP IVIVFRALGV VPDRDILEHI CYDPNDFQML EMMKPCIEEA FVIQDKDIAL DYI GKRGST TGVTREKRLR YAHDILQKEL LPHITTMEGF ETRKAFFLGY MIHRMLLCAL ERREPDDRDH FGKKRLDLAG PLLA SLFRM LFRKMTRDVY KYMQKCVETN REFNLTLAVK SNIITNGLRY SLATGNWGDQ KRSMVNRVGV SQVLNRYTFA STLSH LRRT NTPIGRDGKL AKPRQLHNTH WGMVCPAETP EGQACGLVKN LSLMSYVSVG SPSAPIIEFL EEWGLETLED YNPSAS PNA TKVFVNGVWL GVHRDPAHLT ETLRSLRRRL DISAEVSIVR DIREKELRLF TDAGRICRPL FIVDNNPNSE RRGELCI RK EHIQQLIEDK DRYDIDPEQR FGWTALVSSG LIEYLDAEEE ETVMIAMSPE DLEASRQMQA GYEVKEELDP AQRVKPAP N PHVHAWTHCE IHPAMILGIL ASIIPFPDHN QSPRNTYQSA MGKQAMGVYL TNYQVRMDTM ANILYYPQKP LATTRSMEY LKFRELPAGQ NAIVAILCYS GYNQEDSIIM NQASIDRGLF RSIFYRTYTD QEKKIGMTVM EEFERPVRST TLRMKHGTYD KLEDDGLIA PGTRVSGEDI IIGKTAPIPL DHEELGQRTQ LHAKRDVSTP LRSTESGIVD QVMVTTNQEG LKFVKVRMRS T RIPQIGDK FASRHGQKGT IGMTYRHEDM PFSAQGIVPD IIINPHAIPS RMTVAHLVEC QLSKVSALSG FEGDATPFTD VT VEAVSKL LRSHGFQSRG FEVMYHGHTG RKLVAQVFLG PTYYQRLKHL VDDKIHARAR GPVQILTRQP VEGRSRDGGL RFG EMERDC QISHGCSSVL RERLFDCSDA YRVIVCDICG LIAIASYKKD SYECRSCQNR TRFSQVYLPY AAKLLFQELM SMNI APRLF TKNHK

UniProtKB: DNA-directed RNA polymerase II subunit RPB2

+
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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 33.748816 KDa
SequenceString: MDSETHITIR NISKNSVDFV LTNTSLAVAN SLRRVVLAEI PTVAIDLVEI NVNTSVMPDE FLAHRLGMIP LDSSNIDEPP PVGLEYTRN CDCDQYCPKC SVELFLNAKC TGEGTMEIYA RDLVVSSNSS LGHPILADPK SRGPLICKLR KEQEISLRCI A KKGIAKEH ...String:
MDSETHITIR NISKNSVDFV LTNTSLAVAN SLRRVVLAEI PTVAIDLVEI NVNTSVMPDE FLAHRLGMIP LDSSNIDEPP PVGLEYTRN CDCDQYCPKC SVELFLNAKC TGEGTMEIYA RDLVVSSNSS LGHPILADPK SRGPLICKLR KEQEISLRCI A KKGIAKEH AKWSPTSAVA FEYDPWNKLQ HTDYWFENDA DAEWPKSKNA DWEEPPREGE PFNFQEEPRR FYMDVESVGS IP PNEIMVQ GLRILQEKLA VLVRDLDEEQ PTQLSANELN MEENAEMNWS PYQNGEENTW

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

+
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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 23.954504 KDa
SequenceString: MSAEEKNIVR VFRAWKTAHQ LVHDRGYGVS QAELDLTLDQ FKAMHCGMGR NLDRTTLSFY AKPSNDSNKG TIYIEFAKEP SVGIKEMRT FVHTLGDHNH KTGILIYANS MTPSAAKIIA TVTGQFTIET FQESDLIVNI THHELVPKHI LLSPDEKKEL L DRYKLRET ...String:
MSAEEKNIVR VFRAWKTAHQ LVHDRGYGVS QAELDLTLDQ FKAMHCGMGR NLDRTTLSFY AKPSNDSNKG TIYIEFAKEP SVGIKEMRT FVHTLGDHNH KTGILIYANS MTPSAAKIIA TVTGQFTIET FQESDLIVNI THHELVPKHI LLSPDEKKEL L DRYKLRET QLPRIQLADP VARYLGLKRG EVVKIVRRSE TSGRYNSYRI CA

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

+
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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 15.742497 KDa
SequenceString:
MSDYEEDEAF GMDGAVMEEE VDELEMIDEN GQSQQGVSHP GEPSTTVITE DVASSKTAQS GKAVAKEDRT TTPYMTKYER ARILGTRAL QISMNAPVLV DLEGETDPLQ IAMKELAQKK IPLLVRRYLP DGSYEDWSVA ELI

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

+
Macromolecule #6: DNA-directed RNA polymerase II subunit rpb7

MacromoleculeName: DNA-directed RNA polymerase II subunit rpb7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 19.121982 KDa
SequenceString:
MPFFLKELSL TISLHPSYFG PRMQDYLKAK LLADVEGTCS GQYGYIICVL DSNTIDIDKG RVVPGQGFAE FEVKYRAVLW RPFRGEVVD AIVTTVNKMG FFANIGPLNV FVSSHLVPPD MKFDPTANPP NYSGEDQVIE KGSNVRLKIV GTRTDATEIF A IATMKEDY LGVL

UniProtKB: DNA-directed RNA polymerase II subunit rpb7

+
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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 14.317318 KDa
SequenceString:
MSESVLLDEI FTVTSVDKQK YQRVSRITAV SGQNDMNLTL DINSQIYPLE KDATFSLQIT SNLNSPDLKE AADYIMYGKV YRVEEAKDE KVSVYVSFGG LLMAIEGSHR KLYRLSLDHV YLLLRR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

+
Macromolecule #8: DNA-directed RNA polymerase II subunit RPB9,RBP9

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9,RBP9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 16.2538 KDa
SequenceString:
MSNFQYCIEC NNMLYPREDK VDRVLRLACR NCDYSEIAAT SKVYRHELQS SNVENTTVSH DASTDPTLPR SDKECPRCHQ HEAVFYQTH SRRGDTMMTL IYVCVHCGFA FEEQGGGGGG DYKDHDGDYK DHDIDYKDDD DK

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

+
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: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 8.286801 KDa
SequenceString:
MIIPIRCFSC GKVIGDKWDT YLTLLQEDNT EGEALDKLGL QRYCCRRMIL THVDLIEKLL CYNPLSKQKN L

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

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

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 14.143276 KDa
SequenceString:
MNQPERYELI ELMGLPKVTY ELDSKSPNAA VVTLEKEDHT LANMLANQLL SDERVLFAGY KVPHPLNHNF ILRVQTVEDC SPKQVIVDA AKSLITHLEE IKVNFMREWE LKMISVEGVE MEFS

UniProtKB: DNA-directed RNA polymerase II subunit RPB11

+
Macromolecule #11: 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: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 7.216495 KDa
SequenceString:
MNHPTSTGGT AFNPPRPATM IYLCADCGAR NTIQAKEVIR CRECGHRVMY KMRTKRMVQF EAR

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

+
Macromolecule #12: Transcription elongation factor spt5

MacromoleculeName: Transcription elongation factor spt5 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 123.489242 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKHHHHHHPM SDKIIHLTDD SFDTDVLKAD GAILVDFWAE WCGPCKMIAP ILDEIADEYQ GKLTVAKLNI DQNPGTAPKY GIRGIPTLL LFKNGEVAAT KVGALSKGQL KEFLDANLAG SGSGSENLYF QGAMDTNSPK SIDKDANSTE VDAAEQDAAS V KINSTRAS ...String:
MKHHHHHHPM SDKIIHLTDD SFDTDVLKAD GAILVDFWAE WCGPCKMIAP ILDEIADEYQ GKLTVAKLNI DQNPGTAPKY GIRGIPTLL LFKNGEVAAT KVGALSKGQL KEFLDANLAG SGSGSENLYF QGAMDTNSPK SIDKDANSTE VDAAEQDAAS V KINSTRAS PNGSDLLNDD SEAAKITTNE KQSSPVDSHN ESPNDTTINK GEDGNENEVD NVNNNDKKED EDNVEENEEE AD ANEEEEE DEEDDEEDEE DEDESGGGRR KRARHDRRNQ FLDIEAEVDE DEEELEDEED EIGREDGFIE EEVGADYVGD DRR HRELDR QRQELQSVDA ERLAEEYREK YGRSQTVVGD TSNVPQRLLL PSVNDPNIWA VRCKIGKEKD IVFTIMRKAM DLQY TSSPL EIISAFQRDS LVGYIYVEAR KQSHVLDALN GVLNVYTNNM ILVPIKEMPD LLKVQKQVVE LLPGAYVRIR RGKYA GDLA QVDNLSENGL TARVRIVPRI DYSDGLKRKN SATRPQARLF NESEAFKSNP SKFSKRGPRL FLFNNEEFED GFLVKD IRI SSLITEGVNP TLDEVSKFNP NNEDLDLSSL ALSVKGGHAE FQPGDHVEVY VGEQTGVSGV VENVRGSVIT MVSSDGL RL DVPSRGLRKR FRHGDYVKVI AGKYKDDTGM VVRISKDEVT FLSDTLMTEL TVFSRDLGEA SSAQAVNSAY ELHDLVQL D VNTVACIFSV DRDTYKVIDQ NGGVRTVLAS QITMRHSNRR GVATDRNGAE IRIGDKVKEV GGEGKQGTIL HIYRAFVFL HNRDIAENNG VFSARSRNVA TIAAKGARIS ADLTKMNPAL SNGPALPPVA NLKRTIGRDK AIGATVRIRR GPMKGLLGVI KDTTDANAR VELHTGNKMV TIPKENLLYT TKTGELISYT EFIERSRGIR PGSISTADGP NVPNWAQGAR TPAVANGSRT P AWNTGSRT PAWNSGSKTP AWNSGSRTPA WNSGNKTPAW NAGSRTPAWN SGNKTPAWNV GNKTPAWNSG AKTPAWNAGN KT PSWNNGT KTPAWNANQT PMVANGTNTS WGQTPAYGGF SETNWDTEDN SKPYTAPTPG AWAAPTPGGW DDEEGDSPKY VPP SP

UniProtKB: Transcription elongation factor spt5

+
Macromolecule #16: 5'-3' exoribonuclease 2

MacromoleculeName: 5'-3' exoribonuclease 2 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 102.208312 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGVPALFRLL SRKFAKVITP VIEAPTEKLP DGTEIEPDLS LPNPNGVECD NLYLDMNGIV HPCSHPEDRP APETEDEMMV AVFEYTDRI LAMVRPRQLL FIAIDGVAPR AKMNQQRSRR FRSSREAALK EEELQAFIEE AKQQGIPIDE NATKKKSWDS N CITPGTPF ...String:
MGVPALFRLL SRKFAKVITP VIEAPTEKLP DGTEIEPDLS LPNPNGVECD NLYLDMNGIV HPCSHPEDRP APETEDEMMV AVFEYTDRI LAMVRPRQLL FIAIDGVAPR AKMNQQRSRR FRSSREAALK EEELQAFIEE AKQQGIPIDE NATKKKSWDS N CITPGTPF MDTLAKSLRY YIINKLNSDP CWRNVRFILS DASVPGEGEH KIMEFIRSQR VKPEYDPNTH HVVYGLDAAL IM LGLATHE PHFRVLREDV FFQQGSTKKT KEERLGIKRL DDVSETNKVP VKKPFIWLNV SILREYLEVE LYVPNLPFPF DLE RAIDDW VFFIFFVGND FLPHLPSLDI RDGAVERLTE IWRASLPHMG GYLTLDGSVN LARAEVILSA VGNQEDDIFK RLKQ QEDRR NENYRRRQQR ESNQESESYV DNVVIQRSVE TQSTEVVTSS KSTSVDTKPP KKTQKIDAPA PVDLVNLSEK TSNRS LGAT NRELINNRAA NRLGLSREAA AVSSVNKLAA SALKAQLVSN ETLQNVPLED SIASSSAYED TDSIESSTPV VHPIDT KVS NVGQKRKAPD STEENENTDT VRLYEPGYRE RYYEQKFHIS PDEPEKIREA VKHYVHGLCW VLLYYYQGCP SWTWYYP YH YAPFAADFKD LASIDVKFEL NQPFKPYEQL LGVLPAASKN NLPEKLQTLM TDENSEIIDF YPENFTIDLN GKKFEWQG V ALLPFIDENR LLNAVSKIYP QLTEEESKRN EDGSTLLFIS EHHPMFSELV KQLYSKKRQG KPLKLSGKMA HGLFGKVNT NDSVIPNVSV QCPIDVTSAD ALQKYGSIDD NQSISLVFEV PKSHFVHKSM LLRGVKMPNR VLTPEDINQV RAERSFSSRR NNGNSGSGH HHHHHHH

UniProtKB: 5'-3' exoribonuclease 2

+
Macromolecule #13: DNA none template (34-MER)

MacromoleculeName: DNA none template (34-MER) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 14.917541 KDa
SequenceString:
(DC)(DC)(DG)(DT)(DG)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DG)(DA)(DA)(DA) (DT)(DG)(DG)(DT)(DT)(DT)(DG)(DT)(DG) (DT)(DC)(DT)(DG)(DC)(DT)(DT)(DA)(DT)(DC) (DG) (DG)(DT)(DA)(DG)(DA)(DG)(DT)(DG)

+
Macromolecule #15: DNA template (40-MER)

MacromoleculeName: DNA template (40-MER) / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 14.659406 KDa
SequenceString:
(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DC)(DC)(DG) (DA)(DT)(DA)(DA)(DG)(DC)(DA)(DG)(DA)(DC) (DG)(DT)(DA)(DC)(DC)(DT)(DC)(DT)(DC) (DG)(DA)(DC)(DC)(DC)(DT)(DG)(DT)(DG)(DC) (DT) (DA)(DG)(DA)(DC)(DA)(DC)(DG)(DG)

+
Macromolecule #14: RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3')

MacromoleculeName: RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') / type: rna / ID: 14 / Number of copies: 1
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 8.245842 KDa
SequenceString:
UGAAUCUAUU UCUUUUAUCG AGAGGU

+
Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
25.0 mMHEPES
100.0 mMNaCl
0.05 %Tween 20
GridSupport film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 24.0 µm / Nominal defocus min: 5.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2200000
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V3.8) / Number images used: 215000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.8)
Final 3D classificationNumber classes: 10 / Avg.num./class: 95000 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8qsz:
Structure of s. pombe RNA polymerase II in complex with DSIF and Rat1/Rai1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more