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- PDB-9epc: Cryo-EM structure of the Plastid-encoded RNA polymerase from Sina... -

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Basic information

Entry
Database: PDB / ID: 9epc
TitleCryo-EM structure of the Plastid-encoded RNA polymerase from Sinapis alba
Components
  • (DNA-directed RNA polymerase subunit ...) x 3
  • FLN2
  • PAP1, pTAC3
  • PAP10, TRXz
  • PAP11, MurE-like
  • PAP12, pTAC7
  • PAP2, pTAC2
  • PAP3, pTAC10
  • PAP4, FSD3
  • PAP5, pTAC12, HEMERA
  • PAP6, FLN1
  • PAP7, pTAC14
  • PAP8, pTAC6
  • PAP9, FSD2
  • PRIN2, PLASTID REDOX INSENSITIVE 2
  • RpoB, subunit beta
  • pTAC18
KeywordsTRANSCRIPTION / RNA polymerase Chloroplast Sinapis alba Cryo-EM
Function / homology
Function and homology information


: / DNA-directed RNA polymerase complex / chloroplast / : / : / : / : / : / : / DNA-directed RNA polymerase ...: / DNA-directed RNA polymerase complex / chloroplast / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity / magnesium ion binding / mitochondrion / DNA binding / zinc ion binding
Similarity search - Function
: / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type ...: / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / : / S-ADENOSYL-L-HOMOCYSTEINE / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta''
Similarity search - Component
Biological speciesSinapis alba (white mustard)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsEffantin, G. / Blanvillain, R. / Cobessi, D.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0031 France
CitationJournal: To Be Published
Title: Cryo-EM structure of the Plastid-encoded RNA polymerase from Sinapis alba
Authors: Effantin, G. / Blanvillain, R. / Cobessi, D.
History
DepositionMar 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: RpoB, subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit beta''
F: PAP1, pTAC3
G: PAP2, pTAC2
H: PAP3, pTAC10
I: PAP4, FSD3
J: PAP5, pTAC12, HEMERA
K: PAP6, FLN1
L: PAP7, pTAC14
M: PAP8, pTAC6
N: PAP9, FSD2
O: PAP10, TRXz
P: PAP10, TRXz
Q: PAP11, MurE-like
R: PAP12, pTAC7
S: FLN2
T: pTAC18
U: PRIN2, PLASTID REDOX INSENSITIVE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,262,24929
Polymers1,261,41421
Non-polymers8358
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA-directed RNA polymerase subunit ... , 3 types, 4 molecules ABDE

#1: Protein DNA-directed RNA polymerase subunit alpha


Mass: 37945.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: S67F mutation found from electron density analyses / Source: (natural) Sinapis alba (white mustard) / References: UniProt: A0A6C0M610
#3: Protein DNA-directed RNA polymerase subunit beta' / PEP / Plastid-encoded RNA polymerase subunit beta' / RNA polymerase subunit beta'


Mass: 78761.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
References: UniProt: A0A6C0M5W0, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit beta''


Mass: 156388.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard) / References: UniProt: A0A6C0M829

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Protein , 16 types, 17 molecules CFGHIJKLMNOPQRSTU

#2: Protein RpoB, subunit beta


Mass: 121223.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: S113F muation found from electron density analysis / Source: (natural) Sinapis alba (white mustard)
#5: Protein PAP1, pTAC3


Mass: 103467.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#6: Protein PAP2, pTAC2


Mass: 122664.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE ...Details: Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA,Full sequence: MNLAIPNPNSHHLSFLIQNSTFIGNRRFANSNHLSFLSGGKRPCSVAKINAKTKDLVLGNPSVSVEKGKYSYDVESLINK LSSLPPRGSIARCLDIFKNKLSLNDFALVFKEFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKCLE VFEEMPSQGVARSVFSYTALINAYGRNGRYETSLELLDRMKSEKISPSILTYNTVINACARGGLDWEGLLGLFAEMRHEG IQPDIVTYNTLLSACAIRGLGDEAEMVFRTMNDGGIVPDLTTYSHLVETFGKLGRLEKVSDLLSEMASGGSLPDITSYNV LLEAYAKSGSIKEAMGVFHQMQAAGCSPNANTYSVLLNLFGQNGRYDDVRQLFLEMKSSNTDPDAATYNILIDVFGEGGY FKEVVTLFHDMVEENIEPDMETYEGIIFACGKGGLHEDARKILQYMTAKDVVPSSKAYTGVIEAFGQAALYEEALVAFNT MHEVGSNPSIETFHSLLYSFARGGLFKESEVILSRLVNSGIPRNRDTFNATIEAYKQGGKFEEAVKTYVDMEKSRCDPDE RTLEAVLSVYSCARLVDECREQFEEMKASDILPSIMCYCMMLSVYGKTESWDDVNELLEEMLSNRVSNIHQVIGQMIKGN YDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQKERAARVLNEATKRGIFPELFRKNKLVWSVDVHRMSEGG MYTALSVWLNDLSDILVKGQDLPQLAVVVSVRGQLEKSSAARESPITRAAFSFLQDHVSSSFSFTGWNGGRIMCQRSQLK QLLSTQEPTSEESPKSNIVALTNSPIFAAGTRTSTSSDTNHSGGNPSQRKTKMKKELAGSPA
Source: (natural) Sinapis alba (white mustard)
#7: Protein PAP3, pTAC10


Mass: 79815.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#8: Protein PAP4, FSD3


Mass: 30418.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#9: Protein PAP5, pTAC12, HEMERA


Mass: 60884.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#10: Protein PAP6, FLN1


Mass: 52435.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#11: Protein PAP7, pTAC14


Mass: 55675.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#12: Protein PAP8, pTAC6


Mass: 38039.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#13: Protein PAP9, FSD2


Mass: 34008.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#14: Protein PAP10, TRXz


Mass: 20954.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#15: Protein PAP11, MurE-like


Mass: 85121.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#16: Protein PAP12, pTAC7


Mass: 18835.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#17: Protein FLN2


Mass: 68527.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#18: Protein pTAC18


Mass: 16430.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)
#19: Protein PRIN2, PLASTID REDOX INSENSITIVE 2


Mass: 20915.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sinapis alba (white mustard)

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Non-polymers , 6 types, 8 molecules

#20: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Plastid-encoded RNA polymerase / Type: COMPLEX / Entity ID: #1-#19 / Source: NATURAL
Molecular weightValue: 1.15 MDa / Experimental value: NO
Source (natural)Organism: Sinapis alba (white mustard)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
7PHENIXmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105796 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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