PDB entry 6j9e

View 6j9e on RCSB PDB site
Description: cryo-em structure of xanthomonos oryzae transcription elongation complex with nusa and the bacteriophage protein p7
Deposited on 2019-01-22, released 2019-07-17
The last revision was dated 2019-11-06, with a file datestamp of 2019-11-01.
Experiment type: EM
Resolution: 3.41 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: Xanthomonas oryzae pv. oryzae (strain PXO99A) [TaxId:360094]
    Gene: rpoA, PXO_04496
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: DNA-directed RNA polymerase subunit alpha
    Species: Xanthomonas oryzae pv. oryzae (strain PXO99A) [TaxId:360094]
    Gene: rpoA, PXO_04496
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: DNA-directed RNA polymerase subunit beta
    Species: Xanthomonas oryzae pv. oryzae PXO99A [TaxId:360094]
    Gene: rpoB, PXO_04530
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: DNA-directed RNA polymerase subunit beta'
    Species: Xanthomonas oryzae pv. oryzae PXO99A [TaxId:360094]
    Gene: rpoC, PXO_04529
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: DNA-directed RNA polymerase subunit omega
    Species: Xanthomonas oryzae pv. oryzae [TaxId:64187]
    Gene: rpoZ
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: Transcription termination/antitermination protein NusA
    Species: Xanthomonas oryzae pv. oryzae PXO99A [TaxId:360094]
    Gene: nusA
    Database cross-references and differences (RAF-indexed):
    • PDB 6J9E
  • Chain 'G':
    Compound: DNA (29-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'H':
    Compound: DNA (29-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'I':
    Compound: RNA (5'-r(*gp*cp*ap*up*up*cp*ap*ap*ap*gp*cp*gp*gp*ap*gp*ap*gp*gp*up*a)-3')
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'J':
    Compound: 45l
    Species: Xanthomonas virus Xp10 [TaxId:232237]
    Database cross-references and differences (RAF-indexed):
  • Heterogens: 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:
    >6j9eA (A:)
mgsshhhhhhsqdpmtvtanqvlrprgpqierltdnrakvvieplergyghtlgnalrrv
llssipgfaiteveidgvlheyttveglqedvldvllnlkdvairmhsgdsatlslskqg
pgtvtaadirtdhnveiingdhvichltkdtalnmrlkiergfgyqpaaarrrpdeetrt
igrlmldasfspvrrvayaveaarveqrtdldklvidietngtidaeeavrtaadilsdq
lsvfgdfthrdrgaakpaasgvdpvllrpiddleltvrsanclkaesiyyigdliqktev
ellktpnlgkkslteikevlaqrglalgmklenwppagvaqhgmlg

    Sequence, based on observed residues (ATOM records):
    >6j9eA (A:)
prgpqierltdnrakvvieplergyghtlgnalrrvllssipgfaiteveidgvlheytt
veglqedvldvllnlkdvairmhsgdsatlslskqgpgtvtaadirtdhnveiingdhvi
chltkdtalnmrlkiergfgyqpaaargrlmldasfspvrrvayaveaarveqrtdldkl
vidietngtidaeeavrtaadilsdqlsvfg

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6j9eB (B:)
mgsshhhhhhsqdpmtvtanqvlrprgpqierltdnrakvvieplergyghtlgnalrrv
llssipgfaiteveidgvlheyttveglqedvldvllnlkdvairmhsgdsatlslskqg
pgtvtaadirtdhnveiingdhvichltkdtalnmrlkiergfgyqpaaarrrpdeetrt
igrlmldasfspvrrvayaveaarveqrtdldklvidietngtidaeeavrtaadilsdq
lsvfgdfthrdrgaakpaasgvdpvllrpiddleltvrsanclkaesiyyigdliqktev
ellktpnlgkkslteikevlaqrglalgmklenwppagvaqhgmlg

    Sequence, based on observed residues (ATOM records):
    >6j9eB (B:)
lrprgpqierltdnrakvvieplergyghtlgnalrrvllssipgfaiteveidgvlhey
ttveglqedvldvllnlkdvairmhsgdsatlslskqgpgtvtaadirtdhnveiingdh
vichltkdtalnmrlkiergfgyqpaalmldasfspvrrvayaveaarveqrtdldklvi
dietngtidaeeavrtaadilsdqlsvf

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6j9eC (C:)
mtsysftekkrirkdfgkqrsilevpfllaiqvdsyreflqedvestkrkdlglhaalks
vfpissysgnaaleyvgyklgqpvfderecrqrgmsygaplrvtvrlviydresstkaik
yvkeqevylgeiplmtgngtfivngtervivsqlhrspgvffdhdrgkthssgkllysar
iipyrgswldfefdpkdalftridrrrklpvsillralgynneemlaeffeintfhinpd
egvqlelvperlrgetlnfdladgdkviveagkritarhvkqleaagvaalavpddylvg
rilshdvvdgstgellanandeisedqltafrkagvdavgtlwvndldrgpylsntlrid
ptktqlealveiyrmmrpgepptkeaaqnlfhnlfftferydlstvgrmkfnrrvgrkdv
lgesvlydkkyfaerndeeskrlvaehtdtsdilevikvlteirngrgvvddidhlgnrr
vrsvgemaenvfrvglvrveravkerlsmaesegltpqelinakpvaaaikeffgssqls
qfmdqnnplsevthkrrvsalgpggltreragfevrdvhpthygrvctietpegpnigli
nslavfartnqygfletpyrkvldgkvsddveylsaieeneyviaqanaltdaknmlteq
fvpcrfqgesllkppsevhfmdvspmqtvsvaaalvpflehddanralmganmqrqavpt
lrsqkplvgtgieravardsgvtvnalrggvieqidaarivvkvneaeigggtdagvdiy
nlikytrsnqntcinqrplvnvgdviargdvladgpstdigelalgqnmliafmpwngyn
fedsillservveedryttihieeltcvardtklgpeeisadipnvseqalnrldesgvv
yigaevragdimvgkvtpkgesqltpeekllraifgekasdvkdsslrvppgmdgtvidv
qvftrdgiekdkrarqieeneikrvkkdfddqfrileaaiyarlrsqivgkvangganlk
kgdsvtdayldglkksdwfqlrmkdedaadaieraqkqiqahekefearfadkrgkitqg
ddlapgvlkmvkvflavkrriqpgdkmagrhgnkgvvsnvvpvedmpymatgesvdivln
plgvpsrmnigqilevhlgwaakglgrkiqrmleaqaavselrkflddiynhdnainaqr
vdlsqfsdeellnlgknlidgvpmatpvfdgaseaeikrmleladlpqsgqtqlydgrtg
eafdrkttvgymhylklnhlvddkmharstgpyslvtqqplggkaqfggqrfgemevwal
eaygaaytlqemltvksddvqgrnqmyknivdgehemvagmpesfnvlvkeirslaihme
lee

    Sequence, based on observed residues (ATOM records):
    >6j9eC (C:)
sysftekkrirkdfgkqrsilevpfllaiqvdsyreflqedrkdlglhaalksvfpissy
sgnaaleyvgyklgqpvfderecrqrgmsygaplrvtvrlviydresstkaikyvkeqev
ylgeiplmtgngtfivngtervivsqlhrspgvffdhdrgkthssgkllysariipyrgs
wldfefdpkdalftridrrrklpvsillralgynneemlaeffeintfhivqlelvperl
rgearhvkqleaagvaalavpddylvgrilshdvvdgstgellanandeisedqltafrk
agvdavgtlwvndldrgpylsntlridptktqlealveiyrmmrpgepptkeaaqnlfhn
lfftferydlstvgrmkfnrrvgrkdvlgesvlydkkyfaerndeeskrlvaehtdtsdi
levikvlteirngrgvvddidhlgnrrvrsvgemaenvfrvglvrveravkerlsmaltp
qelinakpvaaaikeffgssqlsqfmdqnnplsevthkrrvsalgpggltreragfevrd
vhpthygrvctietpegpniglinslavfartnqygfletpyrkvldgkvsddveylsai
eeneyviaqanaltdaknmlteqfvpcrfqgesllkppsevhfmdvspmqtvsvaaalvp
flehddanralmganmqrqavptlrsqkplvgtgieravardsgvtvnalrggvieqida
arivvkvneaeiagvdiynlikytrsnqntcinqrplvnvgdviargdvladgpstdige
lalgqnmliafmpwngynfedsillservveedryttihieeltcvardtklgpeeisad
ipnvseqalnrldesgvvyigaevragdimvgkvtpkgtpeekllraifgekasdvkdss
lrvpmdgtvidvqvftrdgiekdkrarqieeneikrvkkdfddqfrileaaiyarlrsqi
vgieraqkqiqahekefearfadkrgkitqgddlapgvlkmvkvflavkrriqpgdkmag
rhgnkgvvsnvvpvedmpymatgesvdivlnplgvpsrmnigqilevhlgwaakglgrki
qrmleaqaavselrkflddiynhdqrvdlsqfsdeellnlgknlidgvpmatpvfdgase
aeikrmleladlpqsgqtqlydgrtgeafdrkttvgymhylklnhlvddkmharstgpys
lvtqqplggkaqfggqrfgemevwaleaygaaytlqemltvksddvqgrnqmyknivdge
hemvagmpesfnvlvkeirslaihmele

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6j9eD (D:)
mkdllnlfnqqrqtldfdaikialaspdlirswsygevkkpetinyrtfkperdglfcaa
ifgpikdyeclcgkykrmkhrgvvcekcgtevtlakvrrermghidlaspvahiwflksl
psriglmldmtlrdiervlyfeayvvtepgltplerrqllteeqyltarqeynddfdaam
gaeavyellrtidlqsemtrlreeiastgsetklkrltkriklieaflesgnrpewmvmt
vlpvlppdlrplvpldggrfatsdlndlyrrvinrnnrlrrllelnapdiivrnekrmlq
esvdalldngrrgraitgtnkrplksladmikgkqgrfrqnllgkrvdysgrsvitvgpy
lklhqcglpkkmalelfkpfvfaklqrrglattikaakklvereeaevwdileevirehp
vllnraptlhrlgiqafepvliegkaiqlhplvctafnadfdgdqmavhvplsleaqlea
ralmmstnnilspangepiivpsqdvvlglyymsralenkkgegmvfantsevkraydnr
vvelhakvkvritqvdvdavdgkrtsgtsivdttvgrallseilpeglpfqlantemtkk
nisrlinssyrllglkdtvvfadklmytgyayatragvsigiddmlipdekkgilteaea
evleiqeqyqsglvtagerynkvvdiwsrtseriakammdtigtekvenakgetidqksm
nslyimadsgargsqaqirqlagmrglmarpdgsiietpikanfreglnvqeyfnsthga
rkgladtalktansgyltrrlvdvaqdvviteidcgtteglimtpiveggdvveplkerv
lgrvvaedvylpgndeepivtrntlldeawvakledasvqsvkvrstiscessfgvcarc
ygrdlarghqvnigeavgviaaqsigepgtqltmrtfhiggaasraaavdnitvkttgsv
kfnnlksvahasgslvavsrsgelsvldghgrereryklpygatitakdgdavkagqsva
nwdphnhpivsevagfirfidfvdgvtviektdeltglasreitdpkrrgahakelrpiv
rivdgkgndltipntdlpaqyllpprsivnlqdgaavgvgdvvakipqeasktrditggl
prvadlfearkpkdpailaersgiisfgkdtkgkqrliikdtdgseheelipkyrqiivf
egehvtkgetvvdgepspqdilrllgveplaaylvkeiqdvyrlqgvkindkhievitrq
mlrkveivdqgnskflngeqverqrvieenarlvkrnelpakydpvllgitkaslatesf
isaasfqettrvlteaavrgtrdnlrglkenvivgrlipagtglayhagrrkasgltdse
metlsgkpagaepvaaladagadee

    Sequence, based on observed residues (ATOM records):
    >6j9eD (D:)
mkdllnlfnqqrqtldfdaikialaspdlirswsygevkkpetinyrtfkperdglfcaa
ifgpikdyeclcgkykrmkhrgvvcekcgtevtlakvrrermghidlaspvahiwflksl
psriglmldmtlrdiervlyfeayvvtrrqllteeqyltarqeynddfdaamgaeavyel
lrtidlqsemtrlreeiastgsetklkrltkriklieaflesgnrpewmvmtvlpvlppd
lrplvpldggrfatsdlndlyrrvinrnnrlrrllelnapdiivrnekrmlqesvdalld
ngrrgraikrplksladmikgkqgrfrqnllgkrvdysgrsvitvgpylklhqcglpkkm
alelfkpfvfaklqrrglattikaakklvereeaevwdileevirehpvllnraptlhrl
giqafepvliegkaiqlhplvctafnadfdgdqmavhvplsleaqlearalmmstnnils
pangepiivpsqdvvlglyymsralenkkgegmvfantsevkraydnrvvelhakvkvri
tqvdvdrtsgtsivdttvgrallseilpeglpfqlantemtkknisrlinssyrllglkd
tvvfadklmytgyayatragvsigiddmlipdekkgilteaeaevleiqeqyqsglvtag
erynkvvdiwsrtseriakammdtigtekvenakgetidqksmnslyimadsgargsqaq
irqlagmrglmarpdgsiietpikanfreglnvqeyfnsthgarkgladtalktansgyl
trrlvdvaqdvviteidcgtteglimtpiveggdvveplkervlgrvvaedvvtrntlld
eawvakledasvqsvkvrstiscessfgvcarcygrdlarghqvnigeavgviaaqsige
pgtqltdnitvkttgsvkfnnlkavsrsgelsvldghgrereryklpygatitaavkagq
svanwdpglprvadlfearkpkdpailaersgiisfgkdtkgkqrliikdtdgseheeli
pkyrqiivfegehvtkgetvvdgepspqdilrllgveplaaylvkeiqdvyrlqgvkind
khievitrqmlrkveivdqgnskflngeqverqrvieenarlvkrnelpakydpvllgit
kaslatesfisaasfqettrvlteaavrgtrdnlrglkenvivgrlipagtglayhagrr

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6j9eE (E:)
maritvedclevvnnrfelvmmaskrarqlangvqplienaaasdkptvmalreiaarri
dnalidevekaereraerealewaaaevvadedmskndd

    Sequence, based on observed residues (ATOM records):
    >6j9eE (E:)
vedclevvnnrfelvmmaskrarqlangvqplidkptvmalreiaarridnalideveka
erera

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6j9eF (F:)
gamdmskelllvvdavanekgvprevifdaieaalasaakkrypdqdvlarvtidhkdgt
yetyrrwevvaddvvmespdrqvrlmdaideadgvdvgdyieeqienpdfgriaaqaakq
vivqrvreaerqqvvdawkdrvgelitgvvkraergnifvdlggnaeafipkdkgiprdv
lrpgdrvrgylaevrseprgpqlfisraapefmielfklevpevgqglveinacardpgd
rakiaviahdartdpigacigmrgsrvqavsnelngervdivlwnenpanfvinamapae
vqsiivdedkhsmdlavaedrlaqaigkggqnvrlasrltgwqlnvmtadqvaakseaeq
aaarqlfmdrlevdeeisailvsegfntveeiayvpvgellavegfdediveelrarard
allnaalaeeeglegtqptedllalegmdeetavalaehgvrtsedlsdlaadeivdfgi
egltqeraaalilaaraeeiarlerge

    Sequence, based on observed residues (ATOM records):
    >6j9eF (F:)
mskelllvvdavanekgvprevifdaieaalasaakkrypdqdvlarvtidhkdgtyety
rrwieeqienpdfgriaaqaakqvivqrvreaerqqvvdawkdrvgelitgvvkraergn
ifvdlnaeafipkdrvrgylaevrseprgpqlfisraapefmiel

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    Sequence, based on SEQRES records:
    >6j9eJ (J:)
gamamneftqisgyvnafgsqrgsvltvkvendegwtlveedfdradygsdpefvaevss
ylkrnggikdltkvltr

    Sequence, based on observed residues (ATOM records):
    >6j9eJ (J:)
neftqisgyvnafgsqrgsvltvkvendegwtlveedfdradygsdpefvaevssylkrn
ggikdl