8YFR
Cryo em structure of komagataella phaffii rat1-rai1 complex bound within the rnapii cleft
PDB DOI: 10.2210/pdb8yfr/pdb
Classification: TRANSCRIPTION Organism(s): Komagataella Phaffii
Deposited: 2024-02-25 Deposition Author(s): Ehara, H. , Murayama, Y. , Sekine, S. , Yanagisawa, T.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.4 Å
Cryo em structure of komagataella phaffii rat1-rai1 complex bound within the rnapii cleft
Ehara, H. , Murayama, Y. , Sekine, S. , Yanagisawa, T.
Primary Citation of Related Structures: 8YFR
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| DNA-directed RNA polymerase subunit | A | 1743 | Komagataella Phaffii | MSQFPYSSAPLRSVKEVQFGLLSPEEIRAISVVKIEYPEIMDESRQRPREGGLNDPKLGSIDRNFKCQTCGEGMAECPGHFGHMELAKPVFHIGFIPKIKKVCECICMNCGKLLLDETNPTMAQAIRIRDPKKRFNAVWQLCKTKMVCEADAPVDEYSEQKVVSRGGCGNTQPVVRKDGMKLWGTWKKSGFSDRDAQPERKLLTPGEILNVFKHISPEDCFRLGFNEDYARPEWMIITVLPVPPPQVRPSIAMDETTQGQDDLTHKLSDILKANINVQKLEMDGSPQHIINEVEQLLQFHVATYMDNDIAGQPQALQKSGRPVKAIRARLKGKEGRLRGNLMGKRVDFSARTVISGDPNLELDQVGVPISIAKTLSYPETVTQYNIHRLTEYVRNGPNEHPGAKYVIRDNGDRIDLRYHKRAGDIVLQYGWKVERHLMDDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPVMGIVQDTLCGVRKMTLRDTFIEYEQVMNMLFWVPSWDGVVPQPAILKPKPLWTGKQLLSIAIPSGIHLQRTDGGNSLLSPKDNGMLIVDGKVMFGVVDKKTVGSGGGGLIHTVMREKGPKICAELFGNIQKVVNYWLLHNGFSIGIGDAIADASTMKEITHAISSAKEQVQEIIYKAQHNELELKPGMTLRESFEGEVSRTLNDARDSAGRSAEMNLKDLNNVKQMVSAGSKGSFINIAQMSACVGQQMVEGKRIAFGFADRSLPHFTKDDFSPESKGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDGTTRNSLGDIIQFLYGEDGLDGTQVERQTIDTIPGSDKAFHKRYYVDLMDEKNSIKPDVIEYAADILGDVELQKELNSEYEQLVSDRKFLREIVFVNGDHNWPLPVNLRRIIQNAQQIFHLDRAKASDLTIPEIIHGVRDLCKKLFVLRGENELIKEAQQNATSLFQCLVRARLATRRILEEFRLNRDAFEWVLGTIEAQFQRSLVHPGEMVGVIAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKNIKTPALTVYLDREIALDIEKAKVIQSSIEYTTLKNVTSATEIYYDPDPTSTVIEEDFDTVEAYFSIPDEKVEETIDKQSPWLLRLELDRARMLDKQLTMNQVADKISEVFSDDLFVMWSEDNADKLIIRCRVIRDPKAMDEELEAEEDQMLKRIEAHMLDLIALRGIPGISKVYMVKHKVSVPDESGEYKNEELWALETDGINLAEVMAVPGVDSSRTYSNSFVEILSVLGIEATRSSLYKEILNVIAFDGSYVNYRHMALLVDVMTSRGYLMAITRHGINRADTGALMRCSFEETVEILFEAGAAAELDDCRGVSENVMLGQLAPMGTGAFDVMIDEKLLTSLPADYAPTMPLFKGKATQGSATPYDNNAQYDDEFNHDDVADVMFSPMAETGSGDDRSGGLTEYAGIQSPYQPTSPGLSATSPGFAPTSPGFAPTSPRYSPTSPGYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPASPQYSPSRHSPNGESKEGE |
| RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III | J | 72 | Komagataella Phaffii | MIIPVRCFSCGKVVGDKWDAYLRLLEEGKQEGDALDELKLKRYCCRRMVLTHVDLIEKFLRYNPLEKKDFDS |
| RNA polymerase II subunit B12.5 | K | 118 | Komagataella Phaffii | MNAPDRFELFILPDDVPKLKITPDSRVPNCIIIKFEREDHTLANLLREELALYPDVTFVAYKVEHPLFANFVMRLQTEEGTRPKQALERACASIINKLKTLDHKFNEEWNIKNFSLND |
| RNA polymerase subunit ABC10-alpha | L | 72 | Komagataella Phaffii | MSREGFVAPSGTDLAAAASGVAPNKHYGVKYTCGACAHNFSLNKSDPVRCKECGHRVIYKARTKRMIQFDAR |
| 5'-3' exoribonuclease | R | 1006 | Komagataella Phaffii | MGVPALFRWLSRKYPKIISPVIQDEDVDIDGESRPTRYEDPNPNGELDNLYLDMNGIVHPCSHPEHKPVPETEDEMMLDVFAYTENVIMMARPRKVIYIAVDGVAPRAKMNQQRSRRFRSAQDAKDANEKKAAELKEMEKKGEIIDDAIKNKKTWDSNAITPGTPFMHRLADSLRYWAAYKLTTDPGWSGIEVIISDASVPGQGQHKIMSYVRSLRSSPKHDPNTTHCIYGLNANLIFLGLATHEPHFKILREDVFAQDKKSYSLQDQLRMTDIERQELKDKKTPFLWLHLNILREYLQIELNVPGLSFPFDLEKSIDDWVFICFFCGNNFLPHLPSLDVRDNSITTLVTIWKQILPTMKGYLTTDGYLNLPAVERLLAELAKKEDYIFRKRYEDEKRSLENQKRRKLAQEQSSARSQNAPNISTGKDKAPLTPNQNIPLYTTSGESVGIKMTDSEMVNNSALITKANEANKSIAELLKQNLQNEINKKRKISNEEQEVVKESVEEVVEEEDDVLVTSDPEDSSTEILIPKNEEIRLWEPGYRKRYYETKFHTKDPQKVKKIARNMVQKYIEGVSWVLLYYYQGCPSWNWYYPYHYAPFAADFVNLSELKIEFVEGTPFRPYEQLMSVLPAASSHNLPDVFRSLMSDANSEIIDFYPEEFPLDMNGKKVIWQAIPLLPFIDENRLLKAVQSKYDQLTEDEKFRNTNRSEILVLGRSHSHYPTLVKELYEEGKDSYEFQVDSSGVSGVAIKLQSFDRSGVLRLPVKQLEGYRHYPDISNRDFLMVEFKQLPKSHAKSMILSGLIPHLRRLTQEDKDSILYGGTNFYGRNRFSPEENADFKQYIGPHGKSQYLPRQGGYKAFIQIHSDEAKGHRHGIYHGGSHTETEFRRGGGYHQHGNRGGRGGYQGNQGYQANSGGYQNSYQGSYQGGYRGGYQGGSQGRYQAGYQSGYQGGYQGEYKNGYQGGYQGNQGNQGYNRQTYNASKSGTLPMKRRHNSGPSSGLEVLFQ |
| Decapping nuclease | S | 384 | Komagataella Phaffii | GPGMSKEKILPLAARSKKAMLRQPKQVAYFSRDLNYKTHPDRSNLSYYYLPDGDIDNSIDLSVGSKHFLLGDSVELSKLDPILLALKEIEKESGAKTKDRIITWRGIMRKLLTLPYDSEEDFVLDVVSFDGQLFIQFNVPYLKSKDVQKQGDTEFHKKLQFSGYKFEKMATLPKPWPECTRKEIDSRAKSKCNNIEQYGAIVRTGISRIKILIGGAVACTADYYDENDPLSRYIELKTTRTINQYKDMIAFEKKLFRTWAQCFLLGIPKIIYGFRDDNCILRTVEEFSTNDIPLMVKNNPLNEQPKKENCYMSSINFYGAVVEWLNESVKDDQVWKLSYAKRNRQYLVLKEVTDENEKQQIVDSAIPAWFKEWRSELRNSEGNI |
| DNA-directed RNA polymerase subunit beta | B | 1227 | Komagataella Phaffii | MSYDPYSIDDTITTEDCWTVISAFFEEKGLVSQQLDSFDEFMETSIQDLVWEEPRLILDQPAQHTNEKDNINKRYEIRFGKIYLSRPTMTEADGTTHAMFPQEARLRNLTYSSPVYLDMEKSMFTSIDDEGNPNATLDWQQVHEPIKDGVEEGNKVHIGKVPIMLRSKFCSLRTLDEVDLYKMKECPYDMGGYFVINGSEKVLIAQERSAANIVQVFKKAAPSPISHVAEIRSALEKGSRLISTMQIKLYGREDKGTGRTIKATLPYVKQDIPIVIVFRALGVVPDGEILQHICYDENDWQMLEMLKPCIEEGFVIQDKEVALDFIGRRGSAALGIRREKRIQYAKDILQKELLPHITQEEGFETRKTFFLGYMVNRLLLCALERKDQDDRDHFGKKRLDLAGPLLANLFRILFRKLTREIYRYMQRCIETDRDFNLNLAVKSTTITSGLKYSLATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLLSGISIGSPSEPIINFLEEWGMEPLEDYDPAQHTKSTRIFVNGVWTGIHRDPSMLVSTMRDLRRSGAISPEVSIIRDIREREFKIFTDVGRVYRPLFIVEDDESKDNKGELRITKEHIRKIQQGYDDDAMNDDSEEQEQDVYGWSSLVTSGVIEYVDGEEEETIMIAMTPEDLQTRSLEQKEIDLNDTAKRIKPEMSTSSHHTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLAKTQAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKRFGISIVEEFEKPTRATTLRLKHGTYEKLDEDGLIAPGVRVSGDDIIIGKTTPIPPDTEELGQRTKYHTKRDASTPLRSTENGIVDQVLLTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFSAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVGSIRGYEGDATPFTDLTVDAVSNLLRDNGYQSRGFEVMYNGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAAGFLKERLMEASDAFRVHVCGICGLMSVIANLKKNQFECRSCKNKTNIYQLHIPYAAKLLFQELMAMNIAPRLYTERSGVSMRS |
| RNA polymerase II third largest subunit B44, part of central core | C | 304 | Komagataella Phaffii | MSKEPKVNIINAQDDEVELMLSDVNLSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMKYSRDCTCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILLCKLRNHQELNIRCIAKKGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDSKYATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKANQVFSRGIKTLQEKLANVLFELENSRPANTTAYGGATAYGGQTVYGRETSYGGNTNYGDYNAPY |
| RNA polymerase II subunit B32 | D | 186 | Komagataella Phaffii | MNVSTSTVGARRRRAKQQVDDEENATLLRLGPEFALKQYDHDGNEHDLIALSLSESRLLIREALKARSRARNGGVDIESSNGEIDDDELAKVTSGAVANGVVKKTLDYLNTFARFKDEETCTAVDQLLHNSSDCSVLHPFEIAQLSSLGCEDVDEAITLIPSLAAKKEVNLQRILDELNRLEDPYK |
| DNA-directed RNA polymerases I, II, and III subunit RPABC1 | E | 214 | Komagataella Phaffii | MEDNNRIISRLWRSFRTVKEMAADRGYFISQEEMDQSLEEFRSKICDSMGNPQRKLMSFLANPTPEALEKYSDLGTLWVEFCDEPSVGIKTMRNFCLRIQEKNFSTGIFIYQNNITPSANKMIPTVSPAIIETFQESDLVVNITHHELVPKHIRLSDGEKSQLLQRYKLKESQLPRIQREDPVARYLGLKRGQVVKIIRRSETSGRYASYRICL |
| RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III | F | 155 | Komagataella Phaffii | MSEDEAFNEQTENFENFEDEHFSDDNFEDRSTQPEDYAVGVTADGRQIINGDGIQEVNGTIKAHRKRSNKELAILKEERTTTPYLTKYERARILGTRALQISMNAPVLVDIEGETDPLQIAMKELSQRKIPLVIRRYLPDGSYEDWGCDELIVDN |
| RNA polymerase II subunit | G | 171 | Komagataella Phaffii | MFFLKDLSLILTLHPSYFGPQMNQYLREKLLTDVEGTCTGQFGYIVTVLDGMNIDVGKGRIIPGSGSAEFEVKYRAVVWKPFKGEVVDAIVSNVSPIGFFADVGPLNVFVSTRLIPDNLVYNPSNSPPAYMSNDELITKGSKVRLKVVGTRTDVNEIYAIGSIKEDFLGAI |
| DNA-directed RNA polymerases I, II, and III subunit RPABC3 | H | 145 | Komagataella Phaffii | MSSALFDDIFTVQTVDNGRYNKVSRIIGISTTNSAIKLTLDINNEMFPVSQDDSLTVTLANSLSLDGEDESANFSKSWRPPKPTDKSLADDYDYVMFGTVYKFEEGDEDKIKVYVSFGGLLMCLEGGYKSLASLKQDNLYILIRR |
| DNA-directed RNA polymerase subunit | I | 115 | Komagataella Phaffii | MASFRFCLECNNMLYPKEDKENQRLLYSCRNCDYTELAEDPKVYRHELITNIGETAGIVDDIGQDPTLPRSDKECPECHSRDCVFFQSQQRRKDTNMTLFYVCLNCKKTFRDESE |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2024-02-25 Deposition Author(s): Ehara, H. , Murayama, Y. , Sekine, S. , Yanagisawa, T.