PDB entry 5ipl

View 5ipl on RCSB PDB site
Description: sigmas-transcription initiation complex with 4-nt nascent rna
Deposited on 2016-03-09, released 2016-03-30
The last revision was dated 2016-06-22, with a file datestamp of 2016-06-17.
Experiment type: XRAY
Resolution: 3.6 Å
R-factor: N/A
AEROSPACI score: 0.08 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '1':
    Compound: synthetic nontemplate strand DNA (50-MER)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain '2':
    Compound: synthetic template strand DNA (50-MER)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain '3':
    Compound: nascent RNA 4-mer
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'A':
    Compound: DNA-directed RNA polymerase subunit alpha
    Species: Escherichia coli [TaxId:562]
    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 [TaxId:562]
    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 [TaxId:562]
    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 [TaxId:562]
    Gene: rpoC, tabB, b3988, JW3951
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: DNA-directed RNA polymerase subunit omega
    Species: Escherichia coli [TaxId:562]
    Gene: rpoZ, b3649, JW3624
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: RNA polymerase sigma factor RpoS
    Species: Escherichia coli [TaxId:562]
    Gene: rpoS, appR, katF, nur, otsX, sigS, b2741, JW5437
    Database cross-references and differences (RAF-indexed):
    • Uniprot P13445
      • conflict (328)
  • Heterogens: DPO, ZN, MG

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 '1':
    No sequence available.

  • Chain '2':
    No sequence available.

  • Chain '3':
    No sequence available.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >5iplA (A:)
    ahhhhhhmqgsvteflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpg
    cavteveidgvlheystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaa
    dithdgdveivkpqhvichltdenasismrikvqrgrgyvpastrihseederpigrllv
    dacyspveriaynveaarveqrtdldklviemetngtidpeeairraatilaeqleafvd
    lr
    

    Sequence, based on observed residues (ATOM records):
    >5iplA (A:)
    teflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpgcavteveidgvl
    heystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaadithdgdveivk
    pqhvichltdenasismrikvqrgrgyvpastrihseederpigrllvdacyspveriay
    nveaarveqrtdldklviemetngtidpeeairraatilaeqleafvdlr
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >5iplB (B:)
    ahhhhhhmqgsvteflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpg
    cavteveidgvlheystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaa
    dithdgdveivkpqhvichltdenasismrikvqrgrgyvpastrihseederpigrllv
    dacyspveriaynveaarveqrtdldklviemetngtidpeeairraatilaeqleafvd
    lr
    

    Sequence, based on observed residues (ATOM records):
    >5iplB (B:)
    teflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpgcavteveidgvl
    heystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaadithdgdveivk
    pqhvichltdenasismrikvqrgrgyvpastrihseederpigrllvdacyspveriay
    nveaarveqrtdldklviemetngtidpeeairraatilaeqleafvd
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >5iplC (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):
    >5iplC (C:)
    ysytekkrirkdfgkrpqvldvpyllsiqldsfqkfieqdpegqygleaafrsvfpiqsy
    sgnselqyvsyrlgepvfdvqecqirgvtysaplrvklrlviyereapegtvkdikeqev
    ymgeiplmtdngtfvingtervivsqlhrspgvffdsdkgkthssgkvlynariipyrgs
    wldfefdpkdnlfvridrrrklpatiilralnytteqildlffekvifeirdnklqmelv
    perlrgetasfdieangkvyvekgrritarhirqlekddvklievpveyiagkvvakdyi
    destgelicaanmelsldllaklsqsghkrietlftndldhgpyisetlrvdptndrlsa
    lveiyrmmrpgepptreaaeslfenlffsedrydlsavgrmkfnrsllreeiegsgilsk
    ddiidvmkklidirngkgevddidhlgnrrirsvgemaenqfrvglvrveravkerlslg
    dldtlmpqdminakpisaavkeffgssqlsqfmdqnnplseithkrrisalgpggltrer
    agfevrdvhpthygrvcpietpegpniglinslsvyaqtneygfletpyrkvtdgvvtde
    ihylsaieegnyviaqansnldeeghfvedlvtcrskgesslfsrdqvdymdvstqqvvs
    vgaslipflehddanralmganmqrqavptlradkplvgtgmeravavdsgvtavakrgg
    vvqyvdasrivikvnedemypgeagidiynltkytrsnqntcinqmpcvslgepvergdv
    ladgpstdlgelalgqnmrvafmpwngynfedsilvservvqedrfttihiqelacvsrd
    tklgpeeitadipnvgeaalskldesgivyigaevtggdilvgkvtpkgetqltpeekll
    raifgekasdvkdsslrvpngvsgtvidvqvftrdgvekdkraleieemqlkqakkdlse
    elqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelk
    hefekkleakrrkitqgddlapgvlkivkvylavkrriqpgdkmagrhgnkgviskinpi
    edmpydengtpvdivlnplgvpsrmnigqilethlgmaakgigdkinamlkqqqevaklr
    efiqraydlgadvrqkvdlstfsdeevmrlaenlrkgmpiatpvfdgakeaeikellklg
    dlptsgqirlydgrtgeqferpvtvgymymlklnhlvddkmharstgsyslvtqqplggk
    aqfggqrfgemevwaleaygaaytlqemltvksddvngrtkmyknivdgnhqmepgmpes
    fnvllkeirslginielede
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >5iplD (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):
    >5iplD (D:)
    eefdaikialaspdmirswsfgevkkpetinyrtfkperdglfcarifgpvkdyeclcgk
    ykrlkhrgvicekcgvevtqtkvrrermghielasptahiwflkslpsrigllldmplrd
    iervlyfesyvvieggmtnlerqqilteeqyldaleefgdefdakmgaeaiqallksmdl
    eqeceqlreelnetnsetkrkkltkriklleafvqsgnkpewmiltvlpvlppdlrplvp
    ldggrfatsdlndlyrrvinrnnrlkrlldlaapdiivrnekrmlqeavdalldngrrgr
    aitgsnkrplksladmikgkqgrfrqnllgkrvdysgrsvitvgpylrlhqcglpkkmal
    elfkpfiygklelrglattikaakkmvereeavvwdildevirehpvllnraptlhrlgi
    qafepvliegkaiqlhplvcaaynadfdgdqmavhvpltleaqlearalmmstnnilspa
    ngepiivpsqdvvlglyymtrdcvnakgegmvltgpkeaerlyrsglaslharvkvrite
    yekdangelvaktslkdttvgrailwmivpkglpysivnqalgkkaiskmlntcyrilgl
    kptvifadqimytgfayaarsgasvgiddmvipekkheiiseaeaevaeiqeqfqsglvt
    agerynkvidiwaaandrvskammdnlqtetvinrdgqeekqvsfnsiymmadsgargsa
    aqirqlagmrglmakpdgsiietpitanfreglnvlqyfisthgarkgladtalktansg
    yltrrlvdvaqdlvvteddcgthegimmtpvieggdvkeplrdrvlgrvtaedvlkpgta
    dilvprntllheqwcdlleensvdavkvrsvvscdtdfgvcahcygrdlarghiinkgea
    igviaaqsigepgtqltmrtfhiggaaskditgglprvadlfearrpkepailaeisgiv
    sfgketkgkrrlvitpvdgsdpyeemipkwrqlnvfegervergdvisdgpeaphdilrl
    rgvhavtryivnevqdvyrlqgvkindkhievivrqmlrkativnagssdflegeqveys
    rvkianreleangkvgatysrdllgitkaslatesfisaasfqettrvlteaavagkrde
    lrglkenvivgrlipagtgyayhqdrmrrraag
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >5iplE (E:)
    arvtvqdavekignrfdlvlvaarrarqmqvggkdplvpeendkttvialreieeglinn
    qildvrerqeqqeqeaaelqavtaiaegrr
    

    Sequence, based on observed residues (ATOM records):
    >5iplE (E:)
    arvtvqdavekignrfdlvlvaarrarqmqvggkdplvpeendkttvialreieeglinn
    qildvrerqeqqeqeaael
    

  • Chain 'F':
    Sequence, based on SEQRES records:
    >5iplF (F:)
    mgqntlkvhdlnedaefdengvevfdekalveeepsdndlaeeellsqgatqrvldatql
    ylgeigysplltaeeevyfarralrgdvasrrrmiesnlrlvvkiarrygnrglalldli
    eegnlgliravekfdpergfrfstyatwwirqtieraimnqtrtirlpihivkelnvylr
    tarelshkldhepsaeeiaeqldkpvddvsrmlrlneritsvdtplggdsekalldilad
    ekengpedttqdddmkqsivkwlfelnakqrevlarrfgllgyeaatledvgreigltre
    rvrqiqveglrrlreilqtqglniealflehhhhhh
    

    Sequence, based on observed residues (ATOM records):
    >5iplF (F:)
    rvldatqlylgeigysplltaeeevyfarralrgdvasrrrmiesnlrlvvkiarrygnr
    glalldlieegnlgliravekfdpergfrfstyatwwirqtieraimnqtrtirlpihiv
    kelnvylrtarelshkldhepsaeeiaeqldkpvddvsrmlrlneritsvdtplggdsek
    alldiladekengpedttqdddmkqsivkwlfelnakqrevlarrfgllgyeaatledvg
    reigltrervrqiqveglrrlreilqtqglniealfl