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- EMDB-18496: Structure of the plastid-encoded RNA polymerase complex (PEP) fro... -

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Basic information

Entry
Database: EMDB / ID: EMD-18496
TitleStructure of the plastid-encoded RNA polymerase complex (PEP) from Sinapis alba
Map dataComposite Map (Map G).
Sample
  • Complex: Plastid-encoded DNA-dependent RNA polymerase (PEP)
    • Protein or peptide: x 17 types
  • Ligand: x 3 types
KeywordsTranscription / Chloroplasts / Gene Expression / RNA / Polymerase
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / chloroplast / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding
Similarity search - Function
: / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily ...: / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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, 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 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta' / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
Authorsdo Prado PFV / Ahrens FM / Pfannschmidt T / Hillen HS
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2848 Germany
German Research Foundation (DFG)SFB1190 Germany
German Research Foundation (DFG)SFB1565 Germany
German Research Foundation (DFG)EXC 2067/1 390729940 Germany
German Research Foundation (DFG)PF323-7 Germany
CitationJournal: Mol Cell / Year: 2024
Title: Structure of the multi-subunit chloroplast RNA polymerase.
Authors: Paula F V do Prado / Frederik M Ahrens / Monique Liebers / Noah Ditz / Hans-Peter Braun / Thomas Pfannschmidt / Hauke S Hillen /
Abstract: Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase ...Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. Here, we report the cryo-EM structure of a 19-subunit PEP complex from Sinapis alba (white mustard). The structure reveals that the PEP core resembles prokaryotic and nuclear RNAPs but contains chloroplast-specific features that mediate interactions with the PAPs. The PAPs are unrelated to known transcription factors and arrange around the core in a unique fashion. Their structures suggest potential functions during transcription in the chemical environment of chloroplasts. These results reveal structural insights into chloroplast transcription and provide a framework for understanding photosynthesis gene expression.
History
DepositionSep 21, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18496.png

Downloads & links

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Map

FileDownload / File: emd_18496.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite Map (Map G).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 440 pix.
= 462. Å		1.05 Å/pix.
x 440 pix.
= 462. Å		1.05 Å/pix.
x 440 pix.
= 462. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.05553045 - 2.7619514
Average (Standard dev.)0.025998646 (±0.051533367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 461.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Plastid-encoded DNA-dependent RNA polymerase (PEP)

EntireName: Plastid-encoded DNA-dependent RNA polymerase (PEP)
Components
  • Complex: Plastid-encoded DNA-dependent RNA polymerase (PEP)
    • Protein or peptide: PAP4
    • Protein or peptide: PAP5
    • Protein or peptide: PAP8
    • Protein or peptide: PAP9
    • Protein or peptide: PAP10
    • Protein or peptide: PAP11
    • Protein or peptide: PAP12 (DNA-directed RNA polymerase subunit omega)
    • Protein or peptide: PTAC18
    • Protein or peptide: PAP6
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta''
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: PAP1
    • Protein or peptide: PAP3
    • Protein or peptide: FLN2
    • Protein or peptide: PAP7
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
  • Ligand: FE (III) ION
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINE

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Supramolecule #1: Plastid-encoded DNA-dependent RNA polymerase (PEP)

SupramoleculeName: Plastid-encoded DNA-dependent RNA polymerase (PEP) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: PAP4

MacromoleculeName: PAP4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 30.404408 KDa
SequenceString: MASCVVTTSS FCTLSDSNIR LKSSKLVHLS NQQRRRFPLG SRGGLKVEAY YGLKTPPYPL DALEPYMSRR TLEVHWGKHH RGYVDNLNK QLGKDDKLYG YTMEELIKAT YNNGNPLPEF NNAAQVYNHD FFWESMQPGG GDMPQKGVLE QIEKDFGSFT N FREKFTNA ...String:
MASCVVTTSS FCTLSDSNIR LKSSKLVHLS NQQRRRFPLG SRGGLKVEAY YGLKTPPYPL DALEPYMSRR TLEVHWGKHH RGYVDNLNK QLGKDDKLYG YTMEELIKAT YNNGNPLPEF NNAAQVYNHD FFWESMQPGG GDMPQKGVLE QIEKDFGSFT N FREKFTNA ALTQFGSGWV WLVLKREERR LEVVKTSNAI NPLVWDDIPI ISLDVWEHSY YLDYKNERGK YINTFLNHLV SW NAAMSRM ARAEAFVNLG EPNIPIA

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Macromolecule #2: PAP5

MacromoleculeName: PAP5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 60.884246 KDa
SequenceString: MASISTTSWL YRDKLCTESG KLGTCILQRP VKCGFPVKRL YVGITSKDVL MRDCIKCKKD DDDDDASEGS SKKDGQGYEY VSVERAPYY SYMDSTSGKM EPASGARASI PGEDYWPEGT SSRVRAARAP QPAGESSSFP SYGKNPGSRR KKNRKATEGN A AVETYDEV ...String:
MASISTTSWL YRDKLCTESG KLGTCILQRP VKCGFPVKRL YVGITSKDVL MRDCIKCKKD DDDDDASEGS SKKDGQGYEY VSVERAPYY SYMDSTSGKM EPASGARASI PGEDYWPEGT SSRVRAARAP QPAGESSSFP SYGKNPGSRR KKNRKATEGN A AVETYDEV SDSEDSSEEE ESDSSNGFVV YNNEVEGEDE EETGFELDKK LGRPHPFIDP TKKKQIETTL TSDESWWNWR KP EKEQWSR WQRRRPDVET VFLKAMAETG QVKLYGKEPT LTETSLYRAR RHLFKEERLQ AERERLAKEG PMAFYSEWVK AWK RDTSRE AVQKHFEETG EDENTQLIEM FSHQTDREYR IMMGTDVRIK RDPLAMRMKE DQIKQIWGGD PVYPTINYIQ APDA VMDFR GPDFHEPTPN MLSYLKENCK VISREMHETL LAKEKTEQVE VPDIDDAMAQ AVDIGENDDE EEDTEEAEKD EKVAR NWSV LKSTPELRNS KPKPKKEGRM SLDEAVDDSE NLTDFLMDFD EETDP

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Macromolecule #3: PAP8

MacromoleculeName: PAP8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 38.039504 KDa
SequenceString: MASSAASPSL SLLSLTPKPP PSPSTASATS HRLFPSFRTN GCFAPLTLKP RRGRSIIVKV DDGDADGGGQ DEYDMDDEEV EEVDNKKDY DVEYDPLAAA MAAASGGGGD GDIAFVQSKS FISTQGWDSE MVVDYRINED EFHKISLLDC DFFIRKPPDP D NDVYDFRE ...String:
MASSAASPSL SLLSLTPKPP PSPSTASATS HRLFPSFRTN GCFAPLTLKP RRGRSIIVKV DDGDADGGGQ DEYDMDDEEV EEVDNKKDY DVEYDPLAAA MAAASGGGGD GDIAFVQSKS FISTQGWDSE MVVDYRINED EFHKISLLDC DFFIRKPPDP D NDVYDFRE MYVTPPDTDI YSVPRVLAPM PQKYIRCAMS DYGCYDVTEP PIDAPRDPLY KSEREISKVF LTKHYRNRRL ND PEFVLDF EEIYVIDSKT KSITRARVLV TVPGGRKRDR KDDLLVIRDN GNSFKIIHVG ERDDPTTVIE REEWTKTRED MEK HLRKLR DFSVSNWF

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Macromolecule #4: PAP9

MacromoleculeName: PAP9 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 34.008883 KDa
SequenceString: MMTSTCSFLS SCSLLPSQEP NQRMQWKRHE KRQFSRKVAV SGVIRAGFEL KPPPYPLDAL EPHMSRETLD YHWGKHHKTY VENLNKQIV GTDLDGLSLE EVVLLSYNRG NMLPAFNNAA QAWNHEFFWE SIQPGGGGKP SGDLLRLIER DFGSFSDFVE R FKAAAASN ...String:
MMTSTCSFLS SCSLLPSQEP NQRMQWKRHE KRQFSRKVAV SGVIRAGFEL KPPPYPLDAL EPHMSRETLD YHWGKHHKTY VENLNKQIV GTDLDGLSLE EVVLLSYNRG NMLPAFNNAA QAWNHEFFWE SIQPGGGGKP SGDLLRLIER DFGSFSDFVE R FKAAAASN FGSGWTWLAY KANRLDVANA VNPLPKEEDK KLVIVKTPNA VNPLVWDYSP LLTIDTWEHA YYLDFENRRI EY INTFMEK LVSWETVSTR LESAMARAAQ REQEGSDTEA EENPDDEEPE VYLDDASEVD

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Macromolecule #5: PAP10

MacromoleculeName: PAP10 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 20.851234 KDa
SequenceString:
MALVQSIALL PHLNVPLSPI LSTLHAPSSL FLRKENRPVT SPFLSSTSGN SHFSPLTHPR KLLCTPPRGK FVREDYLVRK LTAEELQEL VKGERKVPLI VDFYATWCGP CILMAQELEM LAVEYESNAM IVKVDTDDEY EFARDMQVRG LPTLFFISPD P SKDAIRTE GLIPLQMMRD IIDNDM

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Macromolecule #6: PAP11

MacromoleculeName: PAP11 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 85.061648 KDa
SequenceString: MAFTFFSPHP VFLPLGRTTS SFSYKPVYSP FPRNSRNLQL AAGPARRNSY PNPADDDPPE APEDSMHGVS KFQQIQRQAA RARKLEEED FEKNRNTYLS AIADVEDAPE TGRDDVESGG DLFSDIDRAI SMKRSEFVKK GLLQPNPPKT TSSKKLDEEE D DVTDVVDE ...String:
MAFTFFSPHP VFLPLGRTTS SFSYKPVYSP FPRNSRNLQL AAGPARRNSY PNPADDDPPE APEDSMHGVS KFQQIQRQAA RARKLEEED FEKNRNTYLS AIADVEDAPE TGRDDVESGG DLFSDIDRAI SMKRSEFVKK GLLQPNPPKT TSSKKLDEEE D DVTDVVDE LDEEEVVDLD EIDKLTGLTE VSDEEDWVDE EGNPRINKKK ETGSDHHFEF DLDDFGGSKA RIVEPKFRLS LA ELLDESK VVPISVYGDL DVEITGIQHD SRGVSSGDLF VCCENEGDSV LSEADKRGAV AVVASKEIDI EDTLGCRALV IVE DTEAVL AALASSFYRH PSKNMAVIGV TGTNGKTTTT YLIKSLYEAM GVRTGMFSTV SCYVHGDNKM DSPTTTSPDA VLVQ SMMAK MLHNGTEALV MEASPQELAS GKCDEVDFDI AVFTNLTRED SDFRGTDEEY RDAEAKLFAR MVDPERHRKV VNIDD PNAA FFVQQGNPDV PVVTFAMENT KADVHPLKFE LSLFETQVLV NTPQGILEIS SGLLGRHNIC NILAAVAVGI AVGAPL EDI VRGVEEVDAV PGRCELIDEE QAFGVIVDHA NTPDGLSRLL DSVRELKPRR IITVIGCAGE NERGKRPVMT KIATEKS DV TMLTSDNPGN EDPLDILDDM LSGIGWTMQE YLKHGEHDYY PPLSNGHRLF LHDVRRVAVR CAVAMGEEGD MVVVAGKG H ESYQLEGDKK EFYDDREECR EALQYVDELH QAGIDTSEFP WRLPESH

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Macromolecule #7: PAP12 (DNA-directed RNA polymerase subunit omega)

MacromoleculeName: PAP12 (DNA-directed RNA polymerase subunit omega) / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 18.835195 KDa
SequenceString:
MFCSSFTSSI SRIGDARSGN SRASSFTFQT QVSCGIQRDD NGRRIWRRRT LTKKDDMLRY KLQRVPFVEE QVRKIKEVGK VMTMDIERL LLSEDNRFEF VNSVAAEATE YVEKNRDEYG GTKKAIFHVL SNRVNDLGFD RPEAYAESDP YKPGPGYLKE Y YT

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Macromolecule #8: PTAC18

MacromoleculeName: PTAC18 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 16.430916 KDa
SequenceString:
MASLIMTTPF SGSLTQCKKK TNNLSVNRAF FKVTCSMQTP LEELYNVKVE RKVSQRRLDE LGVSRWSVWK TGKCKLPWDW QVDQLVYIE EGEVRVVPEG SKRFMQFLAG DLVRYPKWLE ADLFFNAPYS ERYCFKAYAD D

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Macromolecule #9: PAP6

MacromoleculeName: PAP6 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 52.435281 KDa
SequenceString: MASLHLFPHL HHFDSIIHRR EIAAHSRRQF LSPKASINGG VVTNGASAAE TAKPSRKGRN KKKQTEETNP DSDPALVDYD DGIDFPYDD PPLVCCFGAV QKEFVPVVRV HDNPMHPDIY SQWKMLQWDP PEFGRAPGGP PSNVAISHVR LGGRAAFMGK V GGDDYGEE ...String:
MASLHLFPHL HHFDSIIHRR EIAAHSRRQF LSPKASINGG VVTNGASAAE TAKPSRKGRN KKKQTEETNP DSDPALVDYD DGIDFPYDD PPLVCCFGAV QKEFVPVVRV HDNPMHPDIY SQWKMLQWDP PEFGRAPGGP PSNVAISHVR LGGRAAFMGK V GGDDYGEE LVLMMNKERV QTRGVKFDEG ASTACTRVKI KFEDGKMKAE TVKEPPEDSL LASELNLAVL KEARIFHFNS EV LTSPTME STLFKAIQWS KKFGGLIFFD LNLPLPLWRS RNETRKLIKK SWDEANIIEV SQQELEFLLD EEYYERRRNY TPQ YFAEDF EQTKNRRDYY HYTPEEIKPL WHDDLKLLVV TDGTLRLHYY TPKFDGVVVG TEDVLITPFT CDRTGSGDAV VAGI MRKLT TCPEMFEDQD VLERQLRFAV AAGIISQWTI GAVRGFPTES ATQNLKEQVY VPSMW

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Macromolecule #10: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 121.163047 KDa
SequenceString: MLGDGKEGTS TIPGFNQIQF EGFYRFIDQG LIEELSKFPK IEDIDHEIEF QLFVETYQLV EPLIKERDAV YESLTYSSEL YVSAGLIWK TNRNMQEQRI FIGNIPLMNS LGTSIVNGIY RVVINQILQS PGIYYQSELD HNGISVYTGT IISDWGGRLE L EIDKKARI ...String:
MLGDGKEGTS TIPGFNQIQF EGFYRFIDQG LIEELSKFPK IEDIDHEIEF QLFVETYQLV EPLIKERDAV YESLTYSSEL YVSAGLIWK TNRNMQEQRI FIGNIPLMNS LGTSIVNGIY RVVINQILQS PGIYYQSELD HNGISVYTGT IISDWGGRLE L EIDKKARI WARVSRKQKI SILVLSSAMG SNLREILENV CYPEIFLSFL TDKEKKKIGS KENAILEFYQ QFSCVGGDPI FS ESLCKEL QKKFFHQRCE LGRIGRRNIN WRLNLNIPQN NIFLLPRDIL AAADHLIGMK FGMGTLDDMN HLKNKRIRSV ADL LQDQLG LALARLENVV KGTIGGAIRH KLIPTPQNLV TSTPLTTTYE SFFGLHPLSQ VLDRTNPLTQ IVHGRKLSYL GPGG LTGRT ANFRIRDIHP SHYGRICPID TSEGINVGLI GSLSIHARIG DWGSLESPFY ELVEKSKKAQ IRMLFLSPSQ DEYYM IAAG NSLALNRGIQ EEQVVPARYR QEFLTIAWEE VHLRSIFPFQ YFSIGASLIP FIEHNDANRA LMSSNMQRQA VPLSRS EKC IVGTGLERQV ALDSGVPAIA EHEGKILYTD TEKIILSGNE NTLSIPLIMY QRSNKNTCMH QKPQVRRGKC IKKGQIL AD GAATVGGELA LGKNILVAYM PWEGYNFEDA VLISECLVYG DIYTSFHIRK YEIQTHVTTQ GPERITKEIP HLEGRLLR N LDKNGIVMLG SWVETGDILV GKLTPQVAKE SSYAPEDRLL RAILGIQVST SKETCLKLPI GGRGRVIDVR WVQKKGGSS YNPEIIRVYI SQKREIKVGD KVAGRHGNKG IISKILPRQD MPYLQDGRPV DMVFNPLGVP SRMNVGQIFE CSLGLAGSLL DRHYRIAPF DERYEQEASR KLVFSELYEA SKQTANPWVF EPEYPGKSRI FDGRTGDPFE QPVIIGKPYI LKLIHQVDDK I HGRSSGHY ALVTQQPLRG RSKQGGQRVG EMEVWALEGF GVAHILQEML TYKSDHIRAR QEVLGTTIIG GTIPKPEDAP ES FRLLVRE LRSLALELNH FLVSEKNFQI NRKEV

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #11: DNA-directed RNA polymerase subunit beta''

MacromoleculeName: DNA-directed RNA polymerase subunit beta'' / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 156.388719 KDa
SequenceString: MAERANLVFH NKVIDGTAIK RLISRLIDHF GMAYTSHILD QVKTLGFQQA TATSISLGID DLLTIPSKGW LVQDAEQQSL ILEKHHHYG NVHAVEKLRQ SIEIWYATSE YLRQEMNPNF RMTDPFNPVH MMSFSGARGN ASQVHQLVGM RGLMSDPQGQ M IDLPIQSN ...String:
MAERANLVFH NKVIDGTAIK RLISRLIDHF GMAYTSHILD QVKTLGFQQA TATSISLGID DLLTIPSKGW LVQDAEQQSL ILEKHHHYG NVHAVEKLRQ SIEIWYATSE YLRQEMNPNF RMTDPFNPVH MMSFSGARGN ASQVHQLVGM RGLMSDPQGQ M IDLPIQSN LREGLSLTEY IISCYGARKG VVDTAVRTSD AGYLTRRLVE VVQHIVVRRT DCGTIRGISV SPRNKSRMMS ER IFIQTLI GRVLADDIYI GSRCVAFRNQ DLGIGLVNRF ITFGTQSISI RTPFTCRSTS WICRLCYGRS PTHGDLVELG EAV GIIAGQ SIGEPGTQLT LRTFHTGGVF TGGTAEHVRA PYNGKIKFNE DLVHPTRTRH GHPAFLCYID LSVIIESEDI IHSV TIPPK SFLLVQNDQY VESEQVIAEI REGTYTFHFK ERVRKYIYSD SEGEMHWSTD VSHAPEFTYS NVHLLPKTSH LWILS GGSC GSSLILFSIH KDQDQMNIPF LSVERKSISS LSVNNDQVSQ KFFSSDFSDK KKSGIPNYSE LNGIVGTSHY NFIYSA IFH ENSDLLAKRR RNRFLIPFQS IQEQEQEKEF IPHSGISVEI PINGIFRRNS IFAFFDDPRY RRKSSGILKY GTLKADS II QKEDMIEYRG VQKFKTKYEM KVDRFFFIPE EVHILPESSA IMVENYSIIG VDTRITLNIR SQVGGLIRVE RKKKRIEL K IFSGDIHFPD KTDKISRHSG ILIPPGRGKT NSKESKNLKN WIYVQRITPT KKKFFVLVRP VATYEIADSI NLATLFPKD LFREKDNIQL RVFNYILYGN GKPTRGISDT SIQLVRTCLV LNWDQDNKNS SLEEVRAFFV EVNTKGLIRD FIRIGLVKSH ISYIRKRNN PPDSGLISAD SMNPFYSISP KAGILHQSLR QNHGTIRMFL NRNKESQSLL ILSSSNCFRI GPFNHVKYHN V INQSIKKK PLITIKNSSG PLGTAIQISN FYSFLPLLTY NQISVIKYLQ LDNFKYIFQV IHSYLIDENG RIFNLDPYSN LV LNPFKLN WYFLHQNYNN NYCEETSTII SLGQFFCENV CIAKKEPYLK SGQVLIVQRD SVVIRSAKPY LATPGAKVHG HYR EILYEG DTLVTFIYEK SRSGDITQGL PKVEQVLEVR SIDSISLNLE KRIKGWNRCI TRILGIPWGF LIGAELTIVQ SRIS LVNKI QKVYRSQGVQ IHNRHIEIIV RQITSKVLVS EEGMSNVFLP GELIGLLRAE RTGRALEEAI CYRAVLLGIT RASLN TQSF ISEASFQETA RVLAKAALRG RIDWLKGLKE NVVLGGVIPA GTGFNKGLVH CSRQHTNILL EKKTKNLSLL EGDMRD ILF YHREFCDSSI

UniProtKB: DNA-directed RNA polymerase subunit beta''

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Macromolecule #12: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 37.885652 KDa
SequenceString: MVREKVKVST RTLQWKCVES RRDSKRLYYG RFILSPLMKG QADTIGIAMR RALLGEIEGT CITRAKSENI PHDYSNIVGI QESVHEILM NLNEIVLKSN LYGTRNALIC VQGPGYITAR DIILPPSVEI VDNTQHIATL TEPINLCIGL KIERNRGYSL K MSNNFEDR ...String:
MVREKVKVST RTLQWKCVES RRDSKRLYYG RFILSPLMKG QADTIGIAMR RALLGEIEGT CITRAKSENI PHDYSNIVGI QESVHEILM NLNEIVLKSN LYGTRNALIC VQGPGYITAR DIILPPSVEI VDNTQHIATL TEPINLCIGL KIERNRGYSL K MSNNFEDR SYPIDAVFMP VQNANHSIHS YGNGNEKQEI LFIEIWTNGS LTPKEALHEA SRNLINLFIP FLHVEEETFY LE NNQHQVT LPLFPFHNKL VNLRQKKKEL AFQYIFIDQL ELPPRIYNCL KKSNIHTLLD LLNNSQEDLI KMEHFHIEDV KKL LDILEK K

UniProtKB: DNA-directed RNA polymerase subunit alpha

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Macromolecule #13: PAP1

MacromoleculeName: PAP1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 103.467867 KDa
SequenceString: MSLFFLNPAL PSNSIHPIPR RAAGISSIRC SISAPEKKPR RRRKQQQKRE NEDSSSFGSS EAVSALERSL RLTFMDELME RARNRDPSG VSEVIYDMIA AGLSPGPRSF HGLVVAHALN GDEQGAMHSL RKELGAGQRP LPETMIALVR LSGSKGNAQR G LELLAAME ...String:
MSLFFLNPAL PSNSIHPIPR RAAGISSIRC SISAPEKKPR RRRKQQQKRE NEDSSSFGSS EAVSALERSL RLTFMDELME RARNRDPSG VSEVIYDMIA AGLSPGPRSF HGLVVAHALN GDEQGAMHSL RKELGAGQRP LPETMIALVR LSGSKGNAQR G LELLAAME KLNYDIRQAW LILVEELVRT NHLEEANKVF LKGARGGMRA TDQLYDLMIE EDCKAGDHSN ALDISYEMEA AG RFATTFH FNCLLSVQAT CGIPEVAYAT FENMEYGEDF MKPDTETYNW VIQAYTRADS YDRVQDVAEL LGMMVEDYKR VQP NVKTHA LLVECFTKYC VVKEAIRHFR ALKNFEGGTK VLHNAGNFED PLSLYLRALC REGRIVELID ALDAMRRDNQ PIPP RAMIM SRKYRTLVSS WIEPLQEEAE LGYEIDYLAR YVEEGGLTGE RKRWVPRRGK TPLDPDAAGF IYSNPIETSF KQRCL EDWK VHHRKLLRTL QSEGLPVLGD ASESDYMRVM ERLRNIIKGP AQNLLKPKAA SKMVVSELKE ELEAQGLPID GTRNVL YQR VQKARRINKS RGRPLWVPPI EEEEEEVDEE VDELICRIKL HEGDTEFWKR RFLGEGLIET TAETKETDES SVATGEI EN KTEVVAKEAD DDEDDEEEEQ EGDEDDDENE EEEEAVVVEP ENRAEGEDLI KNKAADAKRH LQMIGVQLLK ESDEANRT K KRGKRASRMT LEDDADEDWF PEEPFEAFKE MRERKVFDVS DMYTIADVWG WTWEKDFKNK TPRRWSQEWE VELAIVLMA KVIELGGVPT IGDCAVILRA AIRAPMPSSF LKILQTTHSL GYAFGSPLYD EIITLCLDLG ELDAAIAIVA DMETTGITVP DQTLDKVIS ARQSNEIPKS EHEEPPSSSE SS

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Macromolecule #14: PAP3

MacromoleculeName: PAP3 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 79.815469 KDa
SequenceString: MQICQATLTT FTFTNPSNPN FCKPKPLFPS FQPPRRVTLP PCRGFSSDEF PVDETFLEKF GPKDKDTEDE ARRRNWIERG WAPWEEILT PEADFARKSL NEGEEVPLQS PEAIEAFKML RPSYRKKKIK EMGITEDEWY AKQFEIRGDK PPPLDTSWAG P LVVRQIPP ...String:
MQICQATLTT FTFTNPSNPN FCKPKPLFPS FQPPRRVTLP PCRGFSSDEF PVDETFLEKF GPKDKDTEDE ARRRNWIERG WAPWEEILT PEADFARKSL NEGEEVPLQS PEAIEAFKML RPSYRKKKIK EMGITEDEWY AKQFEIRGDK PPPLDTSWAG P LVVRQIPP RDWPPKGWEV DRKELEFIRE AHKLMAERVW LEDLDKDLKV GEDATVDKMC LERFKVFLKQ YNEWVEANKD RL EEDSYKY DQDFYPGRRI RGKDYKEGMY ELPFYYPGMI CEGTVTTLHL YQGAFVDIGG VHEGWVPIKG NDWFWIRHFI RVG MHVIVE ITAKRDPYRF RFPLELRFVH PNIDHMIFNK FDFPPIFHRD GDTNPDEIRR DCGRPPEPRK DPGSKPEEEG LLSD HPYVD KLWQLHVAEQ MILDDYEANP EKYKGKKLSE LSDDEGFDER KEIEHGEAYY KKTKLPKVIL KTSVKELDLE AALIE RKYH NKLMMEAKAR GEGYKIEKLR RNIEMDEYDS LHWRRSLEER EALLRDISSR QALGLPLEEP GRYKPGSFFG KDQYDP TSA LYQYDYWGEP KNSEISKQER MKDAHNKSIV GKGNVWYDMS YDDAIKQTIE RRKAESNVVT QKEEETESKE EEEDDDD EY EFDDFDYSIL SDESSIGYSE QQPLVNGTQV FTD

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Macromolecule #15: FLN2

MacromoleculeName: FLN2 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 68.527102 KDa
SequenceString: MASLSFTQFL PFPRCSVDVP CLQPHGFVKF RGERWKGKHS FLMVAGRRKL SESAPLDEDD GGNGAVGGKK PTKVPKKSGA RTAKKKVVA KDEPLEESSQ LLVDSDNVSD NESDTKEPVR RTRKKAAASS DVNEGKTEKK VRRKRTVKKD KEVEDGLVTY D EASDVEEA ...String:
MASLSFTQFL PFPRCSVDVP CLQPHGFVKF RGERWKGKHS FLMVAGRRKL SESAPLDEDD GGNGAVGGKK PTKVPKKSGA RTAKKKVVA KDEPLEESSQ LLVDSDNVSD NESDTKEPVR RTRKKAAASS DVNEGKTEKK VRRKRTVKKD KEVEDGLVTY D EASDVEEA LTVEATDADS EGEEIDLSKH ESEDISHTYG WPPLVCCFGS AQHAFVPSGR PANRLLDYER QERMKDAVWA PE KYIRAPG GCAGGVAIAL ASLGGKAAFM GKLGDDDFGQ AMLYYLNVCQ VQTRSVKIDS KRVTACSTMK ISKRGRLKST CVK PCAEDS LSKSEINVDV LKEAKMFYFT THSLLDKKMM STTLQAIKIS KQLGNVIFYD LNLPLPLWQS LEETKSLIQE VWDL ADVIE VTKQELEFLC GIEPTEEFDT KNNDSSKFVH YEPETVEPLW HENLKILFVT NGTSKIHYYT KEHNGAVLGM EDVPI TPFT RDMSASGDGI VAGLIRMLTV QPDLMNDKGY LERTARYAIE CGVVDQWLLA QTRGYPPKDD MEEEEDDDEE EEMESD PNG IRSITEREYR TSKPYDEPDG PYVMKPVEER EYRKLELVGS MGEDDDSS

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Macromolecule #16: PAP7

MacromoleculeName: PAP7 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 55.675461 KDa
SequenceString: MASPVSLHYL INTFISKPQG FCNGTVSSPR PRSSFVRERQ NSVKPIKVAS LETQPFPLFQ SPASEESSSS ELESADPDFY KIGYVRRVR AYGVEFKEGP DGFGIYASKD IEPRRRARVI MEIPHELMIT IRQKHPWMFF PDIVPIGHPI FDIINSTDPE R DWDLRLAC ...String:
MASPVSLHYL INTFISKPQG FCNGTVSSPR PRSSFVRERQ NSVKPIKVAS LETQPFPLFQ SPASEESSSS ELESADPDFY KIGYVRRVR AYGVEFKEGP DGFGIYASKD IEPRRRARVI MEIPHELMIT IRQKHPWMFF PDIVPIGHPI FDIINSTDPE R DWDLRLAC LLLFSFDRED HFWRLYGDFL PAADECSSLL LATEEDLAEL QDPQLVSTIR QQQKRVLEFW EKNWHSGVPL KI KRLAEDA ERFIWAVSIA QTRCISMKTR IGALVQDLNM MIPYADMLNH SFEPNCFLHW RPKDRILEVM SNAGQAIKKG EEM TINYMP GQKNNMLMER YGFSTPVNPW DAIPFSGDSR IHLNSFLSVF NIFGLPEEYY HDSELSGDDS FVDGAVIAAA RTLP TWSDI DLPPIPSAER KAVKELQDEC RKMLAEYPTT SEQDQKLLDS LSEARTTFAT AVKYRMHRKM FIGKIIKALD IYQER LLF

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Macromolecule #17: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 78.761867 KDa
SequenceString: MIDRYKHQQL RIGLVSPQQI SAWATKKIPN GEIVGEVTKP YTFHYKTNKP EKDGLFCERI FGPIKSGICA CGNYRVIGDE KEDPKFCEQ CGVEFVDSRI RRYQMGYIKL TCPVTHVWYL KRLPSYIANL LDKPLKELEG LVYCDFSFAR PITKKPTFLR L RGSFEYEI ...String:
MIDRYKHQQL RIGLVSPQQI SAWATKKIPN GEIVGEVTKP YTFHYKTNKP EKDGLFCERI FGPIKSGICA CGNYRVIGDE KEDPKFCEQ CGVEFVDSRI RRYQMGYIKL TCPVTHVWYL KRLPSYIANL LDKPLKELEG LVYCDFSFAR PITKKPTFLR L RGSFEYEI QSWKYSIPLF FTTQGFEIFR NREISTGAGA IREQLADLDL RIIIENSLVE WKQLGEEGPT GNEWEDRKIV RR KDFLVRR MELAKHFIRT NIEPEWMVLC LLPVLPPELR PIIQIEGGKL MSSDINELYR RVIYRNNTLT DLLTTSRSTP GEL VMCQEK LVQEAVDTLL DNGIRGQPMR DGHNKVYKSF SDVIEGKEGR FRETLLGKRV DYSGRSVIVV GPSLSLHRCG LPRE IAIEL FQTFVIRGLI RQHLASNIGV AKSQIREKKP IVWEILQEVM QGHPVLLNRA PTLHRLGIQS FQPILVEGRT ICLHP LVCK GFNADFDGDQ MAVHVPLSLE AQAEARLLMF SHMNLLSPAI GDPISVPTQD MLIGLYVLTS GTRRGICANR YNPCNR KNY QNERIYETNY KYMKEPFFCN SYDAIGAYRQ KRINLDSPLW LRWQLDQRVI ASKEVPIEVH YESFGNYHEI YAHYLIV RS VKKETLYIYI RTTVGHISFY REIEEAIQGF SQACSYDT

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #18: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #19: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #20: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 20 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
Component:
ConcentrationNameFormula
50.0 mMTris
0.1 mMEDTA
10.0 mMMagnesium chlorideMgCl2
0.1 mMSodium fluorideNaF
0.1 mMPMSF
1.0 mM2-mercapto ethanol
GridModel: Quantifoil R2/1 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.7 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123874
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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