Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Yeast PIC-Mediator structure with RNA polymerase II C-terminal domain. Authors: Sandra Schilbach / Haibo Wang / Christian Dienemann / Patrick Cramer / Abstract: For transcription initiation, RNA polymerase II (Pol II) forms a preinitiation complex (PIC) that associates with the general coactivator Mediator. Whereas atomic models of the human PIC-Mediator ...For transcription initiation, RNA polymerase II (Pol II) forms a preinitiation complex (PIC) that associates with the general coactivator Mediator. Whereas atomic models of the human PIC-Mediator structure have been reported, structures for its yeast counterpart remain incomplete. Here, we present an atomic model for the yeast PIC with core Mediator, including the Mediator middle module that was previously poorly resolved and including subunit Med1 that was previously lacking. We observe three peptide regions containing eleven of the 26 heptapeptide repeats of the flexible C-terminal repeat domain (CTD) of Pol II. Two of these CTD regions bind between the Mediator head and middle modules and form defined CTD-Mediator interactions. CTD peptide 1 binds between the Med6 shoulder and Med31 knob domains, whereas CTD peptide 2 forms additional contacts with Med4. The third CTD region (peptide 3) binds in the Mediator cradle and associates with the Mediator hook. Comparisons with the human PIC-Mediator structure show that the central region in peptide 1 is similar and forms conserved contacts with Mediator, whereas peptides 2 and 3 exhibit distinct structures and Mediator interactions.
0: General transcription and DNA repair factor IIH helicase subunit XPD 1: General transcription and DNA repair factor IIH subunit TFB1 2: General transcription and DNA repair factor IIH subunit TFB2 3: RNA polymerase II transcription factor B subunit 3 4: General transcription and DNA repair factor IIH subunit TFB4 5: General transcription and DNA repair factor IIH subunit TFB5 6: General transcription and DNA repair factor IIH subunit SSL1 7: General transcription and DNA repair factor IIH helicase subunit XPB A: DNA-directed RNA polymerase II subunit RPB1 B: DNA-directed RNA polymerase II subunit RPB2 C: DNA-directed RNA polymerase II subunit RPB3 D: DNA-directed RNA polymerase II subunit RPB4 E: DNA-directed RNA polymerases I, II, and III subunit RPABC1 F: DNA-directed RNA polymerases I, II, and III subunit RPABC2 G: DNA-directed RNA polymerase II subunit RPB7 H: DNA-directed RNA polymerases I, II, and III subunit RPABC3 I: DNA-directed RNA polymerase II subunit RPB9 J: DNA-directed RNA polymerases I, II, and III subunit RPABC5 K: DNA-directed RNA polymerase II subunit RPB11 L: DNA-directed RNA polymerases I, II, and III subunit RPABC4 M: Transcription initiation factor IIB N: NONTEMPLATE DNA (209-MER) O: TATA-binding protein Q: Transcription initiation factor IIF subunit alpha R: Transcription initiation factor IIF subunit beta T: TEMPLATE DNA (209-MER) U: Transcription initiation factor IIA large subunit V: Transcription initiation factor IIA subunit 2 W: Transcription initiation factor IIE subunit alpha X: Transcription initiation factor IIE subunit beta a: Mediator of RNA polymerase II transcription subunit 6 b: Mediator of RNA polymerase II transcription subunit 8 c: Mediator of RNA polymerase II transcription subunit 11 d: Mediator of RNA polymerase II transcription subunit 17 e: Mediator of RNA polymerase II transcription subunit 18 f: Mediator of RNA polymerase II transcription subunit 20 g: Mediator of RNA polymerase II transcription subunit 22 h: Mediator of RNA polymerase II transcription subunit 4 i: Mediator of RNA polymerase II transcription subunit 7 j: Mediator of RNA polymerase II transcription subunit 9 k: Mediator of RNA polymerase II transcription subunit 10 l: Mediator of RNA polymerase II transcription subunit 14 m: Mediator of RNA polymerase II transcription subunit 19 n: Mediator of RNA polymerase II transcription subunit 21 o: Mediator of RNA polymerase II transcription subunit 31 p: Mediator of RNA polymerase II transcription subunit 1 hetero molecules
Mass: 72993.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Trichoplusia ni (cabbage looper)
Mass: 58602.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Trichoplusia ni (cabbage looper)
Mass: 37506.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Trichoplusia ni (cabbage looper)
Mass: 8243.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Trichoplusia ni (cabbage looper)
Mass: 52370.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Trichoplusia ni (cabbage looper)
+
Protein , 3 types, 3 molecules 3MO
#4: Protein
RNApolymeraseIItranscriptionfactorBsubunit3
Mass: 38188.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Trichoplusia ni (cabbage looper)
#21: Protein
TranscriptioninitiationfactorIIB / General transcription factor TFIIB / Transcription factor E
Mass: 39215.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SUA7, YPR086W, P9513.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P29055
#23: Protein
TATA-bindingprotein
Mass: 27042.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SPT15 / Production host: Escherichia coli (E. coli) / References: UniProt: G4XSG8
DNA-directedRNApolymeraseIIsubunitRPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220
Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#10: Protein
DNA-directedRNApolymeraseIIsubunitRPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide
Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#11: Protein
DNA-directedRNApolymeraseIIsubunitRPB3 / RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II ...RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide
Mass: 38635.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16370
#12: Protein
DNA-directedRNApolymeraseIIsubunitRPB4 / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide
Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20433
#15: Protein
DNA-directedRNApolymeraseIIsubunitRPB7 / RNA polymerase II subunit B7 / B16
Mass: 19909.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34087
#17: Protein
DNA-directedRNApolymeraseIIsubunitRPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9
Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27999
#19: Protein
DNA-directedRNApolymeraseIIsubunitRPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide
Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38902
+
DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#13: Protein
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide
Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434
#14: Protein
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide
Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435
#16: Protein
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide
Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20436
#18: Protein
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide
Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22139
#20: Protein
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha
Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422
+
DNA chain , 2 types, 2 molecules NT
#22: DNA chain
NONTEMPLATEDNA (209-MER)
Mass: 64290.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#26: DNA chain
TEMPLATEDNA (209-MER)
Mass: 64754.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Mass: 82320.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#25: Protein
TranscriptioninitiationfactorIIFsubunitbeta / TFIIF medium subunit / TFIIF-beta / Transcription factor G 54 kDa subunit
Mass: 46684.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TFG2, YGR005C / Production host: Escherichia coli (E. coli) / References: UniProt: P41896
Mass: 32230.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#28: Protein
TranscriptioninitiationfactorIIAsubunit2
Mass: 13473.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PACBIOSEQ_LOCUS3356, PACBIOSEQ_LOCUS3547, PACBIOSEQ_LOCUS3591, PACBIOSEQ_LOCUS3602, PACBIOSEQ_LOCUS3607, PACBIOSEQ_LOCUS3639, PACBIOSEQ_LOCUS3680, PACBIOSEQ_LOCUS3892, PACBIOSEQ_LOCUS3963 Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PRZ0
TranscriptioninitiationfactorIIEsubunitalpha / TFIIE-alpha / Factor A 66 kDa subunit / Transcription factor A large subunit
Mass: 55951.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TFA1, YKL028W / Production host: Escherichia coli (E. coli) / References: UniProt: P36100
#30: Protein
TranscriptioninitiationfactorIIEsubunitbeta / TFIIE-beta / Factor A 43 kDa subunit / Transcription factor A small subunit
Mass: 37050.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TFA2, YKR062W / Production host: Escherichia coli (E. coli) / References: UniProt: P36145
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Mediator of RNA polymerase II transcription subunit ... , 16 types, 16 molecules abcdefghijklmnop
#31: Protein
MediatorofRNApolymeraseIItranscriptionsubunit6
Mass: 32844.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#32: Protein
MediatorofRNApolymeraseIItranscriptionsubunit8
Mass: 25297.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#33: Protein
MediatorofRNApolymeraseIItranscriptionsubunit11
Mass: 13324.189 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#34: Protein
MediatorofRNApolymeraseIItranscriptionsubunit17
Mass: 78582.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#35: Protein
MediatorofRNApolymeraseIItranscriptionsubunit18
Mass: 34316.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#36: Protein
MediatorofRNApolymeraseIItranscriptionsubunit20
Mass: 22918.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#37: Protein
MediatorofRNApolymeraseIItranscriptionsubunit22
Mass: 13875.731 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#38: Protein
MediatorofRNApolymeraseIItranscriptionsubunit4
Mass: 32244.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#39: Protein
MediatorofRNApolymeraseIItranscriptionsubunit7
Mass: 25616.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#40: Protein
MediatorofRNApolymeraseIItranscriptionsubunit9
Mass: 17400.377 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#41: Protein
MediatorofRNApolymeraseIItranscriptionsubunit10
Mass: 17927.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#42: Protein
MediatorofRNApolymeraseIItranscriptionsubunit14
Mass: 84746.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#43: Protein
MediatorofRNApolymeraseIItranscriptionsubunit19
Mass: 24885.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#44: Protein
MediatorofRNApolymeraseIItranscriptionsubunit21
Mass: 16093.368 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#45: Protein
MediatorofRNApolymeraseIItranscriptionsubunit31
Mass: 14747.739 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
#46: Protein
MediatorofRNApolymeraseIItranscriptionsubunit1
Mass: 64314.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli)
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