PDB entry 7khi

View 7khi on RCSB PDB site
Description: escherichia coli rna polymerase and rrnbp1 promoter complex with dksa/ppgpp
Deposited on 2020-10-21, released 2020-10-28
The last revision was dated 2021-02-03, with a file datestamp of 2021-01-29.
Experiment type: EM
Resolution: 3.62 Å
R-factor: N/A
AEROSPACI score: 0.14 (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: RNA polymerase sigma factor rpoD
    Species: Escherichia coli (strain K12) [TaxId:83333]
    Gene: rpoD, alt, b3067, JW3039
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: RNA polymerase-binding transcription factor DksA
    Species: Escherichia coli (strain K12) [TaxId:83333]
    Gene: dksA, b0145, JW0141
    Database cross-references and differences (RAF-indexed):
  • Chain 'X':
    Compound: DNA (36-mer)
    Species: Escherichia coli K-12 [TaxId:83333]
  • Chain 'Y':
    Compound: DNA (28-mer)
    Species: Escherichia coli K-12 [TaxId:83333]
  • Heterogens: 1N7, G4P, MG, ZN

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:
    >7khiA (A:)
    mqgsvteflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpgcavteve
    idgvlheystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaadithdgd
    veivkpqhvichltdenasismrikvqrgrgyvpastrihseederpigrllvdacyspv
    eriaynveaarveqrtdldklviemetngtidpeeairraatilaeqleafvdlrd
    

    Sequence, based on observed residues (ATOM records):
    >7khiA (A:)
    eflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpgcavteveidgvlh
    eystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaadithdgdveivkp
    qhvichltdenasismrikvqrgrgyvpastrihseederpigrllvdacyspveriayn
    veaarveqrtdldklviemetngtidpeeairraatilaeqleafvdlrd
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >7khiB (B:)
    mqgsvteflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpgcavteve
    idgvlheystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaadithdgd
    veivkpqhvichltdenasismrikvqrgrgyvpastrihseederpigrllvdacyspv
    eriaynveaarveqrtdldklviemetngtidpeeairraatilaeqleafvdlrd
    

    Sequence, based on observed residues (ATOM records):
    >7khiB (B:)
    teflkprlvdieqvssthakvtleplergfghtlgnalrrillssmpgcavteveidgvl
    heystkegvqedileillnlkglavrvqgkdeviltlnksgigpvtaadithdgdveivk
    pqhvichltdenasismrikvqrgrgyvpastrihseederpigrllvdacyspveriay
    nveaarveqrtdldklviemetngtidpeeairraatilaeqleafvd
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >7khiC (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):
    >7khiC (C:)
    vysytekkrirkdfgkrpqvldvpyllsiqldsfqkfieqdpegqygleaafrsvfpiqs
    ysgnselqyvsyrlgepvfdvqecqirgvtysaplrvklrlviyereapegtvkdikeqe
    vymgeiplmtdngtfvingtervivsqlhrspgvffdsdkgkthssgkvlynariipyrg
    swldfefdpkdnlfvridrrrklpatiilralnytteqildlffekvifeirdnklqmel
    vperlrgetasfdieangkvyvekgrritarhirqlekddvklievpveyiagkvvakdy
    idestgelicaanmelsldllaklsqsghkrietlftndldhgpyisetlrvdptndrls
    alveiyrmmrpgepptreaaeslfenlffsedrydlsavgrmkfnrsllreeiegsgils
    kddiidvmkklidirngkgevddidhlgnrrirsvgemaenqfrvglvrveravkerlsl
    gdldtlmpqdminakpisaavkeffgssqlsqfmdqnnplseithkrrisalgpggltre
    ragfevrdvhpthygrvcpietpegpniglinslsvyaqtneygfletpyrkvtdgvvtd
    eihylsaieegnyviaqansnldeeghfvedlvtcrskgesslfsrdqvdymdvstqqvv
    svgaslipflehddanralmganmqrqavptlradkplvgtgmeravavdsgvtavakrg
    gvvqyvdasrivikvnedemypgeagidiynltkytrsnqntcinqmpcvslgepvergd
    vladgpstdlgelalgqnmrvafmpwngynfedsilvservvqedrfttihiqelacvsr
    dtklgpeeitadipnvgeaalskldesgivyigaevtggdilvgkvtpkgetqltpeekl
    lraifgekasdvkdsslrvpngvsgtvidvqvftrdgvekdkraleieemqlkqakkdls
    eelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydel
    khefekkleakrrkitqgddlapgvlkivkvylavkrriqpgdkmagrhgnkgviskinp
    iedmpydengtpvdivlnplgvpsrmnigqilethlgmaakgigdkinamlkqqqevakl
    refiqraydlgadvrqkvdlstfsdeevmrlaenlrkgmpiatpvfdgakeaeikellkl
    gdlptsgqirlydgrtgeqferpvtvgymymlklnhlvddkmharstgsyslvtqqplgg
    kaqfggqrfgemevwaleaygaaytlqemltvksddvngrtkmyknivdgnhqmepgmpe
    sfnvllkeirslginielede
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >7khiD (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):
    >7khiD (D:)
    teefdaikialaspdmirswsfgevkkpetinyrtfkperdglfcarifgpvkdyeclcg
    kykrlkhrgvicekcgvevtqtkvrrermghielasptahiwflkslpsrigllldmplr
    diervlyfesyvvieggmtnlerqqilteeqyldaleefgdefdakmgaeaiqallksmd
    leqeceqlreelnetnsetkrkkltkriklleafvqsgnkpewmiltvlpvlppdlrplv
    pldggrfatsdlndlyrrvinrnnrlkrlldlaapdiivrnekrmlqeavdalldngrrg
    raitgsnkrplksladmikgkqgrfrqnllgkrvdysgrsvitvgpylrlhqcglpkkma
    lelfkpfiygklelrglattikaakkmvereeavvwdildevirehpvllnraptlhrlg
    iqafepvliegkaiqlhplvcaaynadfdgdqmavhvpltleaqlearalmmstnnilsp
    angepiivpsqdvvlglyymtrdcvnakgegmvltgpkeaerlyrsglaslharvkvrit
    eyekdangelvaktslkdttvgrailwmivpkglpysivnqalgkkaiskmlntcyrilg
    lkptvifadqimytgfayaarsgasvgiddmvipekkheiiseaeaevaeiqeqfqsglv
    tagerynkvidiwaaandrvskammdnlqtetvinrdgqeekqvsfnsiymmadsgargs
    aaqirqlagmrglmakpdgsiietpitanfreglnvlqyfisthgarkgladtalktans
    gyltrrlvdvaqdlvvteddcgthegimmtpvieggdvkeplrdrvlgrvtaedvlkpgt
    adilvprntllheqwcdlleensvdavkvrsvvscdtdfgvcahcygrdlarghiinkge
    aigviaaqsigepgtqltmrtfhiggaasraaaessiqvknkgsiklsnvksvvnssgkl
    vitsrntelklidefgrtkesykvpygavlakgdgeqvaggetvanwdphtmpvitevsg
    fvrftdmidgqtitrqtdeltglsslvvldsaertaggkdlrpalkivdaqgndvlipgt
    dmpaqyflpgkaivqledgvqissgdtlaripqesggtkditgglprvadlfearrpkep
    ailaeisgivsfgketkgkrrlvitpvdgsdpyeemipkwrqlnvfegervergdvisdg
    peaphdilrlrgvhavtryivnevqdvyrlqgvkindkhievivrqmlrkativnagssd
    flegeqveysrvkianreleangkvgatysrdllgitkaslatesfisaasfqettrvlt
    eaavagkrdelrglkenvivgrlipagtgyayhqdrmrrraag
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >7khiE (E:)
    marvtvqdavekignrfdlvlvaarrarqmqvggkdplvpeendkttvialreieeglin
    nqildvrerqeqqeqeaaelqavtaiaegrr
    

    Sequence, based on observed residues (ATOM records):
    >7khiE (E:)
    arvtvqdavekignrfdlvlvaarrarqmqvggkdplvpeendkttvialreieeglinn
    qildvrerqeqqeqea
    

  • Chain 'F':
    Sequence, based on SEQRES records:
    >7khiF (F:)
    meqnpqsqlkllvtrgkeqgyltyaevndhlpedivdsdqiediiqmindmgiqvmeeap
    daddlmlaentadedaaeaaaqvlssveseigrttdpvrmymremgtvelltregeidia
    kriedginqvqcsvaeypeaitylleqydrveaeearlsdlitgfvdpnaeedlaptath
    vgselsqedldddededeedgdddsadddnsidpelarekfaelraqyvvtrdtikakgr
    shataqeeilklsevfkqfrlvpkqfdylvnsmrvmmdrvrtqerlimklcveqckmpkk
    nfitlftgnetsdtwfnaaiamnkpwseklhdvseevhralqklqqieeetgltieqvkd
    inrrmsigeakarrakkemveanlrlvisiakkytnrglqfldliqegniglmkavdkfe
    yrrgykfstyatwwirqaitrsiadqartiripvhmietinklnrisrqmlqemgreptp
    eelaermlmpedkirkvlkiakepismetpigddedshlgdfiedttlelpldsattesl
    raathdvlagltareakvlrmrfgidmntdytleevgkqfdvtrerirqieakalrklrh
    psrsevlrsfldd
    

    Sequence, based on observed residues (ATOM records):
    >7khiF (F:)
    qsqlkllvtrgkeqgyltyaevndhlpedivdsdqiediiqmindmgiqvmeeapdaddl
    mlaentadedaaeaaaqvlssveseigrttdpvrmymremgtvelltregeidiakried
    ginqvqcsvaeypeaitylleqydrveaeearlsdlitgfvddpelarekfaelraqyvv
    trdtikataqeeilklsevfkqfrlvpkqfdylvnsmrvmmdrvrtqerlimklcveqck
    mpkknfitlftgnetsdtwfnaaiamnkpwseklhdvseevhralqklqqieeetgltie
    qvkdinrrmsigeakarrakkemveanlrlvisiakkytnrglqfldliqegniglmkav
    dkfeyrrgykfstyatwwirqaitrsiadqartiripvhmietinklnrisrqmlqemgr
    eptpeelaermlmpedkirkvlkiakepismetpigddedshlgdfiedttlelpldsat
    teslraathdvlagltareakvlrmrfgidmntdytleevgkqfdvtrerirqieakalr
    klrhpsrsevlrsfld
    

  • Chain 'M':
    Sequence, based on SEQRES records:
    >7khiM (M:)
    mqegqnrktsslsilaiagvepyqekpgeeymneaqlahfrrileawrnqlrdevdrtvt
    hmqdeaanfpdpvdraaqeeefslelrnrdrerklikkiektlkkvededfgycescgve
    igirrlearptadlcidcktlaeirekqmag
    

    Sequence, based on observed residues (ATOM records):
    >7khiM (M:)
    sslsilaiagvepyqekpgeeymneaqlahfrrileawrnqlrdevdrtvthmqdeaanf
    pdpvdraaqeeefslelrnrdrerklikkiektlkkvededfgycescgveigirrlear
    ptadlcidcktlaeirekqmag
    

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    No sequence available.