[English] 日本語
Yorodumi
- EMDB-42437: Composite map of PIC_delta_TFIIK form2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42437
TitleComposite map of PIC_delta_TFIIK form2
Map datacomposite map of PIC_delta_TFIIK form2
Sample
  • Complex: composite map of PIC_deltaTFIIK form 2
    • Protein or peptide: x 28 types
    • DNA: x 2 types
  • Ligand: x 3 types
Keywordspol II / Transcription
Function / homology
Function and homology information


regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / TFIIA-class transcription factor complex binding / regulation of mRNA 3'-end processing / RNA polymerase III transcription regulatory region sequence-specific DNA binding / phosphatidylinositol-5-phosphate binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / TFIIA-class transcription factor complex binding / regulation of mRNA 3'-end processing / RNA polymerase III transcription regulatory region sequence-specific DNA binding / phosphatidylinositol-5-phosphate binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / regulation of transcription by RNA polymerase III / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / transcription factor TFIIF complex / DNA 5'-3' helicase / phosphatidylinositol-3-phosphate binding / RNA polymerase I preinitiation complex assembly / transcription factor TFIIA complex / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA binding, bending / RNA Polymerase I Transcription Initiation / transcription preinitiation complex / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / 3'-5' DNA helicase activity / DNA 3'-5' helicase / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / poly(A)+ mRNA export from nucleus / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of TC-NER Pre-Incision Complex / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / RNA polymerase II complex binding / Estrogen-dependent gene expression / ATPase activator activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / protein phosphatase activator activity / positive regulation of translational initiation / Dual incision in TC-NER / positive regulation of RNA polymerase II transcription preinitiation complex assembly / ATP-dependent activity, acting on DNA / positive regulation of transcription initiation by RNA polymerase II / transcription by RNA polymerase III / transcription by RNA polymerase I / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II core promoter sequence-specific DNA binding / transcription-coupled nucleotide-excision repair / DNA helicase activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA-directed RNA polymerase activity / transcription antitermination / RNA polymerase II transcription regulatory region sequence-specific DNA binding / isomerase activity / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / : / : / :
Similarity search - Function
: / Tfa2 E-tether / Bacterial type XPD DNA helicase, FeS cluster domain / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. ...: / Tfa2 E-tether / Bacterial type XPD DNA helicase, FeS cluster domain / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Helical and beta-bridge domain / Helical and beta-bridge domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIH subunit TTDA/Tfb5 / Transcription initiation factor TFIIE, beta subunit / TFB5-like superfamily / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / Transcription factor TFIIH complex subunit Tfb5 / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription factor TFIIH complex subunit Tfb5 / ATP-dependent helicase Rad3/Chl1-like / : / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / TFIIS/LEDGF domain superfamily / Zinc finger, TFIIB-type / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...DNA-directed RNA polymerase II subunit RPB1 / General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2 / General transcription and DNA repair factor IIH subunit TFB1 / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIE subunit alpha / Transcription initiation factor IIE subunit beta / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit alpha / Transcription initiation factor IIF subunit beta / General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 / General transcription and DNA repair factor IIH subunit TFB2 / General transcription and DNA repair factor IIH subunit SSL1 / General transcription and DNA repair factor IIH subunit TFB4 / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYang C / Murakami K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2024
Title: Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3.
Authors: Chun Yang / Pratik Basnet / Samah Sharmin / Hui Shen / Craig D Kaplan / Kenji Murakami /
Abstract: RNA polymerase II (pol II) initiates transcription from transcription start sites (TSSs) located ∼30-35 bp downstream of the TATA box in metazoans, whereas in the yeast Saccharomyces cerevisiae, ...RNA polymerase II (pol II) initiates transcription from transcription start sites (TSSs) located ∼30-35 bp downstream of the TATA box in metazoans, whereas in the yeast Saccharomyces cerevisiae, pol II scans further downstream TSSs located ∼40-120 bp downstream of the TATA box. Previously, we found that removal of the kinase module TFIIK (Kin28-Ccl1-Tfb3) from TFIIH shifts the TSS in a yeast in vitro system upstream to the location observed in metazoans and that addition of recombinant Tfb3 back to TFIIH-ΔTFIIK restores the downstream TSS usage. Here, we report that this biochemical activity of yeast TFIIK in TSS scanning is attributable to the Tfb3 RING domain at the interface with pol II in the pre-initiation complex (PIC): especially, swapping Tfb3 Pro51-a residue conserved among all fungi-with Ala or Ser as in MAT1, the metazoan homolog of Tfb3, confers an upstream TSS shift in vitro in a similar manner to the removal of TFIIK. Yeast genetic analysis suggests that both Pro51 and Arg64 of Tfb3 are required to maintain the stability of the Tfb3-pol II interface in the PIC. Cryo-electron microscopy analysis of a yeast PIC lacking TFIIK reveals considerable variability in the orientation of TFIIH, which impairs TSS scanning after promoter opening.
History
DepositionOct 20, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42437.png

Downloads & links

-
Map

FileDownload / File: emd_42437.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map of PIC_delta_TFIIK form2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum0.0 - 0.054039262
Average (Standard dev.)0.0004053079 (±0.0022373893)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: consensus map before focused refinement

Fileemd_42437_additional_1.map
Annotationconsensus map before focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : composite map of PIC_deltaTFIIK form 2

EntireName: composite map of PIC_deltaTFIIK form 2
Components
  • Complex: composite map of PIC_deltaTFIIK form 2
    • Protein or peptide: Transcription initiation factor IIB
    • 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 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: Transcription initiation factor IIF subunit alpha
    • Protein or peptide: Transcription initiation factor IIF subunit beta
    • Protein or peptide: Transcription elongation factor S-II
    • Protein or peptide: TATA-box-binding protein
    • Protein or peptide: Transcription initiation factor IIA large subunit
    • Protein or peptide: Transcription initiation factor IIA subunit 2
    • Protein or peptide: Transcription initiation factor IIE subunit alpha
    • Protein or peptide: Transcription initiation factor IIE subunit beta
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB4
    • Protein or peptide: DNA-directed RNA polymerase II subunit RPB7
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPD/RAD3
    • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB1
    • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB4
    • Protein or peptide: General transcription and DNA repair factor IIH subunit SSL1
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPB
    • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB2
    • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB5
    • DNA: non-template strand
    • DNA: template strand
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: IRON/SULFUR CLUSTER

+
Supramolecule #1: composite map of PIC_deltaTFIIK form 2

SupramoleculeName: composite map of PIC_deltaTFIIK form 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1 MDa

+
Macromolecule #1: Transcription initiation factor IIB

MacromoleculeName: Transcription initiation factor IIB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 38.25734 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MMTRESIDKR AGRRGPNLNI VLTCPECKVY PPKIVERFSE GDVVCALCGL VLSDKLVDTR SEWRTFSNDD HNGDDPSRVG EASNPLLDG NNLSTRIGKG ETTDMRFTKE LNKAQGKNVM DKKDNEVQAA FAKITMLCDA AELPKIVKDC AKEAYKLCHD E KTLKGKSM ...String:
MMTRESIDKR AGRRGPNLNI VLTCPECKVY PPKIVERFSE GDVVCALCGL VLSDKLVDTR SEWRTFSNDD HNGDDPSRVG EASNPLLDG NNLSTRIGKG ETTDMRFTKE LNKAQGKNVM DKKDNEVQAA FAKITMLCDA AELPKIVKDC AKEAYKLCHD E KTLKGKSM ESIMAASILI GCRRAEVART FKEIQSLIHV KTKEFGKTLN IMKNILRGKS EDGFLKIDTD NMSGAQNLTY IP RFCSHLG LPMQVTTSAE YTAKKCKEIK EIAGKSPITI AVVSIYLNIL LFQIPITAAK VGQTLQVTEG TIKSGYKILY EHR DKLVDP QLIANGVVSL DNLPGVEKK

UniProtKB: Transcription initiation factor IIB

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

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 191.821578 KDa
SequenceString: MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKP VFHVGFIAKI KKVCECVCMH CGKLLLDEHN ELMRQALAIK DSKKRFAAIW TLCKTKMVCE TDVPSEDDPT Q LVSRGGCG ...String:
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKP VFHVGFIAKI KKVCECVCMH CGKLLLDEHN ELMRQALAIK DSKKRFAAIW TLCKTKMVCE TDVPSEDDPT Q LVSRGGCG NTQPTIRKDG LKLVGSWKKD RATGDADEPE LRVLSTEEIL NIFKHISVKD FTSLGFNEVF SRPEWMILTC LP VPPPPVR PSISFNESQR GEDDLTFKLA DILKANISLE TLEHNGAPHH AIEEAESLLQ FHVATYMDND IAGQPQALQK SGR PVKSIR ARLKGKEGRI RGNLMGKRVD FSARTVISGD PNLELDQVGV PKSIAKTLTY PEVVTPYNID RLTQLVRNGP NEHP GAKYV IRDSGDRIDL RYSKRAGDIQ LQYGWKVERH IMDNDPVLFN RQPSLHKMSM MAHRVKVIPY STFRLNLSVT SPYNA DFDG DEMNLHVPQS EETRAELSQL CAVPLQIVSP QSNKPCMGIV QDTLCGIRKL TLRDTFIELD QVLNMLYWVP DWDGVI PTP AIIKPKPLWS GKQILSVAIP NGIHLQRFDE GTTLLSPKDN GMLIIDGQII FGVVEKKTVG SSNGGLIHVV TREKGPQ VC AKLFGNIQKV VNFWLLHNGF STGIGDTIAD GPTMREITET IAEAKKKVLD VTKEAQANLL TAKHGMTLRE SFEDNVVR F LNEARDKAGR LAEVNLKDLN NVKQMVMAGS KGSFINIAQM SACVGQQSVE GKRIAFGFVD RTLPHFSKDD YSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGS DAAFEKRYRV DLLNTDHTLD PSLLESGSEI LGDLKLQVLL DEEYKQLVKD RKFLREVFVD GEANWPLPVN I RRIIQNAQ QTFHIDHTKP SDLTIKDIVL GVKDLQENLL VLRGKNEIIQ NAQRDAVTLF CCLLRSRLAT RRVLQEYRLT KQ AFDWVLS NIEAQFLRSV VHPGEMVGVL AAQSIGEPAT QMTLNTFHFA GVASKKVTSG VPRLKEILNV AKNMKTPSLT VYL EPGHAA DQEQAKLIRS AIEHTTLKSV TIASEIYYDP DPRSTVIPED EEIIQLHFSL LDEEAEQSFD QQSPWLLRLE LDRA AMNDK DLTMGQVGER IKQTFKNDLF VIWSEDNDEK LIIRCRVVRP KSLDAETEAE EDHMLKKIEN TMLENITLRG VENIE RVVM MKYDRKVPSP TGEYVKEPEW VLETDGVNLS EVMTVPGIDP TRIYTNSFID IMEVLGIEAG RAALYKEVYN VIASDG SYV NYRHMALLVD VMTTQGGLTS VTRHGFNRSN TGALMRCSFE ETVEILFEAG ASAELDDCRG VSENVILGQM APIGTGA FD VMIDEESLVK YMPEQKITEI EDGQDGGVTP YSNESGLVNA DLDVKDELMF SPLVDSGSND AMAGGFTAYG GADYGEAT S PFGAYGEAPT SPGFGVSSPG FSPTSPTYSP TSPAYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP SYSPTSPSY SPTSPNYSPT SPSYSPTSPG YSPGSPAYSP KQDEQKHNEN ENSR

UniProtKB: DNA-directed RNA polymerase II subunit RPB1

+
Macromolecule #3: DNA-directed RNA polymerase II subunit RPB2

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 138.937297 KDa
SequenceString: MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYE ISFGKIYVTK PMVNESDGVT HALYPQEARL RNLTYSSGLF VDVKKRTYEA IDVPGRELKY ELIAEESEDD S ESGKVFIG ...String:
MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ DIICEDSTLI LEQLAQHTTE SDNISRKYE ISFGKIYVTK PMVNESDGVT HALYPQEARL RNLTYSSGLF VDVKKRTYEA IDVPGRELKY ELIAEESEDD S ESGKVFIG RLPIMLRSKN CYLSEATESD LYKLKECPFD MGGYFIINGS EKVLIAQERS AGNIVQVFKK AAPSPISHVA EI RSALEKG SRFISTLQVK LYGREGSSAR TIKATLPYIK QDIPIVIIFR ALGIIPDGEI LEHICYDVND WQMLEMLKPC VED GFVIQD RETALDFIGR RGTALGIKKE KRIQYAKDIL QKEFLPHITQ LEGFESRKAF FLGYMINRLL LCALDRKDQD DRDH FGKKR LDLAGPLLAQ LFKTLFKKLT KDIFRYMQRT VEEAHDFNMK LAINAKTITS GLKYALATGN WGEQKKAMSS RAGVS QVLN RYTYSSTLSH LRRTNTPIGR DGKLAKPRQL HNTHWGLVCP AETPEGQACG LVKNLSLMSC ISVGTDPMPI ITFLSE WGM EPLEDYVPHQ SPDATRVFVN GVWHGVHRNP ARLMETLRTL RRKGDINPEV SMIRDIREKE LKIFTDAGRV YRPLFIV ED DESLGHKELK VRKGHIAKLM ATEYQDIEGG FEDVEEYTWS SLLNEGLVEY IDAEEEESIL IAMQPEDLEP AEANEEND L DVDPAKRIRV SHHATTFTHC EIHPSMILGV AASIIPFPDH NQSPRNTYQS AMGKQAMGVF LTNYNVRMDT MANILYYPQ KPLGTTRAME YLKFRELPAG QNAIVAIACY SGYNQEDSMI MNQSSIDRGL FRSLFFRSYM DQEKKYGMSI TETFEKPQRT NTLRMKHGT YDKLDDDGLI APGVRVSGED VIIGKTTPIS PDEEELGQRT AYHSKRDAST PLRSTENGIV DQVLVTTNQD G LKFVKVRV RTTKIPQIGD KFASRHGQKG TIGITYRRED MPFTAEGIVP DLIINPHAIP SRMTVAHLIE CLLSKVAALS GN EGDASPF TDITVEGISK LLREHGYQSR GFEVMYNGHT GKKLMAQIFF GPTYYQRLRH MVDDKIHARA RGPMQVLTRQ PVE GRSRDG GLRFGEMERD CMIAHGAASF LKERLMEASD AFRVHICGIC GLMTVIAKLN HNQFECKGCD NKIDIYQIHI PYAA KLLFQ ELMAMNITPR LYTDRSRDF

UniProtKB: DNA-directed RNA polymerase II subunit RPB2

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

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 35.330457 KDa
SequenceString: MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCE DHCDKCSVVL TLQAFGESES TTNVYSKDLV IVSNLMGRNI GHPIIQDKEG NGVLICKLRK GQELKLTCVA K KGIAKEHA ...String:
MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCE DHCDKCSVVL TLQAFGESES TTNVYSKDLV IVSNLMGRNI GHPIIQDKEG NGVLICKLRK GQELKLTCVA K KGIAKEHA KWGPAAAIEF EYDPWNKLKH TDYWYEQDSA KEWPQSKNCE YEDPPNEGDP FDYKAQADTF YMNVESVGSI PV DQVVVRG IDTLQKKVAS ILLALTQMDQ DKVNFASGDN NTASNMLGSN EDVMMTGAEQ DPYSNASQMG NTGSGGYDNA W

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

+
Macromolecule #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.117094 KDa
SequenceString: MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY ...String:
MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY RLKESQLPRI QRADPVALYL GLKRGEVVKI IRKSETSGRY ASYRICM

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

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

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.931834 KDa
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTLK EKAIPKDQRA TTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR IAMKELAEKK IPLVIRRYLP DGSFEDWSVE ELIVDL

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

+
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: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.525363 KDa
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTPA NDSSATRSWR PPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG GLLMRLEGNY RNLNNLKQEN AYLLIRR

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

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

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.308161 KDa
SequenceString:
MTTFRFCRDC NNMLYPREDK ENNRLLFECR TCSYVEEAGS PLVYRHELIT NIGETAGVVQ DIGSDPTLPR SDRECPKCHS RENVFFQSQ QRRKDTSMVL FFVCLSCSHI FTSDQKNKRT QFS

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: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.290732 KDa
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKRD

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: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.633493 KDa
SequenceString:
MNAPDRFELF LLGEGESKLK IDPDTKAPNA VVITFEKEDH TLGNLIRAEL LNDRKVLFAA YKVEHPFFAR FKLRIQTTEG YDPKDALKN ACNSIINKLG ALKTNFETEW NLQTLAADDA F

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: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.729969 KDa
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEAR

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

+
Macromolecule #12: Transcription initiation factor IIF subunit alpha

MacromoleculeName: Transcription initiation factor IIF subunit alpha / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 82.32057 KDa
SequenceString: MSRRNPPGSR NGGGPTNASP FIKRDRMRRN FLRMRMGQNG SNSSSPGVPN GDNSRGSLVK KDDPEYAEER EKMLLQIGVE ADAGRSNVK VKDEDPNEYN EFPLRAIPKE DLENMRTHLL KFQSKKKINP VTDFHLPVRL HRKDTRNLQF QLTRAEIVQR Q KEISEYKK ...String:
MSRRNPPGSR NGGGPTNASP FIKRDRMRRN FLRMRMGQNG SNSSSPGVPN GDNSRGSLVK KDDPEYAEER EKMLLQIGVE ADAGRSNVK VKDEDPNEYN EFPLRAIPKE DLENMRTHLL KFQSKKKINP VTDFHLPVRL HRKDTRNLQF QLTRAEIVQR Q KEISEYKK KAEQERSTPN SGGMNKSGTV SLNNTVKDGS QTPTVDSVTK DNTANGVNSS IPTVTGSSVP PASPTTVSAV ES NGLSNGS TSAANGLDGN ASTANLANGR PLVTKLEDAG PAEDPTKVGM VKYDGKEVTN EPEFEEGTMD PLADVAPDGG GRA KRGNLR RKTRQLKVLD ENAKKLRFEE FYPWVMEDFD GYNTWVGSYE AGNSDSYVLL SVEDDGSFTM IPADKVYKFT ARNK YATLT IDEAEKRMDK KSGEVPRWLM KHLDNIGTTT TRYDRTRRKL KAVADQQAMD EDDRDDNSEV ELDYDEEFAD DEEAP IIDG NEQENKESEQ RIKKEMLQAN AMGLRDEEAP SENEEDELFG EKKIDEDGER IKKALQKTEL AALYSSDENE INPYLS ESD IENKENESPV KKEEDSDTLS KSKRSSPKKQ QKKATNAHVH KEPTLRVKSI KNCVIILKGD KKILKSFPEG EWNPQTT KA VDSSNNASNT VPSPIKQEEG LNSTVAEREE TPAPTITEKD IIEAIGDGKV NIKEFGKFIR RKYPGAENKK LMFAIVKK L CRKVGNDHME LKKE

UniProtKB: Transcription initiation factor IIF subunit alpha

+
Macromolecule #13: Transcription initiation factor IIF subunit beta

MacromoleculeName: Transcription initiation factor IIF subunit beta / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 46.684492 KDa
SequenceString: MSSGSAGAPA LSNNSTNSVA KEKSGNISGD EYLSQEEEVF DGNDIENNET KVYEESLDLD LERSNRQVWL VRLPMFLAEK WRDRNNLHG QELGKIRINK DGSKITLLLN ENDNDSIPHE YDLELTKKVV ENEYVFTEQN LKKYQQRKKE LEADPEKQRQ A YLKKQERE ...String:
MSSGSAGAPA LSNNSTNSVA KEKSGNISGD EYLSQEEEVF DGNDIENNET KVYEESLDLD LERSNRQVWL VRLPMFLAEK WRDRNNLHG QELGKIRINK DGSKITLLLN ENDNDSIPHE YDLELTKKVV ENEYVFTEQN LKKYQQRKKE LEADPEKQRQ A YLKKQERE EELKKKQQQQ KRRNNRKKFN HRVMTDRDGR DRYIPYVKTI PKKTAIVGTV CHECQVMPSM NDPNYHKIVE QR RNIVKLN NKERITTLDE TVGVTMSHTG MSMRSDNSNF LKVGREKAKS NIKSIRMPKK EILDYLFKLF DEYDYWSLKG LKE RTRQPE AHLKECLDKV ATLVKKGPYA FKYTLRPEYK KLKEEERKAT LGELADEQTG SAGDNAQGDA EADLEDEIEM EDVV

UniProtKB: Transcription initiation factor IIF subunit beta

+
Macromolecule #14: Transcription elongation factor S-II

MacromoleculeName: Transcription elongation factor S-II / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 34.903551 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MDSKEVLVHV KNLEKNKSND AAVLEILHVL DKEFVPTEKL LRETKVGVEV NKFKKSTNVE ISKLVKKMIS SWKDAINKNK RSRQAQQHH QDHAPGNAED KTTVGESVNG VQQPASSQSD AMKQDKYVST KPRNSKNDGV DTAIYHHKLR DQVLKALYDV L AKESEHPP ...String:
MDSKEVLVHV KNLEKNKSND AAVLEILHVL DKEFVPTEKL LRETKVGVEV NKFKKSTNVE ISKLVKKMIS SWKDAINKNK RSRQAQQHH QDHAPGNAED KTTVGESVNG VQQPASSQSD AMKQDKYVST KPRNSKNDGV DTAIYHHKLR DQVLKALYDV L AKESEHPP QSILHTAKAI ESEMNKVNNC DTNEAAYKAR YRIIYSNVIS KNNPDLKHKI ANGDITPEFL ATCDAKDLAP AP LKQKIEE IAKQNLYNAQ GATIERSVTD RFTCGKCKEK KVSYYQLQTR SADEPLTTFC TCEACGNRWK FS

UniProtKB: Transcription elongation factor S-II

+
Macromolecule #15: TATA-box-binding protein

MacromoleculeName: TATA-box-binding protein / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.042275 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MADEERLKEF KEANKIVFDP NTRQVWENQN RDGTKPATTF QSEEDIKRAA PESEKDTSAT SGIVPTLQNI VATVTLGCRL DLKTVALHA RNAEYNPKRF AAVIMRIREP KTTALIFASG KMVVTGAKSE DDSKLASRKY ARIIQKIGFA AKFTDFKIQN I VGSCDVKF ...String:
MADEERLKEF KEANKIVFDP NTRQVWENQN RDGTKPATTF QSEEDIKRAA PESEKDTSAT SGIVPTLQNI VATVTLGCRL DLKTVALHA RNAEYNPKRF AAVIMRIREP KTTALIFASG KMVVTGAKSE DDSKLASRKY ARIIQKIGFA AKFTDFKIQN I VGSCDVKF PIRLEGLAFS HGTFSSYEPE LFPGLIYRMV KPKIVLLIFV SGKIVLTGAK QREEIYQAFE AIYPVLSEFR KM

UniProtKB: TATA-box-binding protein

+
Macromolecule #16: Transcription initiation factor IIA large subunit

MacromoleculeName: Transcription initiation factor IIA large subunit / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 32.230805 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSNAEASRVY EIIVESVVNE VREDFENAGI DEQTLQDLKN IWQKKLTETK VTTFSWDNQF NEGNINGVQN DLNFNLATPG VNSSEFNIK EENTGNEGLI LPNINSNNNI PHSGETNINT NTVEATNNSG ATLNTNTSGN TNADVTSQPK IEVKPEIELT I NNANITTV ...String:
MSNAEASRVY EIIVESVVNE VREDFENAGI DEQTLQDLKN IWQKKLTETK VTTFSWDNQF NEGNINGVQN DLNFNLATPG VNSSEFNIK EENTGNEGLI LPNINSNNNI PHSGETNINT NTVEATNNSG ATLNTNTSGN TNADVTSQPK IEVKPEIELT I NNANITTV ENIDDESEKK DDEEKEEDVE KTRKEKEQIE QVKLQAKKEK RSALLDTDEV GSELDDSDDD YLISEGEEDG PD ENLMLCL YDKVTRTKAR WKCSLKDGVV TINRNDYTFQ KAQVEAEWV

UniProtKB: Transcription initiation factor IIA large subunit

+
Macromolecule #17: Transcription initiation factor IIA subunit 2

MacromoleculeName: Transcription initiation factor IIA subunit 2 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.47307 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MAVPGYYELY RRSTIGNSLV DALDTLISDG RIEASLAMRV LETFDKVVAE TLKDNTQSKL TVKGNLDTYG FCDDVWTFIV KNCQVTVED SHRDASQNGS GDSQSVISVD KLRIVACNSK KSE

UniProtKB: Transcription initiation factor IIA subunit 2

+
Macromolecule #18: Transcription initiation factor IIE subunit alpha

MacromoleculeName: Transcription initiation factor IIE subunit alpha / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 54.804809 KDa
SequenceString: MDRPIDDIVK NLLKFVVRGF YGGSFVLVLD AILFHSVLAE DDLKQLLSIN KTELGPLIAR LRSDRLISIH KQREYPPNSK SVERVYYYV KYPHAIDAIK WKVHQVVQRL KDDLDKNSEP NGYMCPICLT KYTQLEAVQL LNFDRTEFLC SLCDEPLVED D SGKKNKEK ...String:
MDRPIDDIVK NLLKFVVRGF YGGSFVLVLD AILFHSVLAE DDLKQLLSIN KTELGPLIAR LRSDRLISIH KQREYPPNSK SVERVYYYV KYPHAIDAIK WKVHQVVQRL KDDLDKNSEP NGYMCPICLT KYTQLEAVQL LNFDRTEFLC SLCDEPLVED D SGKKNKEK QDKLNRLMDQ IQPIIDSLKK IDDSRIEENT FEIALARLIP PQNQSHAAYT YNPKKGSTMF RPGDSAPLPN LM GTALGND SSRRAGANSQ ATLHINITTA SDEVAQRELQ ERQAEEKRKQ NAVPEWHKQS TIGKTALGRL DNEEEFDPVV TAS AMDSIN PDNEPAQETS YQNNRTLTEQ EMEERENEKT LNDYYAALAK KQAKLNKEEE EEEEEEEDEE EEEEEEMEDV MDDN DETAR ENALEDEFED VTDTAGTAKT ESNTSNDVKQ ESINDKTEDA VNATATASGP SANAKPNDGD DDDDDDDDEM DIEFE DV

UniProtKB: Transcription initiation factor IIE subunit alpha

+
Macromolecule #19: Transcription initiation factor IIE subunit beta

MacromoleculeName: Transcription initiation factor IIE subunit beta / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.050434 KDa
SequenceString: MSKNRDPLLA NLNAFKSKVK SAPVIAPAKV GQKKTNDTVI TIDGNTRKRT ASERAQENTL NSAKNPVLVD IKKEAGSNSS NAISLDDDD DDEDFGSSPS KKVRPGSIAA AALQANQTDI SKSHDSSKLL WATEYIQKKG KPVLVNELLD YLSMKKDDKV I ELLKKLDR ...String:
MSKNRDPLLA NLNAFKSKVK SAPVIAPAKV GQKKTNDTVI TIDGNTRKRT ASERAQENTL NSAKNPVLVD IKKEAGSNSS NAISLDDDD DDEDFGSSPS KKVRPGSIAA AALQANQTDI SKSHDSSKLL WATEYIQKKG KPVLVNELLD YLSMKKDDKV I ELLKKLDR IEFDPKKGTF KYLSTYDVHS PSELLKLLRS QVTFKGISCK DLKDGWPQCD ETINQLEEDS KILVLRTKKD KT PRYVWYN SGGNLKCIDE EFVKMWENVQ LPQFAELPRK LQDLGLKPAS VDPATIKRQT KRVEVKKKRQ RKGKITNTHM TGI LKDYSH RV

UniProtKB: Transcription initiation factor IIE subunit beta

+
Macromolecule #20: DNA-directed RNA polymerase II subunit RPB4

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB4 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.451191 KDa
SequenceString: MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL NLSEARLVIK EALVERRRAF KRSQKKHKKK HLKHENAND ETTAVEDEDD DLDEDDVNAD DDDFMHSETR EKELESIDVL LEQTTGGNNK DLKNTMQYLT NFSRFRDQET V GAVIQLLK ...String:
MNVSTSTFQT RRRRLKKVEE EENAATLQLG QEFQLKQINH QGEEEELIAL NLSEARLVIK EALVERRRAF KRSQKKHKKK HLKHENAND ETTAVEDEDD DLDEDDVNAD DDDFMHSETR EKELESIDVL LEQTTGGNNK DLKNTMQYLT NFSRFRDQET V GAVIQLLK STGLHPFEVA QLGSLACDTA DEAKTLIPSL NNKISDDELE RILKELSNLE TLY

UniProtKB: DNA-directed RNA polymerase II subunit RPB4

+
Macromolecule #21: DNA-directed RNA polymerase II subunit RPB7

MacromoleculeName: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 19.081053 KDa
SequenceString:
MFFIKDLSLN ITLHPSFFGP RMKQYLKTKL LEEVEGSCTG KFGYILCVLD YDNIDIQRGR ILPTDGSAEF NVKYRAVVFK PFKGEVVDG TVVSCSQHGF EVQVGPMKVF VTKHLMPQDL TFNAGSNPPS YQSSEDVITI KSRIRVKIEG CISQVSSIHA I GSIKEDYL GAI

UniProtKB: DNA-directed RNA polymerase II subunit RPB7

+
Macromolecule #22: General transcription and DNA repair factor IIH helicase subunit ...

MacromoleculeName: General transcription and DNA repair factor IIH helicase subunit XPD/RAD3
type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA 5'-3' helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 89.899047 KDa
SequenceString: MKFYIDDLPV LFPYPKIYPE QYNYMCDIKK TLDVGGNSIL EMPSGTGKTV SLLSLTIAYQ MHYPEHRKII YCSRTMSEIE KALVELENL MDYRTKELGY QEDFRGLGLT SRKNLCLHPE VSKERKGTVV DEKCRRMTNG QAKRKLEEDP EANVELCEYH E NLYNIEVE ...String:
MKFYIDDLPV LFPYPKIYPE QYNYMCDIKK TLDVGGNSIL EMPSGTGKTV SLLSLTIAYQ MHYPEHRKII YCSRTMSEIE KALVELENL MDYRTKELGY QEDFRGLGLT SRKNLCLHPE VSKERKGTVV DEKCRRMTNG QAKRKLEEDP EANVELCEYH E NLYNIEVE DYLPKGVFSF EKLLKYCEEK TLCPYFIVRR MISLCNIIIY SYHYLLDPKI AERVSNEVSK DSIVIFDEAH NI DNVCIES LSLDLTTDAL RRATRGANAL DERISEVRKV DSQKLQDEYE KLVQGLHSAD ILTDQEEPFV ETPVLPQDLL TEA IPGNIR RAEHFVSFLK RLIEYLKTRM KVLHVISETP KSFLQHLKQL TFIERKPLRF CSERLSLLVR TLEVTEVEDF TALK DIATF ATLISTYEEG FLLIIEPYEI ENAAVPNPIM RFTCLDASIA IKPVFERFSS VIITSGTISP LDMYPRMLNF KTVLQ KSYA MTLAKKSFLP MIITKGSDQV AISSRFEIRN DPSIVRNYGS MLVEFAKITP DGMVVFFPSY LYMESIVSMW QTMGIL DEV WKHKLILVET PDAQETSLAL ETYRKACSNG RGAILLSVAR GKVSEGIDFD HQYGRTVLMI GIPFQYTESR ILKARLE FM RENYRIREND FLSFDAMRHA AQCLGRVLRG KDDYGVMVLA DRRFSRKRSQ LPKWIAQGLS DADLNLSTDM AISNTKQF L RTMAQPTDPK DQEGVSVWSY EDLIKHQNSR KDQGGFIENE NKEGEQDEDE DEDIEMQ

UniProtKB: General transcription and DNA repair factor IIH helicase subunit XPD/RAD3

+
Macromolecule #23: General transcription and DNA repair factor IIH subunit TFB1

MacromoleculeName: General transcription and DNA repair factor IIH subunit TFB1
type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 72.993328 KDa
SequenceString: MSHSGAAIFE KVSGIIAINE DVSPAELTWR STDGDKVHTV VLSTIDKLQA TPASSEKMML RLIGKVDESK KRKDNEGNEV VPKPQRHMF SFNNRTVMDN IKMTLQQIIS RYKDADIYEE KRRREESAQH TETPMSSSSV TAGTPTPHLD TPQLNNGAPL I NTAKLDDS ...String:
MSHSGAAIFE KVSGIIAINE DVSPAELTWR STDGDKVHTV VLSTIDKLQA TPASSEKMML RLIGKVDESK KRKDNEGNEV VPKPQRHMF SFNNRTVMDN IKMTLQQIIS RYKDADIYEE KRRREESAQH TETPMSSSSV TAGTPTPHLD TPQLNNGAPL I NTAKLDDS LSKEKLLTNL KLQQSLLKGN KVLMKVFQET VINAGLPPSE FWSTRIPLLR AFALSTSQKV GPYNVLSTIK PV ASSENKV NVNLSREKIL NIFENYPIVK KAYTDNVPKN FKEPEFWARF FSSKLFRKLR GEKIMQNDRG DVIIDRYLTL DQE FDRKDD DMLLHPVKKI IDLDGNIQDD PVVRGNRPDF TMQPGVDING NSDGTVDILK GMNRLSEKMI MALKNEYSRT NLQN KSNIT NDEEDEDNDE RNELKIDDLN ESYKTNYAII HLKRNAHEKT TDNDAKSSAD SIKNADLKVS NQQMLQQLSL VMDNL INKL DLNQVVPNNE VSNKINKRVI TAIKINAKQA KHNNVNSALG SFVDNTSQAN ELEVKSTLPI DLLESCRMLH TTCCEF LKH FYIHFQSGEQ KQASTVKKLY NHLKDCIEKL NELFQDVLNG DGESMSNTCT AYLKPVLNSI TLATHKYDEY FNEYNNN SN

UniProtKB: General transcription and DNA repair factor IIH subunit TFB1

+
Macromolecule #24: General transcription and DNA repair factor IIH subunit TFB4

MacromoleculeName: General transcription and DNA repair factor IIH subunit TFB4
type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.506422 KDa
SequenceString: MDAISDPTFK HARSRKQVTE ESPSLLTVII EIAPKLWTTF DEEGNEKGSI IKVLEALIVF LNAHLAFNSA NKVAVIAAYS QGIKYLYPE STSALKASES ENKTRSDLKI INSDMYRRFR NVDETLVEEI YKLFELEKKQ IEQNSQRSTL AGAMSAGLTY V NRISKESV ...String:
MDAISDPTFK HARSRKQVTE ESPSLLTVII EIAPKLWTTF DEEGNEKGSI IKVLEALIVF LNAHLAFNSA NKVAVIAAYS QGIKYLYPE STSALKASES ENKTRSDLKI INSDMYRRFR NVDETLVEEI YKLFELEKKQ IEQNSQRSTL AGAMSAGLTY V NRISKESV TTSLKSRLLV LTCGSGSSKD EIFQYIPIMN CIFSATKMKC PIDVVKIGGS KESTFLQQTT DATNGVYLHV ES TEGLIQY LATAMFIDPS LRPIIVKPNH GSVDFRTSCY LTGRVVAVGF ICSVCLCVLS IIPPGNKCPA CDSQFDEHVI AKL KRKPVV PRLKAKKKVT KP

UniProtKB: General transcription and DNA repair factor IIH subunit TFB4

+
Macromolecule #25: General transcription and DNA repair factor IIH subunit SSL1

MacromoleculeName: General transcription and DNA repair factor IIH subunit SSL1
type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 52.370035 KDa
SequenceString: MAPVVISESE EDEDRVAITR RTKRQVHFDG EGDDRVDQQQ QQHSSSHRDR DKHVQRKKKK RLSNRNLQGS NGGYAWEDEI KRSWDLVKV DDEGDMASLV ASIVEARKKR TAKKNITPYQ RGIIRSLILT LDCSEAMLEK DLRPNRHAMI IQYAIDFVHE F FDQNPISQ ...String:
MAPVVISESE EDEDRVAITR RTKRQVHFDG EGDDRVDQQQ QQHSSSHRDR DKHVQRKKKK RLSNRNLQGS NGGYAWEDEI KRSWDLVKV DDEGDMASLV ASIVEARKKR TAKKNITPYQ RGIIRSLILT LDCSEAMLEK DLRPNRHAMI IQYAIDFVHE F FDQNPISQ MGIIIMRNGL AQLVSQVSGN PQDHIDALKS IRKQEPKGNP SLQNALEMAR GLLLPVPAHC TREVLIVFGS LS TTDPGDI HQTIDSLVSE KIRVKVLGLS AQVAICKELC KATNYGDESF YKILLDETHL KELFNEAVTP LPVNKINKGF TLV KMGFPT RIFEDTPTFC SCHSKLVYGG YFCPNCHSKV CSLPTVCPCC DLMLILSTHL ARSYHHLMPL KTFAEVPTTE KFRS EDCFS CQSRFPILKN HKNGKLLTSS RYRCEDCKQE FCVDCDVFIH EILHNCPGCE SKPVIT

UniProtKB: General transcription and DNA repair factor IIH subunit SSL1

+
Macromolecule #26: General transcription and DNA repair factor IIH helicase subunit XPB

MacromoleculeName: General transcription and DNA repair factor IIH helicase subunit XPB
type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 95.461664 KDa
SequenceString: MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKD KALLQDTNSD IPADFVPDSV SGMFRSHDFS YLRLRPDHAS RPLWISPSDG RIILESFSPL AEQAQDFLVT I AEPISRPS ...String:
MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKD KALLQDTNSD IPADFVPDSV SGMFRSHDFS YLRLRPDHAS RPLWISPSDG RIILESFSPL AEQAQDFLVT I AEPISRPS HIHEYKITAY SLYAAVSVGL ETDDIISVLD RLSKVPVAES IINFIKGATI SYGKVKLVIK HNRYFVETTQ AD ILQMLLN DSVIGPLRID SDHQVQPPED VLQQQLQQTA GKPATNVNPN DVEAVFSAVI GGDNEREEED DDIDAVHSFE IAN ESVEVV KKRCQEIDYP VLEEYDFRND HRNPDLDIDL KPSTQIRPYQ EKSLSKMFGN GRARSGIIVL PCGAGKTLVG ITAA CTIKK SVIVLCTSSV SVMQWRQQFL QWCTLQPENC AVFTSDNKEM FQTESGLVVS TYSMVANTRN RSHDSQKVMD FLTGR EWGF IILDEVHVVP AAMFRRVVST IAAHAKLGLT ATLVREDDKI GDLNFLIGPK LYEANWMELS QKGHIANVQC AEVWCP MTA EFYQEYLRET ARKRMLLYIM NPTKFQACQF LIQYHERRGD KIIVFSDNVY ALQEYALKMG KPFIYGSTPQ QERMNIL QN FQYNDQINTI FLSKVGDTSI DLPEATCLIQ ISSHYGSRRQ EAQRLGRILR AKRRNDEGFN AFFYSLVSKD TQEMYYST K RQAFLVDQGY AFKVITHLHG MENIPNLAYA SPRERRELLQ EVLLKNEEAA GIEVGDDADN SVGRGSNGHK RFKSKAVRG EGSLSGLAGG EDMAYMEYST NKNKELKEHH PLIRKMYYKN LKK

UniProtKB: General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2

+
Macromolecule #27: General transcription and DNA repair factor IIH subunit TFB2

MacromoleculeName: General transcription and DNA repair factor IIH subunit TFB2
type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 58.602312 KDa
SequenceString: MSDYSLKHSV TQYLEEIPQQ VQNRLYTSPA TCLAIYRILP PLAKFFIMAM VFNENEVPLL DLDKWVNSNG KLQFQNAIKS MKSLHLLIP NKSSGTLMIN LNPTFKISLR NALTGGEVQN SFGVVVEENV VSLDLLDEYS ANKWETILHF MVGTPLAKIP S EKVLNLLK ...String:
MSDYSLKHSV TQYLEEIPQQ VQNRLYTSPA TCLAIYRILP PLAKFFIMAM VFNENEVPLL DLDKWVNSNG KLQFQNAIKS MKSLHLLIP NKSSGTLMIN LNPTFKISLR NALTGGEVQN SFGVVVEENV VSLDLLDEYS ANKWETILHF MVGTPLAKIP S EKVLNLLK HSKLMEEVNS TGEFKITNEG FQFLLQEINS QLWTLLLQYL KMIETSKMDL VDVLHFIFML GALEVGKAYK ID ALSETQR IMLQDMRDYG LVFQKHSNDS IFYPTKLALM LTSDTKTIRS ASNAMDSVLR QNREEPSVNE DGANGKSTTD ITT SDDLNK AGLKNQDIPD GSLIVETNFK IYSYSNSPLQ IAVLSLFVHL KARFVNMVLG QITRESIRRA LTNGITADQI IAYL ETHAH PQMRRLAEEK LEKKLELDPN CKEPLQVLPP TVVDQIRLWQ LELDRVITYE GSLYSDFETS QEYNLLSKYA QDIGV LLWK DDKKKKFFIS KEGNSQVLDF AKRKLKKKQ

UniProtKB: General transcription and DNA repair factor IIH subunit TFB2

+
Macromolecule #28: General transcription and DNA repair factor IIH subunit TFB5

MacromoleculeName: General transcription and DNA repair factor IIH subunit TFB5
type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.24349 KDa
SequenceString:
MARARKGALV QCDPSIKALI LQIDAKMSDI VLEELDDTHL LVNPSKVEFV KHELNRLLSK NIYNPMDEEE NQ

UniProtKB: General transcription and DNA repair factor IIH subunit TFB5

+
Macromolecule #29: non-template strand

MacromoleculeName: non-template strand / type: dna / ID: 29 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 19.703676 KDa
SequenceString: (DG)(DG)(DT)(DG)(DA)(DA)(DA)(DA)(DC)(DA) (DT)(DA)(DT)(DA)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DC)(DT)(DC)(DT)(DA)(DC)(DA)(DT) (DT)(DC)(DA)(DT)(DT)(DT)(DT)(DT)(DT)(DC) (DA) (DT)(DC)(DG)(DA)(DT)(DG) ...String:
(DG)(DG)(DT)(DG)(DA)(DA)(DA)(DA)(DC)(DA) (DT)(DA)(DT)(DA)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DC)(DT)(DC)(DT)(DA)(DC)(DA)(DT) (DT)(DC)(DA)(DT)(DT)(DT)(DT)(DT)(DT)(DC) (DA) (DT)(DC)(DG)(DA)(DT)(DG)(DA)(DG) (DT)(DA)(DC)(DT)(DT)(DT)(DA)(DC)(DT)(DT) (DG)(DT) (DT)(DA)(DT)(DC)

GENBANK: GENBANK: CP133022.1

+
Macromolecule #30: template strand

MacromoleculeName: template strand / type: dna / ID: 30 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 19.724719 KDa
SequenceString: (DG)(DA)(DT)(DA)(DA)(DC)(DA)(DA)(DG)(DT) (DA)(DA)(DA)(DG)(DT)(DA)(DC)(DT)(DC)(DA) (DT)(DC)(DG)(DA)(DT)(DG)(DA)(DA)(DA) (DA)(DA)(DA)(DT)(DG)(DA)(DA)(DT)(DG)(DT) (DA) (DG)(DA)(DG)(DC)(DC)(DC) ...String:
(DG)(DA)(DT)(DA)(DA)(DC)(DA)(DA)(DG)(DT) (DA)(DA)(DA)(DG)(DT)(DA)(DC)(DT)(DC)(DA) (DT)(DC)(DG)(DA)(DT)(DG)(DA)(DA)(DA) (DA)(DA)(DA)(DT)(DG)(DA)(DA)(DT)(DG)(DT) (DA) (DG)(DA)(DG)(DC)(DC)(DC)(DC)(DT) (DT)(DT)(DT)(DA)(DT)(DA)(DT)(DG)(DT)(DT) (DT)(DT) (DC)(DA)(DC)(DC)

GENBANK: GENBANK: CP133022.1

+
Macromolecule #31: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 31 / Number of copies: 15 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #32: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 32 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #33: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 33 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Details: Initial Model was obtained with 3D InitialModel in Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90136
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Regularized Likelihood Optimization by Relion
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Regularized Likelihood Optimization by Relion

+
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