PDB entry 6gh5

View 6gh5 on RCSB PDB site
Description: cryo-em structure of bacterial rna polymerase-sigma54 holoenzyme transcription open complex
Deposited on 2018-05-04, released 2018-07-04
The last revision was dated 2019-12-18, with a file datestamp of 2019-12-13.
Experiment type: EM
Resolution: 3.4 Å
R-factor: N/A
AEROSPACI score: 0.09 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-directed RNA polymerase subunit alpha
    Species: Escherichia coli (strain K12) [TaxId:83333]
    Gene: rpoA, pez, phs, sez, b3295, JW3257
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: DNA-directed RNA polymerase subunit alpha
    Species: Escherichia coli (strain K12) [TaxId:83333]
    Gene: rpoA, pez, phs, sez, b3295, JW3257
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: DNA-directed RNA polymerase subunit beta
    Species: Escherichia coli (strain K12) [TaxId:83333]
    Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: DNA-directed RNA polymerase subunit beta'
    Species: Escherichia coli (strain K12) [TaxId:83333]
    Gene: rpoC, tabB, b3988, JW3951
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: DNA-directed RNA polymerase subunit omega
    Species: Escherichia coli (strain K12) [TaxId:83333]
    Gene: rpoZ, b3649, JW3624
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: nifH promoter template DNA
    Species: Klebsiella pneumoniae, synthetic [TaxId:573]
  • Chain 'G':
    Compound: NifH promoter non-template DNA
    Species: Klebsiella pneumoniae, synthetic [TaxId:573]
  • Chain 'M':
    Compound: RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor,RNA polymerase sigma-54 factor
    Species: Klebsiella pneumoniae [TaxId:573]
    Gene: SM87_03359
    Database cross-references and differences (RAF-indexed):

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6gh5A (A:)
    mqgsvteflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpgcavteve
    idgvlheystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaadithdgd
    veivkpqhvichltdenasismrikvqrgrgyvpastrihseederpigrllvdacyspv
    eriaynveaarveqrtdldklviemetngtidpeeairraatilaeqleafvdlrdvrqp
    evkeekpefdpillrpvddleltvrsanclkaeaihyigdlvqrtevellktpnlgkksl
    teikdvlasrglslgmrlenwppasiade
    

    Sequence, based on observed residues (ATOM records):
    >6gh5A (A:)
    vteflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpgcavteveidgv
    lheystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaadithdgdveiv
    kpqhvichltdenasismrikvqrgrgyvpastrihseederpigrllvdacyspveria
    ynveaarveqrtdldklviemetngtidpeeairraatilaeqleafvdlrdvefdpill
    rpvddleltvrsanclkaeaihyigdlvqrtevellktpnlgkkslteikdvlasrglsl
    gmrlenwpp
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6gh5B (B:)
    mqgsvteflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpgcavteve
    idgvlheystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaadithdgd
    veivkpqhvichltdenasismrikvqrgrgyvpastrihseederpigrllvdacyspv
    eriaynveaarveqrtdldklviemetngtidpeeairraatilaeqleafvdlrdvrqp
    evkeekpefdpillrpvddleltvrsanclkaeaihyigdlvqrtevellktpnlgkksl
    teikdvlasrglslgmrlenwppasiade
    

    Sequence, based on observed residues (ATOM records):
    >6gh5B (B:)
    svteflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpgcavteveidg
    vlheystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaadithdgdvei
    vkpqhvichltdenasismrikvqrgrgyvpastrihseederpigrllvdacyspveri
    aynveaarveqrtdldklviemetngtidpeeairraatilaeqleafvdlrdvr
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6gh5C (C:)
    mvysytekkrirkdfgkrpqvldvpyllsiqldsfqkfieqdpegqygleaafrsvfpiq
    sysgnselqyvsyrlgepvfdvqecqirgvtysaplrvklrlviyereapegtvkdikeq
    evymgeiplmtdngtfvingtervivsqlhrspgvffdsdkgkthssgkvlynariipyr
    gswldfefdpkdnlfvridrrrklpatiilralnytteqildlffekvifeirdnklqme
    lvperlrgetasfdieangkvyvekgrritarhirqlekddvklievpveyiagkvvakd
    yidestgelicaanmelsldllaklsqsghkrietlftndldhgpyisetlrvdptndrl
    salveiyrmmrpgepptreaaeslfenlffsedrydlsavgrmkfnrsllreeiegsgil
    skddiidvmkklidirngkgevddidhlgnrrirsvgemaenqfrvglvrveravkerls
    lgdldtlmpqdminakpisaavkeffgssqlsqfmdqnnplseithkrrisalgpggltr
    eragfevrdvhpthygrvcpietpegpniglinslsvyaqtneygfletpyrkvtdgvvt
    deihylsaieegnyviaqansnldeeghfvedlvtcrskgesslfsrdqvdymdvstqqv
    vsvgaslipflehddanralmganmqrqavptlradkplvgtgmeravavdsgvtavakr
    ggvvqyvdasrivikvnedemypgeagidiynltkytrsnqntcinqmpcvslgepverg
    dvladgpstdlgelalgqnmrvafmpwngynfedsilvservvqedrfttihiqelacvs
    rdtklgpeeitadipnvgeaalskldesgivyigaevtggdilvgkvtpkgetqltpeek
    llraifgekasdvkdsslrvpngvsgtvidvqvftrdgvekdkraleieemqlkqakkdl
    seelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqyde
    lkhefekkleakrrkitqgddlapgvlkivkvylavkrriqpgdkmagrhgnkgviskin
    piedmpydengtpvdivlnplgvpsrmnigqilethlgmaakgigdkinamlkqqqevak
    lrefiqraydlgadvrqkvdlstfsdeevmrlaenlrkgmpiatpvfdgakeaeikellk
    lgdlptsgqirlydgrtgeqferpvtvgymymlklnhlvddkmharstgsyslvtqqplg
    gkaqfggqrfgemevwaleaygaaytlqemltvksddvngrtkmyknivdgnhqmepgmp
    esfnvllkeirslginielede
    

    Sequence, based on observed residues (ATOM records):
    >6gh5C (C:)
    mvysytekkrirkdfgkrpqvldvpyllsiqldsfqkfieqdpegqygleaafrsvfpiq
    sysgnselqyvsyrlgepvfdvqecqirgvtysaplrvklrlviyereapegtvkdikeq
    evymgeiplmtdngtfvingtervivsqlhrspgvffdsdkgkthssgkvlynariipyr
    gswldfefdpkdnlfvridrrrklpatiilralnytteqildlffekvifeirdnklqme
    lvperlrgetasfdieangkvyvekgrritarhirqlekddvklievpveyiagkvvakd
    yidestgelicaanmelsldllaklsqsghkrietlftndldhgpyisetlrvdptndrl
    salveiyrmmrpgepptreaaeslfenlffsedrydlsavgrmkfnrsllreeiegsgil
    skddiidvmkklidirngkgevddidhlgnrrirsvgemaenqfrvglvrveravkerls
    lgdldtlmpqdminakpisaavkeffgssqlsqfmdqnnplseithkrrisalgpggltr
    eragfevrdvhpthygrvcpietpegpniglinslsvyaqtneygfletpyrkvtdgvvt
    deihylsaieegnyviaqansnldeeghfvedlvtcrskgesslfsrdqvdymdvstqqv
    vsvgaslipflehddanralmganmqrqavptlradkplvgtgmeravavdsgvtavakr
    ggvvqyvdasrivikvnedemypgeagidiynltkytrsnqntcinqmpcvslgepverg
    dvladgpstdlgelalgqnmrvafmpwngynfedsilvservvqedrfttihiqelacvs
    rdtklgpeeitadipnvgeaalskldesgivyigaevtggdilvgkvtpkgetqltpeek
    llraifgekasdvkdsslrvpngvsgtvidvqvftrdgvekdkraleieemqlkqakkdl
    seelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqyde
    lkhefekkleakrrkitqgddlapgvlkivkvylavkrriqpgdkmagrhgnkgviskin
    piedmpydengtpvdivlnplgvpsrmnigqilethlgmaakgigdkinamlkqqqevak
    lrefiqraydlgadvrqkvdlstfsdeevmrlaenlrkgmpiatpvfdgakeaeikellk
    lgdlptsgqirlydgrtgeqferpvtvgymymlklnhlvddkmharstgsyslvtqqplg
    gkaqfggqrfgemevwaleaygaaytlqemltvksddvngrtkmyknivdgnhqmepgmp
    esfnvllkeirslginieled
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6gh5D (D:)
    mkdllkflkaqtkteefdaikialaspdmirswsfgevkkpetinyrtfkperdglfcar
    ifgpvkdyeclcgkykrlkhrgvicekcgvevtqtkvrrermghielasptahiwflksl
    psrigllldmplrdiervlyfesyvvieggmtnlerqqilteeqyldaleefgdefdakm
    gaeaiqallksmdleqeceqlreelnetnsetkrkkltkriklleafvqsgnkpewmilt
    vlpvlppdlrplvpldggrfatsdlndlyrrvinrnnrlkrlldlaapdiivrnekrmlq
    eavdalldngrrgraitgsnkrplksladmikgkqgrfrqnllgkrvdysgrsvitvgpy
    lrlhqcglpkkmalelfkpfiygklelrglattikaakkmvereeavvwdildevirehp
    vllnraptlhrlgiqafepvliegkaiqlhplvcaaynadfdgdqmavhvpltleaqlea
    ralmmstnnilspangepiivpsqdvvlglyymtrdcvnakgegmvltgpkeaerlyrsg
    laslharvkvriteyekdangelvaktslkdttvgrailwmivpkglpysivnqalgkka
    iskmlntcyrilglkptvifadqimytgfayaarsgasvgiddmvipekkheiiseaeae
    vaeiqeqfqsglvtagerynkvidiwaaandrvskammdnlqtetvinrdgqeekqvsfn
    siymmadsgargsaaqirqlagmrglmakpdgsiietpitanfreglnvlqyfisthgar
    kgladtalktansgyltrrlvdvaqdlvvteddcgthegimmtpvieggdvkeplrdrvl
    grvtaedvlkpgtadilvprntllheqwcdlleensvdavkvrsvvscdtdfgvcahcyg
    rdlarghiinkgeaigviaaqsigepgtqltmrtfhiggaasraaaessiqvknkgsikl
    snvksvvnssgklvitsrntelklidefgrtkesykvpygavlakgdgeqvaggetvanw
    dphtmpvitevsgfvrftdmidgqtitrqtdeltglsslvvldsaertaggkdlrpalki
    vdaqgndvlipgtdmpaqyflpgkaivqledgvqissgdtlaripqesggtkditgglpr
    vadlfearrpkepailaeisgivsfgketkgkrrlvitpvdgsdpyeemipkwrqlnvfe
    gervergdvisdgpeaphdilrlrgvhavtryivnevqdvyrlqgvkindkhievivrqm
    lrkativnagssdflegeqveysrvkianreleangkvgatysrdllgitkaslatesfi
    saasfqettrvlteaavagkrdelrglkenvivgrlipagtgyayhqdrmrrraageapa
    apqvtaedasaslaellnaglggsdne
    

    Sequence, based on observed residues (ATOM records):
    >6gh5D (D:)
    llkflkaqtkteefdaikialaspdmirswsfgevkkpetinyrtfkperdglfcarifg
    pvkdyeclcgkykrlkhrgvicekcgvevtqtkvrrermghielasptahiwflkslpsr
    igllldmplrdiervlyfesyvvieggmtnlerqqilteeqyldaleefgdefdakmgae
    aiqallksmdleqeceqlreelnetnsetkrkkltkriklleafvqsgnkpewmiltvlp
    vlppdlrplvpldggrfatsdlndlyrrvinrnnrlkrlldlaapdiivrnekrmlqeav
    dalldngrrgraitgsnkrplksladmikgkqgrfrqnllgkrvdysgrsvitvgpylrl
    hqcglpkkmalelfkpfiygklelrglattikaakkmvereeavvwdildevirehpvll
    nraptlhrlgiqafepvliegkaiqlhplvcaaynadfdgdqmavhvpltleaqlearal
    mmstnnilspangepiivpsqdvvlglyymtrdcvnakgegmvltgpkeaerlyrsglas
    lharvkvriteyekdangelvaktslkdttvgrailwmivpkglpysivnqalgkkaisk
    mlntcyrilglkptvifadqimytgfayaarsgasvgiddmvipekkheiiseaeaevae
    iqeqfqsglvtagerynkvidiwaaandrvskammdnlqtetvinrdgqeekqvsfnsiy
    mmadsgargsaaqirqlagmrglmakpdgsiietpitanfreglnvlqyfisthgarkgl
    adtalktansgyltrrlvdvaqdlvvteddcgthegimmtpvieggdvkeplrdrvlgrv
    taedvlkpgtadilvprntllheqwcdlleensvdavkvrsvvscdtdfgvcahcygrdl
    arghiinkgeaigviaaqsigepgtqltmrtfhiggaasraaaessiqvknkgsiklsnv
    ksvvnssgklvitsrntelklidefgrtkesykvpygavlakgdgeqvaggetvanwdph
    tmpvitevsgfvrftdmidgqtitrqsslvvldsaerrpalkivdaqgndvaqyflpgka
    ivqledgvqissgdtlaripqditgglprvadlfearrpkepailaeisgivsfgketkg
    krrlvitpvdgsdpyeemipkwrqlnvfegervergdvisdgpeaphdilrlrgvhavtr
    yivnevqdvyrlqgvkindkhievivrqmlrkativnagssdflegeqveysrvkianre
    leangkvgatysrdllgitkaslatesfisaasfqettrvlteaavagkrdelrglkenv
    ivgrlipagtgyayhqdrmrrraag
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6gh5E (E:)
    marvtvqdavekignrfdlvlvaarrarqmqvggkdplvpeendkttvialreieeglin
    nqildvrerqeqqeqeaaelqavtaiaegrr
    

    Sequence, based on observed residues (ATOM records):
    >6gh5E (E:)
    marvtvqdavekignrfdlvlvaarrarqmqvggkdplvpeendkttvialreieeglin
    nqildvrerqeqqeq
    

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    No sequence available.

  • Chain 'M':
    Sequence, based on SEQRES records:
    >6gh5M (M:)
    mgsshhhhhhssglvprgshmkqglqlrlsqqlamtpqlqqairllqlstlelqqelqqa
    lesnplleqtdlhdeveakevedresldtvdaleqkempdelpldaswdeiytagtpsgn
    gvdyqddelpvyqgettqtlqdylmwqveltpftdtdraiatsivdavddtgyltiqied
    ivdsigddeigleeveavlkriqrfdpvgvaakdlrdclliqlsqfaketpwleearlii
    sdhldllanhdfrtlmrvtrlkeevlkeavnliqsldxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxxxxxxxxiprlkinqqyaamgnsarndadgqfirsnlqearwlikslesandtl
    lrvsrciveqqqaffeqgeeymkpmvladiaqavemhestisrvttqkylhsprgifxxx
    xxxxxxxxxxxxxeasstairalvkkliaaenpakplsdskltsmlseqgimvarrtvak
    yreslsippsnqrkqlv
    

    Sequence, based on observed residues (ATOM records):
    >6gh5M (M:)
    ddelpvyqgettqtlqdylmwqveltpftdtdraiatsivdavddtgyltiqiedivdsi
    gddeigleeveavlkriqrfdpvgvaakdlrdclliqlsqfaketpwleearliisdhld
    llanhdfrtlmrvtrlkeevlkeavnliqsldxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxrsnlqearwlikslesandtllrvsrciveqqqaffeqgeeymkpmvladiaqa
    vemhestisrvttqkylhsprgixxxxxxxxxxxxxxxxasstairalvkkliaaenpak
    plsdskltsmlseqgimvarrtvakyreslsippsnqr