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9GDP
Cryo-em structure of vibrio cholerae rna polymerase holoenzyme bound to an ompu promoter dna fragment and 5-mer rna
PDB DOI: 10.2210/pdb9gdp/pdb
Classification: TRANSCRIPTION Organism(s): Vibrio Cholerae O395 , Synthetic Construct
Deposited: 2024-08-06 Deposition Author(s): Alcaide-Jimenez, A. , Bantysh, O. , Baudin, F. , Canals, A. , Coll, M. , Fabrega-Ferrer, M. , Krukonis, E.S. , Machon, C. , Muller, C.W. , Murciano, B. , Perez-Luque, R.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.6 Å
Cryo-em structure of vibrio cholerae rna polymerase holoenzyme bound to an ompu promoter dna fragment and 5-mer rna
Alcaide-Jimenez, A. , Bantysh, O. , Baudin, F. , Canals, A. , Coll, M. , Fabrega-Ferrer, M. , Krukonis, E.S. , Machon, C. , Muller, C.W. , Murciano, B. , Perez-Luque, R.
Primary Citation of Related Structures: 9GDP
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| DNA-directed RNA polymerase subunit beta | C | 1341 | Vibrio Cholerae O395 , Synthetic Construct | MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQDPEGQYGLEAAFRSVFPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAGTVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRVLGKTSAEILDIFFEKVNFEVKDQTLMMELVPERLRGETATFDIEADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEYIVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETLRVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGREDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQMQLKEAKKDLTEEFQILEGGLLARVRSVLLAGGYTEAKLSSIERKKWLEQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLGLAAKGIGDKINQMIKEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNLRAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE |
| DNA-directed RNA polymerase subunit beta' | D | 1401 | Vibrio Cholerae O395 , Synthetic Construct | MKDLLNFLKAQHKTEEFDAIKIGLASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRDRMGHIELASPVAHIWFLKSLPSRIGLLMDMPLRDIERVLYFEMYVVTEPGMTDLERGQMLTEEEYLDRLEEWGDEFTAKMGAEAIKDLLASMDLPAEAEQMREELDTTNSETKRKKLTKRLKLVEAFVASGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYSKLETRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARTLMMSTNNILSPASGDPIIVPSQDVVLGLYYMTREKINAKGEGMYLTGPAEAEKAYRTKTAELHARVKVRITETIKHENGKLTTETKMIDTTVGRAMLWQIVPKGLPYSLVNQKLGKKQISNLLNEAYRKLGLKDTVIFADQIMYTGFAYAALSGVSVGIDDMVVPAAKYTEIAEAEEEVREIQEQFQSGLVTAGERYNKVIDIWASTNDRVAKAMMENLSSEQVINRQGEQEKQESFNSIYMMADSGARGSAAQIRQLAGMRGLMARPDGSIIETPITANFKEGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVVTEHDCGTLEGVVMTPHIEGGDVKVALTELALGRVVSEDILKPGTDEVLIPRNTLLDEKWCKVINDNSVDQIKVRSVVTCDSDFGCCAQCYGRDLARGHLVNQGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASTAAAENSIQAKNNGSVKLHNAKFVTNKDGKLVITSRASELTIIDEFGRTKEKHKLPYGSMLSKADGDAVAAGETVANWEAHTMPIITEVAGRVQFVDMIDGVTVSRQTDDLTGLSSSEVTEAAARPAAGKDMRPAIKLVDANGKDVLIPGTDMPAQYFLPGKAIVNLDDGAEVNVGDTLARIPQKSGGNKDITGGLPRVADLFEARKPKEPAILAEHSGTVSFGKETKGKRRLIITRDSGDTYEEMIPKHRQLNVFEGERIERGDVIADGPESPHDILRLRGIHAVTTYIANEVQEVYRLQGVKINDKHIETIVRQMLRKCTITFAGDSEFLPGETVEYSQVKIANRKLVEEGKEPARFERELLGITKASLATESFISAASFQETTRVLTEAAVSGKRDDLRGLKENVIVGRLIPAGTGFAYHQDRQAKRAQEQQGPSAEQATDNLAALLNAGFSSDDE |
| DNA-directed RNA polymerase subunit omega | E | 90 | Vibrio Cholerae O395 , Synthetic Construct | MARVTVQDAVEKIGNRFDLVLVAARRARQMQSGGKDALVPEENDKPTVIALREIEEGLITKDVLDARERQEQQEQEAAELAAVSSIMHNR |
| DNA-directed RNA polymerase subunit alpha | A | 330 | Vibrio Cholerae O395 , Synthetic Construct | MQGSVTEFLKPRLVDIEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAED |
| DNA-directed RNA polymerase subunit alpha | B | 330 | Vibrio Cholerae O395 , Synthetic Construct | MQGSVTEFLKPRLVDIEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAED |
| DNA-directed RNA polymerase subunit alpha | G | 330 | Vibrio Cholerae O395 , Synthetic Construct | MQGSVTEFLKPRLVDIEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAED |
| RNA polymerase sigma factor RpoD | F | 621 | Vibrio Cholerae O395 , Synthetic Construct | MDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATHIGSELSEADLADEDDAVVEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISHRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDE |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| RNA 5-mer (5'-AAUAG-3') | h | 5 | NA | AAUAG |
| ompU promoter non-template DNA strand | t | 69 | NA | GTTGGATTTATATCATTTTACTAACTGATAGCGGAACTTTGGGACACCCACAGGTTACGCGAAAATGGC |
| ompU promoter template DNA strand | l | 69 | NA | GCCATTTTCGCGGCTATTTTTTTACTCCCAAAGTTCCGCTATCAGTTAGTAAAATGATATAAATCCAAC |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2024-08-06 Deposition Author(s): Alcaide-Jimenez, A. , Bantysh, O. , Baudin, F. , Canals, A. , Coll, M. , Fabrega-Ferrer, M. , Krukonis, E.S. , Machon, C. , Muller, C.W. , Murciano, B. , Perez-Luque, R.