8HE5
Rna polymerase ii elongation complex bound with rad26 and elf1, stalled at shl(-3.5) of the nucleosome
PDB DOI: 10.2210/pdb8he5/pdb
Classification: TRANSCRIPTION Organism(s): Homo Sapiens , Komagataella Phaffii , Synthetic Construct
Deposited: 2022-11-07 Deposition Author(s): Ehara, H. , Kagawa, W. , Kinoshita, C. , Kujirai, T. , Kurumizaka, H. , Osumi, K. , Saotome, M. , Sekine, S. , Takizawa, Y.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 6.95 Å
Rna polymerase ii elongation complex bound with rad26 and elf1, stalled at shl(-3.5) of the nucleosome
Ehara, H. , Kagawa, W. , Kinoshita, C. , Kujirai, T. , Kurumizaka, H. , Osumi, K. , Saotome, M. , Sekine, S. , Takizawa, Y.
Primary Citation of Related Structures: 8HE5
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Histone H3.1 | A | 139 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
| RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III | J | 72 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MIIPVRCFSCGKVVGDKWDAYLRLLEEGKQEGDALDELKLKRYCCRRMVLTHVDLIEKFLRYNPLEKKDFDS |
| RNA polymerase II subunit B12.5 | K | 118 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MNAPDRFELFILPDDVPKLKITPDSRVPNCIIIKFEREDHTLANLLREELALYPDVTFVAYKVEHPLFANFVMRLQTEEGTRPKQALERACASIINKLKTLDHKFNEEWNIKNFSLND |
| RNA polymerase subunit ABC10-alpha | L | 72 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MSREGFVAPSGTDLAAAASGVAPNKHYGVKYTCGACAHNFSLNKSDPVRCKECGHRVIYKARTKRMIQFDAR |
| Transcription elongation factor 1 homolog | M | 113 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | GPGMGKRKSSARKPAPKIKQKLETQFTCLFCNHDNSVVCTLDKKNSIGLLECKKCNLSFQAPINSLSQPIDIYSDWIDACEAVAEENADVNGDNFIENDGADREQDDDYDDEF |
| DNA repair protein | O | 1094 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | GPLGSHMNEEPDDLTSLGVELVGQDTLEHQIASMADTAMLERDKELELKRLEKTKSQIQKWQSKQRSLESKINSRNTKISERERFRKELKDIEENELKVLRDDLKEINTRLQETMKASSLKAKETLDEVEQLPNETKKDFLIRTGKITAFGSVNAFTQDNPEAPVEKSHQSLIAPGIDDDDDYVYPGEIEEIEEIETENESDDQAAIISSKKRKRARSIEHDDVYVNSDSTEDEYDTQTTRQSKDEIHNIDDGDDAFYNARLNAWVTKRSQKREVDANPDEEEWFKPHPTKQDAILDDDYRLPGDVYPALFDYQKTCVQWLWELYLQKVGGILGDEMGLGKTVQIISFIAGLHYTKKLNKPVIVVCPATVLRQWCNEFHRWWPPLRVVILHAIGTGLSGSRTSLQNEASIEKLLEEEEYGSTKSLASLKAESRVKELIDSVFTRGHVIITTYVGLRIYSKHLLKRDWGYAILDEGHKIRNPNSDISLTCKQLRTPNRVILSGTPIQNNLTELWSLFDFIFPGRLGTLPVFQNQFAIPINVGGYANATNLQVQVGYKCAVTLKDLISPYLLRRVKADVAKDLPKKSEMVLFCKLTAPQHALYEKFLRSDELSRILQGKRQVLYGIDILRKICNHPDLVDVHAKRRSKKDPTYGSASKSGKMQVVKKLLELWKSQGHKTLLFTQTRQMLDILESFLERLNAKGAEEEDFVPFKFLRMDGTTSIGVRQSLVDVFNNDPSYNVFLLTTRVGGLGVNLTGANRVIIYDPDWNPSTDVQARERAWRLGQKKDVTIYRLMIAGSIEEKIYHRQIFKQFLTNKILKDPKQRRFFKMNELQDLFTLGDPDEKGTETGDMFNGMEYNFKGTKPRHSQKLSNRERSEEPQDDLVKLAQINGVSGLQEFDGSKDEQMDSTSRQEEELMSGLFASSGVHSALQHDSIMDSTEPEQNEAELEARRIAAEAANSLRESRKLARKSKIGVPTWTGKFGSAGKILNKQRFRDNASGVSSSSILQSIRAKRDLDTKKKERPDFNNEDNDRKLLIRRINDFMLVQNGYKADSQTILNSFKEINNIILMRSMLKQICKWDSKEKVWILKDEYVE |
| DNA-directed RNA polymerases I, II, and III subunit RPABC1 | E | 214 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MEDNNRIISRLWRSFRTVKEMAADRGYFISQEEMDQSLEEFRSKICDSMGNPQRKLMSFLANPTPEALEKYSDLGTLWVEFCDEPSVGIKTMRNFCLRIQEKNFSTGIFIYQNNITPSANKMIPTVSPAIIETFQESDLVVNITHHELVPKHIRLSDGEKSQLLQRYKLKESQLPRIQREDPVARYLGLKRGQVVKIIRRSETSGRYASYRICL |
| DNA-directed RNA polymerase subunit beta | B | 1227 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MSYDPYSIDDTITTEDCWTVISAFFEEKGLVSQQLDSFDEFMETSIQDLVWEEPRLILDQPAQHTNEKDNINKRYEIRFGKIYLSRPTMTEADGTTHAMFPQEARLRNLTYSSPVYLDMEKSMFTSIDDEGNPNATLDWQQVHEPIKDGVEEGNKVHIGKVPIMLRSKFCSLRTLDEVDLYKMKECPYDMGGYFVINGSEKVLIAQERSAANIVQVFKKAAPSPISHVAEIRSALEKGSRLISTMQIKLYGREDKGTGRTIKATLPYVKQDIPIVIVFRALGVVPDGEILQHICYDENDWQMLEMLKPCIEEGFVIQDKEVALDFIGRRGSAALGIRREKRIQYAKDILQKELLPHITQEEGFETRKTFFLGYMVNRLLLCALERKDQDDRDHFGKKRLDLAGPLLANLFRILFRKLTREIYRYMQRCIETDRDFNLNLAVKSTTITSGLKYSLATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLLSGISIGSPSEPIINFLEEWGMEPLEDYDPAQHTKSTRIFVNGVWTGIHRDPSMLVSTMRDLRRSGAISPEVSIIRDIREREFKIFTDVGRVYRPLFIVEDDESKDNKGELRITKEHIRKIQQGYDDDAMNDDSEEQEQDVYGWSSLVTSGVIEYVDGEEEETIMIAMTPEDLQTRSLEQKEIDLNDTAKRIKPEMSTSSHHTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLAKTQAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKRFGISIVEEFEKPTRATTLRLKHGTYEKLDEDGLIAPGVRVSGDDIIIGKTTPIPPDTEELGQRTKYHTKRDASTPLRSTENGIVDQVLLTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFSAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVGSIRGYEGDATPFTDLTVDAVSNLLRDNGYQSRGFEVMYNGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAAGFLKERLMEASDAFRVHVCGICGLMSVIANLKKNQFECRSCKNKTNIYQLHIPYAAKLLFQELMAMNIAPRLYTERSGVSMRS |
| RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III | F | 155 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MSEDEAFNEQTENFENFEDEHFSDDNFEDRSTQPEDYAVGVTADGRQIINGDGIQEVNGTIKAHRKRSNKELAILKEERTTTPYLTKYERARILGTRALQISMNAPVLVDIEGETDPLQIAMKELSQRKIPLVIRRYLPDGSYEDWGCDELIVDN |
| RNA polymerase II third largest subunit B44, part of central core | C | 304 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MSKEPKVNIINAQDDEVELMLSDVNLSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMKYSRDCTCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILLCKLRNHQELNIRCIAKKGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDSKYATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKANQVFSRGIKTLQEKLANVLFELENSRPANTTAYGGATAYGGQTVYGRETSYGGNTNYGDYNAPY |
| RNA polymerase II subunit | G | 171 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MFFLKDLSLILTLHPSYFGPQMNQYLREKLLTDVEGTCTGQFGYIVTVLDGMNIDVGKGRIIPGSGSAEFEVKYRAVVWKPFKGEVVDAIVSNVSPIGFFADVGPLNVFVSTRLIPDNLVYNPSNSPPAYMSNDELITKGSKVRLKVVGTRTDVNEIYAIGSIKEDFLGAI |
| RNA polymerase II subunit B32 | D | 186 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MNVSTSTVGARRRRAKQQVDDEENATLLRLGPEFALKQYDHDGNEHDLIALSLSESRLLIREALKARSRARNGGVDIESSNGEIDDDELAKVTSGAVANGVVKKTLDYLNTFARFKDEETCTAVDQLLHNSSDCSVLHPFEIAQLSSLGCEDVDEAITLIPSLAAKKEVNLQRILDELNRLEDPYK |
| DNA-directed RNA polymerases I, II, and III subunit RPABC3 | H | 145 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MSSALFDDIFTVQTVDNGRYNKVSRIIGISTTNSAIKLTLDINNEMFPVSQDDSLTVTLANSLSLDGEDESANFSKSWRPPKPTDKSLADDYDYVMFGTVYKFEEGDEDKIKVYVSFGGLLMCLEGGYKSLASLKQDNLYILIRR |
| DNA-directed RNA polymerase subunit | I | 115 | Homo Sapiens , Komagataella Phaffii , Synthetic Construct | MASFRFCLECNNMLYPKEDKENQRLLYSCRNCDYTELAEDPKVYRHELITNIGETAGIVDDIGQDPTLPRSDKECPECHSRDCVFFQSQQRRKDTNMTLFYVCLNCKKTFRDESE |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| DNA (198-MER) | n | 198 | NA | GCTTACGTCAGTCTGGCCATCTTTGTGTTTGGTGTGTTTGGGTGGTGGCCGTTTTCGTTGTTTTTTTCTGTCTCGTGCCTGGTGTCTTGGGTGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT |
| RNA (5'-R(P*GP*UP*UP*UP*UP*CP*GP*UP*UP*GP*UP*UP*UP*UP*UP*U)-3') | p | 16 | NA | GUUUUCGUUGUUUUUU |
| DNA (198-MER) | t | 198 | NA | ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACACCCAAGACACCAGGCACGAGACAGCAAAAAACAACGAAAACGGCCACCACCCAAACACACCAAACACAAGAGCTAATTGACTGACGTAAGC |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2022-11-07 Deposition Author(s): Ehara, H. , Kagawa, W. , Kinoshita, C. , Kujirai, T. , Kurumizaka, H. , Osumi, K. , Saotome, M. , Sekine, S. , Takizawa, Y.