EMDB-12745: Yeast RNA polymerase II transcription pre-initiation complex with...

Basic information

• Entry: Database: EMDB / ID: EMD-12745
• Title: Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA

Sample

• Complex: Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA
  • Protein or peptide: x 28 types
  • DNA: x 2 types
• Ligand: x 5 types

• Keywords: Pre-initiation complex / TRANSCRIPTION

Function / homology

Function:

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 / 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 / transcription factor TFIIK complex / 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 / cyclin-dependent protein serine/threonine kinase activator activity / : / DNA binding, bending / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / transcription preinitiation complex / 3'-5' DNA helicase activity / Processing of Capped Intron-Containing Pre-mRNA / DNA 3'-5' helicase / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / poly(A)+ mRNA export from nucleus / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 II Pre-transcription Events / RNA-templated transcription / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase III transcription / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II complex binding / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / ATPase activator activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase I / nuclear-transcribed mRNA catabolic process / protein phosphatase activator activity / positive regulation of translational initiation / transcription by RNA polymerase III / Dual incision in TC-NER / ATP-dependent activity, acting on DNA / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase I complex / tRNA transcription by RNA polymerase III / translesion synthesis / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II core promoter sequence-specific DNA binding / transcription-coupled nucleotide-excision repair / DNA helicase activity / RNA polymerase II, core complex / : / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA-directed RNA polymerase activity / isomerase activity / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / transcription coregulator activity / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / : / : / : / :

Domain/homology:

: / Tfa2 E-tether / Bacterial type XPD DNA helicase, FeS cluster 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 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / 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 / Helicase/UvrB, N-terminal / Zinc finger, TFIIB-type / Type III restriction enzyme, res subunit / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / TBP domain superfamily

Component:

DNA-directed RNA polymerase II subunit RPB1 / General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 / 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 / RNA polymerase II transcription factor B subunit 3 / 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

• Biological species: Saccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae YJM984 (yeast)
• Method: single particle reconstruction / cryo EM / Resolution: 3.2 Å
• Authors: Schilbach S / Aibara S

Funding support

Germany, 5 items

Organization	Grant number	Country
H2020 Marie Curie Actions of the European Commission	894862	Germany
German Research Foundation (DFG)	EXC 2067/1 39072994	Germany
German Research Foundation (DFG)	SFB860	Germany
German Research Foundation (DFG)	SPP2191	Germany
European Research Council (ERC)	882357	Germany

• Citation: Journal: Cell / Year: 2021; Title: Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening.; Authors: Sandra Schilbach / Shintaro Aibara / Christian Dienemann / Frauke Grabbe / Patrick Cramer / ; Abstract: Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of the yeast PIC and define the mechanism of initial DNA opening. We trap the PIC in an intermediate state that contains half a turn of open DNA located 30-35 base pairs downstream of the TATA box. The initially opened DNA region is flanked and stabilized by the polymerase "clamp head loop" and the TFIIF "charged region" that both contribute to promoter-initiated transcription. TFIIE facilitates initiation by buttressing the clamp head loop and by regulating the TFIIH translocase. The initial DNA bubble is then extended in the upstream direction, leading to the open promoter complex and enabling start-site scanning and RNA synthesis. This unique mechanism of DNA opening may permit more intricate regulation than in the Pol I and Pol III systems.

History

Deposition	Apr 13, 2021	-
Header (metadata) release	Jun 16, 2021	-
Map release	Jun 16, 2021	-
Update	Jul 10, 2024	-
Current status	Jul 10, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_12745.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.05 Å

Density

Contour Level	By AUTHOR: 2.1 / Movie #1: 2.1
Minimum - Maximum	-40.258778 - 62.913383000000003
Average (Standard dev.)	0.041241013 (±1.0237968)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order Z Y X Origin 0 0 0 Dimensions 380 380 380 Spacing 380 380 380
Cell	A=B=C: 398.99997 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.05	1.05	1.05
M x/y/z	380	380	380
origin x/y/z	0.000	0.000	0.000
length x/y/z	399.000	399.000	399.000
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	380	380	380
MAP C/R/S	3	2	1
start NC/NR/NS	0	0	0
NC/NR/NS	380	380	380
D min/max/mean	-40.259	62.913	0.041

Supplemental data

Mask #1

• File: emd_12745_msk_1.map

Additional map: Locally filtered map (non-composite) of an OC refinement...

• File: emd_12745_additional_1.map
• Annotation: Locally filtered map (non-composite) of an OC refinement performed with a non-binary PIC mask (cPIC < TFIIH)

Additional map: Half-map 1 of focused refinement encompassing the Pol...

• File: emd_12745_additional_10.map
• Annotation: Half-map 1 of focused refinement encompassing the Pol II stalk region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Pol...

• File: emd_12745_additional_11.map
• Annotation: Half-map 2 of focused refinement encompassing the Pol II stalk region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the Rad3/Ssl1...

• File: emd_12745_additional_12.map
• Annotation: Half-map 1 of focused refinement encompassing the Rad3/Ssl1 region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Rad3/Ssl1...

• File: emd_12745_additional_13.map
• Annotation: Half-map 2 of focused refinement encompassing the Rad3/Ssl1 region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Ssl1/Tfb4/Tfb1-3-helix-bundle...

• File: emd_12745_additional_14.map
• Annotation: Half-map 2 of focused refinement encompassing the Ssl1/Tfb4/Tfb1-3-helix-bundle region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the Ssl1/Tfb4/Tfb1-3-helix-bundle...

• File: emd_12745_additional_15.map
• Annotation: Half-map 1 of focused refinement encompassing the Ssl1/Tfb4/Tfb1-3-helix-bundle region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the Ssl2/Tfb2/Tfb5...

• File: emd_12745_additional_16.map
• Annotation: Half-map 1 of focused refinement encompassing the Ssl2/Tfb2/Tfb5 region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Ssl2/Tfb2/Tfb5...

• File: emd_12745_additional_17.map
• Annotation: Half-map 2 of focused refinement encompassing the Ssl2/Tfb2/Tfb5 region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Pol...

• File: emd_12745_additional_18.map
• Annotation: Half-map 2 of focused refinement encompassing the Pol II clamp/TFIIE/Tfb3-RING-finger region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the Pol...

• File: emd_12745_additional_19.map
• Annotation: Half-map 1 of focused refinement encompassing the Pol II clamp/TFIIE/Tfb3-RING-finger region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the TFIIE/Tfb1-PHD...

• File: emd_12745_additional_2.map
• Annotation: Half-map 2 of focused refinement encompassing the TFIIE/Tfb1-PHD region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the Tfb2...

• File: emd_12745_additional_20.map
• Annotation: Half-map 1 of focused refinement encompassing the Tfb2 region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Tfb2...

• File: emd_12745_additional_21.map
• Annotation: Half-map 2 of focused refinement encompassing the Tfb2 region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the upstream...

• File: emd_12745_additional_22.map
• Annotation: Half-map 2 of focused refinement encompassing the upstream complex region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Pol...

• File: emd_12745_additional_23.map
• Annotation: Half-map 2 of focused refinement encompassing the Pol II-protrusion/upstream-complex TFIIE/TFIIF-winged-helix-domain region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the Pol...

• File: emd_12745_additional_24.map
• Annotation: Half-map 1 of focused refinement encompassing the Pol II-protrusion/upstream-complex TFIIE/TFIIF-winged-helix-domain region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the upstream...

• File: emd_12745_additional_25.map
• Annotation: Half-map 1 of focused refinement encompassing the upstream complex region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the Pol...

• File: emd_12745_additional_3.map
• Annotation: Half-map 1 of focused refinement encompassing the Pol II-cleft/DNA region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the TFIIE/Tfb1-PHD...

• File: emd_12745_additional_4.map
• Annotation: Half-map 1 of focused refinement encompassing the TFIIE/Tfb1-PHD region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Pol...

• File: emd_12745_additional_5.map
• Annotation: Half-map 2 of focused refinement encompassing the Pol II-cleft/DNA region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Pol...

• File: emd_12745_additional_6.map
• Annotation: Half-map 2 of focused refinement encompassing the Pol II jaw-lobe/TFIIF region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the Pol...

• File: emd_12745_additional_7.map
• Annotation: Half-map 1 of focused refinement encompassing the Pol II jaw-lobe/TFIIF region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Pol...

• File: emd_12745_additional_8.map
• Annotation: Half-map 2 of focused refinement encompassing the Pol II core region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the Pol...

• File: emd_12745_additional_9.map
• Annotation: Half-map 1 of focused refinement encompassing the Pol II core region of the pre-initiation complex

Half map: #2

• File: emd_12745_half_map_1.map

Half map: #1

• File: emd_12745_half_map_2.map

Sample components

Entire : Yeast RNA polymerase II transcription pre-initiation complex with...

• Entire: Name: Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA

Components

• Complex: Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA
  • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPD
  • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB1
  • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB2
  • Protein or peptide: RNA polymerase II transcription factor B subunit 3
  • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB4
  • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB5
  • 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: 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 polymerase II subunit RPB4
  • 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
  • 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 IIB
  • DNA: Non-template DNA
  • Protein or peptide: TATA-box-binding protein
  • Protein or peptide: Transcription initiation factor IIF subunit alpha
  • Protein or peptide: Transcription initiation factor IIF subunit beta
  • DNA: Template DNA
  • 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
• Ligand: IRON/SULFUR CLUSTER
• Ligand: ZINC ION
• Ligand: BERYLLIUM TRIFLUORIDE ION
• Ligand: MAGNESIUM ION
• Ligand: ADENOSINE-5'-DIPHOSPHATE

Supramolecule #1: Yeast RNA polymerase II transcription pre-initiation complex with...

• Supramolecule: Name: Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
• Molecular weight: Theoretical: 1.37 MDa

Macromolecule #1: General transcription and DNA repair factor IIH helicase subunit XPD

• Macromolecule: Name: General transcription and DNA repair factor IIH helicase subunit XPD; type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 89.899047 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

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 #2: General transcription and DNA repair factor IIH subunit TFB1

• Macromolecule: Name: General transcription and DNA repair factor IIH subunit TFB1; type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 73.194516 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GGSMSHSGAA IFEKVSGIIA INEDVSPAEL TWRSTDGDKV HTVVLSTIDK LQATPASSEK MMLRLIGKVD ESKKRKDNEG NEVVPKPQR HMFSFNNRTV MDNIKMTLQQ IISRYKDADI YEEKRRREES AQHTETPMSS SSVTAGTPTP HLDTPQLNNG A PLINTAKL DDSLSKEKLL TNLKLQQSLL KGNKVLMKVF QETVINAGLP PSEFWSTRIP LLRAFALSTS QKVGPYNVLS TI KPVASSE NKVNVNLSRE KILNIFENYP IVKKAYTDNV PKNFKEPEFW ARFFSSKLFR KLRGEKIMQN DRGDVIIDRY LTL DQEFDR KDDDMLLHPV KKIIDLDGNI QDDPVVRGNR PDFTMQPGVD INGNSDGTVD ILKGMNRLSE KMIMALKNEY SRTN LQNKS NITNDEEDED NDERNELKID DLNESYKTNY AIIHLKRNAH EKTTDNDAKS SADSIKNADL KVSNQQMLQQ LSLVM DNLI NKLDLNQVVP NNEVSNKINK RVITAIKINA KQAKHNNVNS ALGSFVDNTS QANELEVKST LPIDLLESCR MLHTTC CEF LKHFYIHFQS GEQKQASTVK KLYNHLKDCI EKLNELFQDV LNGDGESMSN TCTAYLKPVL NSITLATHKY DEYFNEY NN NSN

UniProtKB: General transcription and DNA repair factor IIH subunit TFB1

Macromolecule #3: General transcription and DNA repair factor IIH subunit TFB2

• Macromolecule: Name: General transcription and DNA repair factor IIH subunit TFB2; type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 58.900602 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GPGSMSDYSL KHSVTQYLEE IPQQVQNRLY TSPATCLAIY RILPPLAKFF IMAMVFNENE VPLLDLDKWV NSNGKLQFQN AIKSMKSLH LLIPNKSSGT LMINLNPTFK ISLRNALTGG EVQNSFGVVV EENVVSLDLL DEYSANKWET ILHFMVGTPL A KIPSEKVL NLLKHSKLME EVNSTGEFKI TNEGFQFLLQ EINSQLWTLL LQYLKMIETS KMDLVDVLHF IFMLGALEVG KA YKIDALS ETQRIMLQDM RDYGLVFQKH SNDSIFYPTK LALMLTSDTK TIRSASNAMD SVLRQNREEP SVNEDGANGK STT DITTSD DLNKAGLKNQ DIPDGSLIVE TNFKIYSYSN SPLQIAVLSL FVHLKARFVN MVLGQITRES IRRALTNGIT ADQI IAYLE THAHPQMRRL AEEKLEKKLE LDPNCKEPLQ VLPPTVVDQI RLWQLELDRV ITYEGSLYSD FETSQEYNLL SKYAQ DIGV LLWKDDKKKK FFISKEGNSQ VLDFAKRKLK KKQ

UniProtKB: General transcription and DNA repair factor IIH subunit TFB2

Macromolecule #4: RNA polymerase II transcription factor B subunit 3

• Macromolecule: Name: RNA polymerase II transcription factor B subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 38.480746 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GPHMLMDEYE ENKDMCPICK TDRYLSPDVK FLVNPECYHR ICESCVDRIF SLGPAQCPYK GCDKILRKNK FKTQIFDDVE VEKEVDIRK RVFNVFNKTI DDFNGDLVEY NKYLEEVEDI IYKLDHGIDV AKTEEKLRTY EELNKQLIMN NLERSRTEIE S FEQRQKFE KEMKLKKRLL ERQIEEEERM NKEWTKKEIV NRLSTTTQDI NETIEGVKNT VKLKKSSARR KLEELNRVLK NN PYFNSNV NVQNSRLKDA VPFTPFNGDR EAHPRFTLKG SVYNDPFIKD LEHRKEFIAS GFNTNYAYER VLTEAFMGLG CVI SEEL

UniProtKB: RNA polymerase II transcription factor B subunit 3

Macromolecule #5: General transcription and DNA repair factor IIH subunit TFB4

• Macromolecule: Name: General transcription and DNA repair factor IIH subunit TFB4; type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 37.778676 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

SNAMDAISDP TFKHARSRKQ VTEESPSLLT VIIEIAPKLW TTFDEEGNEK GSIIKVLEAL IVFLNAHLAF NSANKVAVIA AYSQGIKYL YPESTSALKA SESENKTRSD LKIINSDMYR RFRNVDETLV EEIYKLFELE KKQIEQNSQR STLAGAMSAG L TYVNRISK ESVTTSLKSR LLVLTCGSGS SKDEIFQYIP IMNCIFSATK MKCPIDVVKI GGSKESTFLQ QTTDATNGVY LH VESTEGL IQYLATAMFI DPSLRPIIVK PNHGSVDFRT SCYLTGRVVA VGFICSVCLC VLSIIPPGNK CPACDSQFDE HVI AKLKRK PVVPRLKAKK KVTKP

UniProtKB: General transcription and DNA repair factor IIH subunit TFB4

Macromolecule #6: General transcription and DNA repair factor IIH subunit TFB5

• Macromolecule: Name: General transcription and DNA repair factor IIH subunit TFB5; type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 8.541787 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GPGSMARARK GALVQCDPSI KALILQIDAK MSDIVLEELD DTHLLVNPSK VEFVKHELNR LLSKNIYNPM DEEENQ

UniProtKB: General transcription and DNA repair factor IIH subunit TFB5

Macromolecule #7: General transcription and DNA repair factor IIH subunit SSL1

• Macromolecule: Name: General transcription and DNA repair factor IIH subunit SSL1; type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 52.571215 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GGSMAPVVIS ESEEDEDRVA ITRRTKRQVH FDGEGDDRVD QQQQQHSSSH RDRDKHVQRK KKKRLSNRNL QGSNGGYAWE DEIKRSWDL VKVDDEGDMA SLVASIVEAR KKRTAKKNIT PYQRGIIRSL ILTLDCSEAM LEKDLRPNRH AMIIQYAIDF V HEFFDQNP ISQMGIIIMR NGLAQLVSQV SGNPQDHIDA LKSIRKQEPK GNPSLQNALE MARGLLLPVP AHCTREVLIV FG SLSTTDP GDIHQTIDSL VSEKIRVKVL GLSAQVAICK ELCKATNYGD ESFYKILLDE THLKELFNEA VTPLPVNKIN KGF TLVKMG FPTRIFEDTP TFCSCHSKLV YGGYFCPNCH SKVCSLPTVC PCCDLMLILS THLARSYHHL MPLKTFAEVP TTEK FRSED CFSCQSRFPI LKNHKNGKLL TSSRYRCEDC KQEFCVDCDV FIHEILHNCP GCESKPVIT

UniProtKB: General transcription and DNA repair factor IIH subunit SSL1

Macromolecule #8: General transcription and DNA repair factor IIH helicase subunit XPB

• Macromolecule: Name: General transcription and DNA repair factor IIH helicase subunit XPB; type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 95.461664 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

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 #9: DNA-directed RNA polymerase II subunit RPB1

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 191.821578 KDa

Sequence

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 #10: DNA-directed RNA polymerase II subunit RPB2

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 138.937297 KDa

Sequence

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 #11: DNA-directed RNA polymerase II subunit RPB3

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB3 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 38.635883 KDa
• Recombinant expression: Organism: Saccharomyces cerevisiae S288C (yeast)

Sequence

String:

MGSHHHHHHS NSGLNDIFEA QKIEWHEDTG SSEGPQVKIR EASKDNVDFI LSNVDLAMAN SLRRVMIAEI PTLAIDSVEV ETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCED HCDKCSVVLT LQAFGESEST TNVYSKDLVI VSNLMGRNIG H PIIQDKEG NGVLICKLRK GQELKLTCVA KKGIAKEHAK WGPAAAIEFE YDPWNKLKHT DYWYEQDSAK EWPQSKNCEY ED PPNEGDP FDYKAQADTF YMNVESVGSI PVDQVVVRGI DTLQKKVASI LLALTQMDQD KVNFASGDNN TASNMLGSNE DVM MTGAEQ DPYSNASQMG NTGSGGYDNA W

UniProtKB: DNA-directed RNA polymerase II subunit RPB3

Macromolecule #12: DNA-directed RNA polymerase II subunit RPB4

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 25.451191 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

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

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC1; type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 25.117094 KDa

Sequence

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

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC2; type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 17.931834 KDa

Sequence

String:

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 #15: DNA-directed RNA polymerase II subunit RPB7

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 19.909934 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

MFFIKDLSLN ITLHPSFFGP RMKQYLKTKL LEEVEGSCTG KFGYILCVLD YDNIDIQRGR ILPTDGSAEF NVKYRAVVFK PFKGEVVDG TVVSCSQHGF EVQVGPMKVF VTKHLMPQDL TFNAGSNPPS YQSSEDVITI KSRIRVKIEG CISQVSSIHA I GSIKEDYL GAIHHHHHH

UniProtKB: DNA-directed RNA polymerase II subunit RPB7

Macromolecule #16: DNA-directed RNA polymerases I, II, and III subunit RPABC3

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC3; type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 16.525363 KDa

Sequence

String:

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 #17: DNA-directed RNA polymerase II subunit RPB9

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB9 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 14.308161 KDa

Sequence

String:

MTTFRFCRDC NNMLYPREDK ENNRLLFECR TCSYVEEAGS PLVYRHELIT NIGETAGVVQ DIGSDPTLPR SDRECPKCHS RENVFFQSQ QRRKDTSMVL FFVCLSCSHI FTSDQKNKRT QFS

UniProtKB: DNA-directed RNA polymerase II subunit RPB9

Macromolecule #18: DNA-directed RNA polymerases I, II, and III subunit RPABC5

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC5; type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 8.290732 KDa

Sequence

String:

MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKRD

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

Macromolecule #19: DNA-directed RNA polymerase II subunit RPB11

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB11 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 13.633493 KDa

Sequence

String:

MNAPDRFELF LLGEGESKLK IDPDTKAPNA VVITFEKEDH TLGNLIRAEL LNDRKVLFAA YKVEHPFFAR FKLRIQTTEG YDPKDALKN ACNSIINKLG ALKTNFETEW NLQTLAADDA F

UniProtKB: DNA-directed RNA polymerase II subunit RPB11

Macromolecule #20: DNA-directed RNA polymerases I, II, and III subunit RPABC4

• Macromolecule: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC4; type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 7.729969 KDa

Sequence

String:

MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEAR

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

Macromolecule #21: Transcription initiation factor IIB

• Macromolecule: Name: Transcription initiation factor IIB / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 39.215391 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

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 DNLPGVEKKK HHHHHH

UniProtKB: Transcription initiation factor IIB

Macromolecule #23: TATA-box-binding protein

• Macromolecule: Name: TATA-box-binding protein / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 28.000338 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

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 KHHHHHH

UniProtKB: TATA-box-binding protein

Macromolecule #24: Transcription initiation factor IIF subunit alpha

• Macromolecule: Name: Transcription initiation factor IIF subunit alpha / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 82.531789 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

GPGMSRRNPP GSRNGGGPTN ASPFIKRDRM RRNFLRMRMG QNGSNSSSPG VPNGDNSRGS LVKKDDPEYA EEREKMLLQI GVEADAGRS NVKVKDEDPN EYNEFPLRAI PKEDLENMRT HLLKFQSKKK INPVTDFHLP VRLHRKDTRN LQFQLTRAEI V QRQKEISE YKKKAEQERS TPNSGGMNKS GTVSLNNTVK DGSQTPTVDS VTKDNTANGV NSSIPTVTGS SVPPASPTTV SA VESNGLS NGSTSAANGL DGNASTANLA NGRPLVTKLE DAGPAEDPTK VGMVKYDGKE VTNEPEFEEG TMDPLADVAP DGG GRAKRG NLRRKTRQLK VLDENAKKLR FEEFYPWVME DFDGYNTWVG SYEAGNSDSY VLLSVEDDGS FTMIPADKVY KFTA RNKYA TLTIDEAEKR MDKKSGEVPR WLMKHLDNIG TTTTRYDRTR RKLKAVADQQ AMDEDDRDDN SEVELDYDEE FADDE EAPI IDGNEQENKE SEQRIKKEML QANAMGLRDE EAPSENEEDE LFGEKKIDED GERIKKALQK TELAALYSSD ENEINP YLS ESDIENKENE SPVKKEEDSD TLSKSKRSSP KKQQKKATNA HVHKEPTLRV KSIKNCVIIL KGDKKILKSF PEGEWNP QT TKAVDSSNNA SNTVPSPIKQ EEGLNSTVAE REETPAPTIT EKDIIEAIGD GKVNIKEFGK FIRRKYPGAE NKKLMFAI V KKLCRKVGND HMELKKE

UniProtKB: Transcription initiation factor IIF subunit alpha

Macromolecule #25: Transcription initiation factor IIF subunit beta

• Macromolecule: Name: Transcription initiation factor IIF subunit beta / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 46.684492 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

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 #27: Transcription initiation factor IIA large subunit

• Macromolecule: Name: Transcription initiation factor IIA large subunit / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 32.230805 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

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 #28: Transcription initiation factor IIA subunit 2

• Macromolecule: Name: Transcription initiation factor IIA subunit 2 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 14.431131 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

MAVPGYYELY RRSTIGNSLV DALDTLISDG RIEASLAMRV LETFDKVVAE TLKDNTQSKL TVKGNLDTYG FCDDVWTFIV KNCQVTVED SHRDASQNGS GDSQSVISVD KLRIVACNSK KSEKHHHHHH

UniProtKB: Transcription initiation factor IIA subunit 2

Macromolecule #29: Transcription initiation factor IIE subunit alpha

• Macromolecule: Name: Transcription initiation factor IIE subunit alpha / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae S288C (yeast)
• Molecular weight: Theoretical: 55.951039 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

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 DVAA ALEHHHHH

UniProtKB: Transcription initiation factor IIE subunit alpha

Macromolecule #30: Transcription initiation factor IIE subunit beta

• Macromolecule: Name: Transcription initiation factor IIE subunit beta / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 37.050434 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

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 #22: Non-template DNA

• Macromolecule: Name: Non-template DNA / type: dna / ID: 22 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Saccharomyces cerevisiae YJM984 (yeast)
• Molecular weight: Theoretical: 32.716977 KDa

Sequence

String:

(DC)(DG)(DA)(DG)(DA)(DA)(DC)(DA)(DG)(DT) (DA)(DG)(DC)(DA)(DC)(DG)(DC)(DT)(DG)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DA)(DT) (DA)(DG)(DC)(DT)(DA)(DT)(DG)(DG)(DA)(DA) (DC) (DG)(DT)(DT)(DC)(DG)(DA)(DT)(DT) (DC)(DA)(DC)(DC)(DT)(DC)(DC)(DG)(DA)(DT) (DG)(DT) (DG)(DT)(DG)(DT)(DT)(DG)(DT) (DA)(DC)(DA)(DT)(DA)(DC)(DA)(DT)(DA)(DA) (DA)(DA)(DA) (DT)(DA)(DT)(DC)(DA)(DT) (DA)(DG)(DC)(DA)(DC)(DA)(DA)(DC)(DT)(DG) (DC)(DG)(DC)(DT) (DG)(DT)(DG)(DT)(DC) (DA)

Macromolecule #26: Template DNA

• Macromolecule: Name: Template DNA / type: dna / ID: 26 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Saccharomyces cerevisiae YJM984 (yeast)
• Molecular weight: Theoretical: 32.68092 KDa

Sequence

String:

(DT)(DG)(DA)(DC)(DA)(DC)(DA)(DG)(DC)(DG) (DC)(DA)(DG)(DT)(DT)(DG)(DT)(DG)(DC)(DT) (DA)(DT)(DG)(DA)(DT)(DA)(DT)(DT)(DT) (DT)(DT)(DA)(DT)(DG)(DT)(DA)(DT)(DG)(DT) (DA) (DC)(DA)(DA)(DC)(DA)(DC)(DA)(DC) (DA)(DT)(DC)(DG)(DG)(DA)(DG)(DG)(DT)(DG) (DA)(DA) (DT)(DC)(DG)(DA)(DA)(DC)(DG) (DT)(DT)(DC)(DC)(DA)(DT)(DA)(DG)(DC)(DT) (DA)(DT)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DC)(DA)(DG)(DC)(DG)(DT)(DG)(DC)(DT) (DA)(DC)(DT)(DG) (DT)(DT)(DC)(DT)(DC) (DG)

Macromolecule #31: IRON/SULFUR CLUSTER

• Macromolecule: Name: IRON/SULFUR CLUSTER / type: ligand / ID: 31 / Number of copies: 1 / Formula: SF4
• Molecular weight: Theoretical: 351.64 Da

Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

Macromolecule #32: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 32 / Number of copies: 17 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #33: BERYLLIUM TRIFLUORIDE ION

• Macromolecule: Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 33 / Number of copies: 1 / Formula: BEF
• Molecular weight: Theoretical: 66.007 Da

Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Macromolecule #34: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 34 / Number of copies: 2 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #35: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 35 / Number of copies: 1 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.6
• Grid: Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Specialist optics: Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 29670 / Average exposure time: 9.0 sec. / Average electron dose: 43.6 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
• Sample stage: Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 4300000

Startup model

Type of model: EMDB MAP
EMDB ID:

3846

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23887
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
• Final 3D classification: Software - Name: RELION

Atomic model buiding 1

Initial model

PDB ID:

5oqj

Chain - Source name: PDB / Chain - Initial model type: experimental model

• Refinement: Space: REAL / Protocol: OTHER

Output model

PDB-7o75:
Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA