EMDB-12721: Yeast TFIIH in the contracted state within the pre-initiation complex

Basic information

• Entry: Database: EMDB / ID: EMD-12721
• Title: Yeast TFIIH in the contracted state within the pre-initiation complexTranscription factor II H

Sample

• Complex: Yeast TFIIH in the contracted state within the pre-initiation complexTranscription factor II H
  • Protein or peptide: x 15 types
  • DNA: x 2 types
• Ligand: x 5 types

Function / homology

Function:

: / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / DNA translocase activity / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / RPB4-RPB7 complex / phosphatidylinositol-3-phosphate binding / 5'-3' DNA helicase activity / : / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 3'-5' DNA helicase activity / transcription preinitiation complex / poly(A)+ mRNA export from nucleus / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase II complex binding / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / ATPase activator activity / tRNA transcription by RNA polymerase III / 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 / transcription elongation by RNA polymerase I / positive regulation of translational initiation / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / ATP-dependent activity, acting on DNA / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / DNA helicase activity / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / ubiquitin protein ligase activity / single-stranded DNA binding / ribosome biogenesis / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / single-stranded RNA binding / nucleotide binding / DNA repair / mRNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm

Domain/homology:

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 / Helical and beta-bridge domain / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helical and beta-bridge domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / ATP-dependent helicase Rad3/Chl1-like / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / 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) / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / 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 / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / C1-like domain superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase subunit Rpb7-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / DNA-directed RNA polymerase, subunit RPB6 / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / von Willebrand factor, type A / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain

Component:

DNA-directed RNA polymerase II subunit RPB1 / General transcription and DNA repair factor IIH helicase subunit XPD / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / 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 / General transcription and DNA repair factor IIH helicase subunit XPB / 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 (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (brewer's yeast) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 3.6 Å
• Authors: Schilbach S / Aibara S / Dienemann C / Grabbe F / Cramer P

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 6, 2021	-
Header (metadata) release	Jun 16, 2021	-
Map release	Jun 16, 2021	-
Update	Aug 4, 2021	-
Current status	Aug 4, 2021	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_12721.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: 3.8 / Movie #1: 3.8
Minimum - Maximum	-52.30278 - 89.136986
Average (Standard dev.)	0.027169101 (±0.9774916)

• 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	-52.303	89.137	0.027

Supplemental data

Mask #1

• File: emd_12721_msk_1.map

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

• File: emd_12721_additional_1.map
• Annotation: Locally filtered map (non-composite) of a refinement of PIC-bound TFIIH in the contracted state

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

• File: emd_12721_additional_10.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 Ssl2/Tfb2/Tfb5...

• File: emd_12721_additional_11.map
• Annotation: Half-map 2 of focused refinement encompassing the Ssl2/Tfb2/Tfb5 region of the pre-initiation complex

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

• File: emd_12721_additional_12.map
• Annotation: Half-map 1 of focused refinement encompassing the Tfb2 region of the pre-initiation complex

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

• File: emd_12721_additional_13.map
• Annotation: Half-map 1 of focused refinement encompassing the Ssl2/Tfb2/Tfb5 region of the pre-initiation complex

Additional map: Half-map 1 of focused refinement encompassing the Tfb3-RING-finger/TFIIE/Pol...

• File: emd_12721_additional_14.map
• Annotation: Half-map 1 of focused refinement encompassing the Tfb3-RING-finger/TFIIE/Pol II-stalk region of the pre-initiation complex

Additional map: Half-map 2 of focused refinement encompassing the Tfb3-RING-finger/TFIIE/Pol...

• File: emd_12721_additional_15.map
• Annotation: Half-map 2 of focused refinement encompassing the Tfb3-RING-finger/TFIIE/Pol II-stalk region of the pre-initiation complex

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

• File: emd_12721_additional_2.map
• Annotation: Half-map 1 of focused refinement encompassing the Pol II stalk region of the pre-initiation complex

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

• File: emd_12721_additional_3.map
• Annotation: Half-map 1 of focused refinement encompassing the Pol II-clamp/TFIIE/Tfb1-PHD region of the pre-initiation complex

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

• File: emd_12721_additional_4.map
• Annotation: Half-map 2 of focused refinement encompassing the Pol II-clamp/TFIIE/Tfb1-PHD region of the pre-initiation complex

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

• File: emd_12721_additional_5.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_12721_additional_6.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_12721_additional_7.map
• Annotation: Half-map 2 of focused refinement encompassing the Rad3/Ssl1 region of the pre-initiation complex

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

• File: emd_12721_additional_8.map
• Annotation: Half-map 1 of focused refinement encompassing the Ssl1/Tfb4-eZnF/Tfb1-3-helix-bundle region of the pre-initiation complex

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

• File: emd_12721_additional_9.map
• Annotation: Half-map 2 of focused refinement encompassing the Ssl1/Tfb4-eZnF/Tfb1-3-helix-bundle region of the pre-initiation complex

Half map: #2

• File: emd_12721_half_map_1.map

Half map: #1

• File: emd_12721_half_map_2.map

Sample components

Entire : Yeast TFIIH in the contracted state within the pre-initiation complex

• Entire: Name: Yeast TFIIH in the contracted state within the pre-initiation complexTranscription factor II H

Components

• Complex: Yeast TFIIH in the contracted state within the pre-initiation complexTranscription factor II H
  • 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 RPB1Polymerase
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB2Polymerase
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB4Polymerase
  • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB7Polymerase
  • DNA: Non-template DNA
  • DNA: Template DNA
  • Protein or peptide: Transcription initiation factor IIE subunit alpha
  • Protein or peptide: Transcription initiation factor IIE subunit beta
• Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
• Ligand: ZINC ION
• Ligand: BERYLLIUM TRIFLUORIDE ION
• Ligand: MAGNESIUM ION
• Ligand: ADENOSINE-5'-DIPHOSPHATE

Supramolecule #1: Yeast TFIIH in the contracted state within the pre-initiation complex

• Supramolecule: Name: Yeast TFIIH in the contracted state within the pre-initiation complex; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
• 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 / EC number: DNA helicase
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• 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

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 (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• 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

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 (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• 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

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 (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• 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

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 (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• 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

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 (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 8.541787 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

GPGSMARARK GALVQCDPSI KALILQIDAK MSDIVLEELD DTHLLVNPSK VEFVKHELNR LLSKNIYNPM DEEENQ

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 (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• 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

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 (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• 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

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 / EC number: DNA-directed RNA polymerase
• Source (natural): Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• 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

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 / EC number: DNA-directed RNA polymerase
• Source (natural): Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• 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

Macromolecule #11: DNA-directed RNA polymerase II subunit RPB4

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB4 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• 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

Macromolecule #12: 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: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 17.931834 KDa

Sequence

String:

MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTLK EKAIPKDQRA TTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR IAMKELAEKK IPLVIRRYLP DGSFEDWSVE ELIVDL

Macromolecule #13: DNA-directed RNA polymerase II subunit RPB7

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB7 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• 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

Macromolecule #16: Transcription initiation factor IIE subunit alpha

• Macromolecule: Name: Transcription initiation factor IIE subunit alpha / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast); Strain: ATCC 204508 / S288c
• 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

Macromolecule #17: Transcription initiation factor IIE subunit beta

• Macromolecule: Name: Transcription initiation factor IIE subunit beta / type: protein_or_peptide / ID: 17 / 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

Macromolecule #14: Non-template DNA

• Macromolecule: Name: Non-template DNA / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• 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 #15: Template DNA

• Macromolecule: Name: Template DNA / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• 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 #18: IRON/SULFUR CLUSTER

• Macromolecule: Name: IRON/SULFUR CLUSTER / type: ligand / ID: 18 / Number of copies: 1 / Formula: SF4
• Molecular weight: Theoretical: 351.64 Da

Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

Macromolecule #19: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 19 / Number of copies: 10 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #20: BERYLLIUM TRIFLUORIDE ION

• Macromolecule: Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: BEF
• Molecular weight: Theoretical: 66.007 Da

Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Macromolecule #21: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 21 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #22: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 22 / 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 / Adenosine diphosphate

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
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
• Specialist optics: Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
• Sample stage: Cooling holder cryogen: NITROGEN
• 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
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 4300000
• CTF correction: Software: (Name: Warp, RELION)

Startup model

Type of model: EMDB MAP
EMDB ID:

3846

• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
• Final 3D classification: Software - Name: RELION
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24671

Atomic model buiding 1

Initial model

PDB ID:

5oqj

• Refinement: Space: REAL / Protocol: OTHER

Output model

PDB-7o4k:
Yeast TFIIH in the contracted state within the pre-initiation complex