EMDB-26545: Mediator-PIC Early (Mediator A)

Basic information

Entry

Database: EMDB / ID: EMD-26545

• Title: Mediator-PIC Early (Mediator A)
• Map data: Mediator-PIC Early (Mediator A)

Sample

• Complex: Core Mediator-PICearly (Copy A)
  • Protein or peptide: x 17 types

Function / homology

Function:

meiotic gene conversion / RNA polymerase II complex recruiting activity / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / mediator complex / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / 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 / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TFIID-class transcription factor complex binding / TFIIB-class transcription factor binding / positive regulation of transcription initiation by RNA polymerase II / translesion synthesis / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / transcription corepressor activity / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / DNA recombination / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA repair / regulation of transcription by RNA polymerase II / structural molecule activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / metal ion binding / nucleus / cytosol

Domain/homology:

Mediator complex, subunit Med19, fungi / Rox3 mediator complex subunit / Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes / Mediator of RNA polymerase II transcription subunit 20 / Mediator complex, subunit Med6, fungi / Mediator complex, subunit Med10 / Transcription factor subunit Med10 of Mediator complex / Mediator of RNA polymerase II transcription subunit 9 / RNA polymerase II transcription mediator complex subunit 9 / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med7 superfmaily / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / MED7 protein / Mediator complex, subunit Med20 / Mediator complex, subunit Med14 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex subunit MED14 / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / 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 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5

Component:

DNA-directed RNA polymerase II subunit RPB1 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 19 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 9 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 31 / Mediator of RNA polymerase II transcription subunit 6 / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 11

• Biological species: Saccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast)
• Method: single particle reconstruction / cryo EM / Resolution: 4.3 Å
• Authors: Gorbea Colon JJ / Chen S-F / Tsai KL / Murakami K

Funding support

United States, 1 items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01-GM123233-01	United States

• Citation: Journal: Mol Cell / Year: 2023; Title: Structural basis of a transcription pre-initiation complex on a divergent promoter.; Authors: Jose J Gorbea Colón / Leon Palao / Shin-Fu Chen / Hee Jong Kim / Laura Snyder / Yi-Wei Chang / Kuang-Lei Tsai / Kenji Murakami / ; Abstract: Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.

History

Deposition	Mar 29, 2022	-
Header (metadata) release	Feb 15, 2023	-
Map release	Feb 15, 2023	-
Update	Mar 8, 2023	-
Current status	Mar 8, 2023	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_26545.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Mediator-PIC Early (Mediator A)
• Voxel size: X=Y=Z: 1.38 Å

Density

Contour Level	By AUTHOR: 0.02
Minimum - Maximum	-0.016072115 - 0.07138125
Average (Standard dev.)	0.00032513688 (±0.0036738445)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 360 360 360 Spacing 360 360 360
Cell	A=B=C: 496.8 Å α=β=γ: 90.0 °

Supplemental data

Additional map: Additional map 1

• File: emd_26545_additional_1.map
• Annotation: Additional map 1

Additional map: Additional map 2

• File: emd_26545_additional_2.map
• Annotation: Additional map 2

Additional map: Additional map 3

• File: emd_26545_additional_3.map
• Annotation: Additional map 3

Half map: Half Map 1

• File: emd_26545_half_map_1.map
• Annotation: Half Map 1

Half map: Half Map 2

• File: emd_26545_half_map_2.map
• Annotation: Half Map 2

Sample components

Entire : Core Mediator-PICearly (Copy A)

• Entire: Name: Core Mediator-PICearly (Copy A)

Components

• Complex: Core Mediator-PICearly (Copy A)
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 1
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 4
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 6
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 7
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 8
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 9
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 10
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 11
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 14
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 17
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 18
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 19
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 20
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 21
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 22
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 31
  • Protein or peptide: DNA-directed RNA polymerase II subunit RPB1Polymerase

Supramolecule #1: Core Mediator-PICearly (Copy A)

• Supramolecule: Name: Core Mediator-PICearly (Copy A) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
• Source (natural): Organism: Saccharomyces cerevisiae (brewer's yeast)

Macromolecule #1: Mediator of RNA polymerase II transcription subunit 1

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 64.314953 KDa

Sequence

String:

MVEGDSYVET LDSMIELFKD YKPGSITLEN ITRLCQTLGL ESFTEELSNE LSRLSTASKI IVIDVDYNKK QDRIQDVKLV LASNFDNFD YFNQRDGEHE KSNILLNSLT KYPDLKAFHN NLKFLYLLDA YSHIESDSTS HNNGSSDKSL DSSNASFNNQ G KLDLFKYF TELSHYIRQC FQDNCCDFKV RTNLNDKFGI YILTQGINGK EVPLAKIYLE ENKSDSQYRF YEYIYSQETK SW INESAEN FSNGISLVME IVANAKESNY TDLIWFPEDF ISPELIIDKV TCSSNSSSSP PIIDLFSNNN YNSRIQLMND FTT KLINIK KFDISNDNLD LISEILKWVQ WSRIVLQNVF KLVSTPSSNS NSSELEPDYQ APFSTSTKDK NSSTSNTEPI PRSN RHGSV VEASRRRRSS TNKSKRPSIT EAMMLKEEGL QQFNLHEILS EPAIEEENGD SIKEHSTTMD GANDLGFTAS VSNQE NAGT DIVMEDHGVL QGTSQNYGTA TADDADIEMK DVSSKPSKPE SSVLQLIVSE DHIILDTISE CNLYDDVKCW SKFIEK FQD IVS

Macromolecule #2: Mediator of RNA polymerase II transcription subunit 4

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 32.244895 KDa

Sequence

String:

MSVQDTKAVE FSMGHIRSSS VSLVAEATSN TNSEDKLSKV QLYEDLCRYE DTLSKLVESV DRFKPNLDIA KDLIRTDEAL FENVKLLAE YDNIYRNLQK IDKDSEELDS KTRKILEILN ECHDELKALP MLEQVEFEKN TILQQRSKIN STELLDYATK L SKFTKIPP TFDKGAVGPN NFIWPAEDAL RRGMLAMASL HSKELTRIPG EEVEETEVPT VPPSQSEEQK GQMAKKEGTP KT DSFIFDG TAKEVGDEAD NTKDKEKEEN NDDALDLDLD LFDPDDF

Macromolecule #3: Mediator of RNA polymerase II transcription subunit 6

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 32.844746 KDa

Sequence

String:

MNVTPLDELQ WKSPEWIQVF GLRTENVLDY FAESPFFDKT SNNQVIKMQR QFSQLNDPNA AVNMTQNIMT LPDGKNGNLE EEFAYVDPA RRQILFKYPM YMQLEEELMK LDGTEYVLSS VREPDFWVIR KQRRTNNSGV GSAKGPEIIP LQDYYIIGAN I YQSPTIFK IVQSRLMSTS YHLNSTLESL YDLIEFQPSQ GVHYKVPTDT STTATAATNG NNAGGGSNKS SVRPTGGANM AT VPSTTNV NMTVNTMGTG GQTIDNGTGR TGNGNMGITT EMLDKLMVTS IRSTPNYI

Macromolecule #4: Mediator of RNA polymerase II transcription subunit 7

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 25.616062 KDa

Sequence

String:

MSNDPGNEVS SLYPPPPPYV KFFTQSNLEK LPKYKEKKAA SAKQTAPNNS NGGSEEEITC ALDYLIPPPM PKNQQYRAFG SIWQVKDQL PDLESMGLTQ LYKKSTENES TNYQYKIQEL RKLLKSLLLN YLELIGVLSI NPDMYERKVE NIRTILVNIH H LLNEYRPH QSRESLIMLL EEQLEYKRGE IREIEQVCKQ VHDKLTSIQD TLRTGSQSPP SSSQ

Macromolecule #5: Mediator of RNA polymerase II transcription subunit 8

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 25.297234 KDa

Sequence

String:

MSQSTASLVP EGNQGSLQED VSFDFNGVPG QALDAVRMRL AQLTHSLRRI RDEMSKAELP QWYTLQSQLN VTLSQLVSVT STLQHFQET LDSTVVYPLP KFPTTSHESL VTTLLRKKNI PEVDEWMKYV RETSGVTTAL LKDEEIEKLL QQDREITNWA R TTFRNEYG KHDFKNEESL SEEHASLLVR DSKPSKPFNV DDVLKFTFTG EKPIITGSTS TSSSN

Macromolecule #6: Mediator of RNA polymerase II transcription subunit 9

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 9 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 17.400377 KDa

Sequence

String:

MNLQNNVLNQ IHQILLPTNP TLDKPNAEAT KEEFSSAENR DEKDYLTNQQ PKNLSTPSTS SNGEFIPHIF YSLHQIRKDP NNLSNQLET LTGSIRHRLK LCKSLISENE DTKDLLSKSP SEWQDIIHQR EQELQIKRDV LDDLYRKLQR

Macromolecule #7: Mediator of RNA polymerase II transcription subunit 10

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 10; type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 17.927926 KDa

Sequence

String:

MNGNSTNNEQ LQQELATTQD QVASIIESFV ELGVSIYDFP GTPEATKGMI TNLQRNVDRL YKLNVRSNDP QSSLSKVDIP LEVVQYIED GRNPDIYTRE FVEAIRRSNQ YQRGKMHGLK QLRDSLADKI VDEFPELKEP VEDIIKRTSP IDNVSNTH

Macromolecule #8: Mediator of RNA polymerase II transcription subunit 11

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 11; type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 13.324189 KDa

Sequence

String:

MQPPYIQERL KSLNDIETQL CSMLQEASQV TFIFGELKRG NESVKPQFEN HVKQFYERLD KSTTQLRKEI QLLDENVGTR LLPINVNKK ALGQDTEKME EQLDLLSAIL DPSKSK

Macromolecule #9: Mediator of RNA polymerase II transcription subunit 14

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 14; type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 123.500695 KDa

Sequence

String:

MTTTIGSPQM LANEERLSNE MHALKNRSEQ NGQEQQGPVK NTQLHGPSAT DPETTATQKE SLEMVPKDTS AATMTSAPPP ALPHVEINQ VSLALVIRNL TVFTMKELAQ YMKTNVHTQA NEPNSAKKIR FLQLIIFLRT QFLKLYVLVK WTRTIKQNNF H VLIDLLNW FRTTNMNVNN CIWALKSSLN SMTNAKLPNV DLVTALEVLS LGRPNLPTHN FKLSGVSNSM DMVDGMAKVP IG LILQRLK DLNLTVSIKI ALMNIPKPLN SYHIKNGRIY FTVPNEFEIQ LSTVNRQSPL FFVDLKLLFN TEAEQTVSAV TEA TSTNGD SENNEENSSS NGNNLPLNKP RLEKLINEIL LKSNDPLLSL YNFLHKYVLT LQLYMVHREF LKLANGGKFS KSNL IHNYD SKKSTITVRY WLNGKMDSKG KITIGIQRTT ESLILKWDNQ SASRAKNMPV IYNNIVSNIE GILDEIMFNH ARIIR SELL ARDIFQEDEE NSDVLLFQLP TTCVSMAPIQ LKIDLLSGQF YFRNPTPLLS NYASKINRAE GPEELARILQ QLKLDK IIH VLTTMFENTG WSCSRIIKID KPIRTQVNTG GESVVKKEDN KYAIAGNSTT NSDVSLLLQR DLFIRLPHWP LNWYLIL SI ISSKTSCVVE KRIGKIVSQR GKWNLKYLDN SNVMTVKLES ITYQKIMILQ RTILNRIINH MLIDSLNQLE IRNKICSS E MINEQKLPQY IIQGSNTNDN ISIITLELES FLEGSKALNS ILESSMFLRI DYSNSQIRLY AKFKRNTMMI QCQIDKLYI HFVQEEPLAF YLEESFTNLG IIVQYLTKFR QKLMQLVVLT DVVERLHKNF ESENFKIIAL QPNEISFKYL SNNDEDDKDC TIKISTNDD SIKNLTVQLS PSNPQHIIQP FLDNSKMDYH FIFSYLQFTS SLFKALKVIL NERGGKFHES GSQYSTMVNI G LHNLNEYQ IVYYNPQAGT KITICIELKT VLHNGRDKIQ FHIHFADVAH ITTKSPAYPM MHQVRNQVFM LDTKRLGTPE SV KPANASH AIRLGNGVAC DPSEIEPILM EIHNILKVDS NSSSS

Macromolecule #10: Mediator of RNA polymerase II transcription subunit 17

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 17; type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 78.582836 KDa

Sequence

String:

MTTEDPDSNH LSSETGIKLA LDPNLITLAL SSNPNSSLHS PTSDEPVPES AGKADTSIRL EGDELENKTK KDNDKNLKFL KNKDSLVSN PHEIYGSMPL EQLIPIILRQ RGPGFKFVDL NEKELQNEIK QLGSDSSDGH NSEKKDTDGA DENVQIGEDF M EVDYEDKD NPVDSRNETD HKTNENGETD DNIETVMTQE QFVKRRRDML EHINLAMNES SLALEFVSLL LSSVKESTGM SS MSPFLRK VVKPSSLNSD KIPYVAPTKK EYIELDILNK GWKLQSLNES KDLLRASFNK LSSILQNEHD YWNKIMQSIS NKD VIFKIR DRTSGQKLLA IKYGYEDSGS TYKHDRGIAN IRNNIESQNL DLIPHSSSVF KGTDFVHSVK KFLRVRIFTK IESE DDYIL SGESVMDRDS ESEEAETKDI RKQIQLLKKI IFEKELMYQI KKECALLISY GVSIENENKV IIELPNEKFE IELLS LDDD SIVNHEQDLP KINDKRANLM LVMLRLLLVV IFKKTLRSRI SSPHGLINLN VDDDILIIRP ILGKVRFANY KLLLKK IIK DYVLDIVPGS SITETEVERE QPQENKNIDD ENITKLNKEI RAFDKLLNIP RRELKINLPL TEHKSPNLSL MLESPNY CN ALIHIKFSAG TEANAVSFDT TFSDFKEVED FLHFIVAEYI QQKKV

Macromolecule #11: Mediator of RNA polymerase II transcription subunit 18

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 18; type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 34.316539 KDa

Sequence

String:

MVQQLSLFGS IGDDGYDLLI STLTTISGNP PLLYNSLCTV WKPNPSYDVE NVNSRNQLVE PNRIKLSKEV PFSYLIDETM MDKPLNFRI LKSFTNDKIP LNYAMTRNIL HNTVPQVTNF NSTNEDQNNS KHTEDTVNES RNSDDIIDVD MDASPAPSNE S CSPWSLQI SDIPAAGNNR SVSMQTIAET IILSSAGKNS SVSSLMNGLG YVFEFQYLTI GVKFFMKHGL ILELQKIWQI EE AGNSQIT SGGFLLKAYI NVSRGTDIDR INYTETALMN LKKELQGYIE LSVPDRQSMD SRVAHGNILI

Macromolecule #12: Mediator of RNA polymerase II transcription subunit 19

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 19; 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: 24.885305 KDa

Sequence

String:

MASRVDETTV PSYYYYVDPE TTYTYQQPNP LQDLISVYGL DDISRQVART NLDGTKAVKL RKSYKNQIAD LSGKFSTIPT RENGKGGQI AHILFQNNPD MMIQPPQQGQ NMSEQQWREQ LRNRDIALFQ PPNFDWDLCS SVLSQFERSY PSEFANQNQG G AQAPFDID DLAFDLDGTG KSQSGSNSGN NSKKRKNKSS GSSMATPTHS DSHEDMKRRR LE

Macromolecule #13: Mediator of RNA polymerase II transcription subunit 20

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 20; type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 22.918068 KDa

Sequence

String:

MGKSAVIFVE RATPATLTEL KDALSNSILS VRDPWSIDFR TYRCSIKNLP ADVSKLMYSI TFHHHGRQTV LIKDNSAMVT TAAAADIPP ALVFNGSSTG VPESIDTILS SKLSNIWMQR QLIKGDAGET LILDGLTVRL VNLFSSTGFK GLLIELQADE A GEFETKIA GIEGHLAEIR AKEYKTSSDS LGPDTSNEIC DLAYQYVRAL EL

Macromolecule #14: Mediator of RNA polymerase II transcription subunit 21

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 21; type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 16.093368 KDa

Sequence

String:

MTDRLTQLQI CLDQMTEQFC ATLNYIDKNH GFERLTVNEP QMSDKHATVV PPEEFSNTID ELSTDIILKT RQINKLIDSL PGVDVSAEE QLRKIDMLQK KLVEVEDEKI EAIKKKEKLL RHVDSLIEDF VDGIANSKKS T

Macromolecule #15: Mediator of RNA polymerase II transcription subunit 22

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 22; type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 13.875731 KDa

Sequence

String:

MSNQALYEKL EQTRTILSVK LAELINMTTI ADRNDDDEGS FAQENSELAV ATTSVMMVNN QTMQLIKNVQ DLLILTRSIK EKWLLNQIP VTEHSKVTRF DEKQIEELLD NCIETFVAEK TT

Macromolecule #16: Mediator of RNA polymerase II transcription subunit 31

• Macromolecule: Name: Mediator of RNA polymerase II transcription subunit 31; type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
• Molecular weight: Theoretical: 14.747739 KDa

Sequence

String:

MSSTNGNAPA TPSSDQNPLP TRFEVELEFI QSLANIQYVT YLLTQQQIWK SPNFKNYLKY LEYWCNPPYS QCIVYPNCLF ILKLLNGFM ESAIVNEDGL LEGLDELPKI IQLQGPQWMN EMVERWAN

Macromolecule #17: DNA-directed RNA polymerase II subunit RPB1

• Macromolecule: Name: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 17 / 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

Experimental details

Structure determination

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

Sample preparation

• Concentration: .1 mg/mL

Buffer

pH: 7.6
Component:

Concentration	Formula	Name
80.0 mM	KOAc	Potassium acetate
20.0 mM	HEPES	HEPES
5.0 mM	DTT	Dithiothreitol
2.0 mM	Mg(OAc)2	Magnesium acetate

• Vitrification: Cryogen name: ETHANE / Instrument: LEICA EM CPC

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 64000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Number real images: 40900 / Average exposure time: 3.4 sec. / Average electron dose: 42.0 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 341314