6INQ
Rna polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign dna (+1 position)
PDB DOI: 10.2210/pdb6inq/pdb
Classification: TRANSCRIPTION/RNA/DNA Organism(s): Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct
Deposited: 2018-10-26 Deposition Author(s): Ehara, H. , Fujino, Y. , Kujirai, T. , Kurumizaka, H. , Sekine, S. , Shirouzu, M.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 6.9 Å
Rna polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign dna (+1 position)
Ehara, H. , Fujino, Y. , Kujirai, T. , Kurumizaka, H. , Sekine, S. , Shirouzu, M.
Primary Citation of Related Structures: 6INQ
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Histone H3.3 | A | 139 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA |
| RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III | J | 72 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MIIPVRCFSCGKVVGDKWDAYLRLLEEGKQEGDALDELKLKRYCCRRMVLTHVDLIEKFLRYNPLEKKDFDS |
| RNA polymerase II subunit B12.5 | K | 118 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MNAPDRFELFILPDDVPKLKITPDSRVPNCIIIKFEREDHTLANLLREELALYPDVTFVAYKVEHPLFANFVMRLQTEEGTRPKQALERACASIINKLKTLDHKFNEEWNIKNFSLND |
| RNA polymerase subunit ABC10-alpha | L | 72 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MSREGFVAPSGTDLAAAASGVAPNKHYGVKYTCGACAHNFSLNKSDPVRCKECGHRVIYKARTKRMIQFDAR |
| RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III | E | 214 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MEDNNRIISRLWRSFRTVKEMAADRGYFISQEEMDQSLEEFRSKICDSMGNPQRKLMSFLANPTPEALEKYSDLGTLWVEFCDEPSVGIKTMRNFCLRIQEKNFSTGIFIYQNNITPSANKMIPTVSPAIIETFQESDLVVNITHHELVPKHIRLSDGEKSQLLQRYKLKESQLPRIQREDPVARYLGLKRGQVVKIIRRSETSGRYASYRICL |
| DNA-directed RNA polymerase subunit beta | B | 1227 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MSYDPYSIDDTITTEDCWTVISAFFEEKGLVSQQLDSFDEFMETSIQDLVWEEPRLILDQPAQHTNEKDNINKRYEIRFGKIYLSRPTMTEADGTTHAMFPQEARLRNLTYSSPVYLDMEKSMFTSIDDEGNPNATLDWQQVHEPIKDGVEEGNKVHIGKVPIMLRSKFCSLRTLDEVDLYKMKECPYDMGGYFVINGSEKVLIAQERSAANIVQVFKKAAPSPISHVAEIRSALEKGSRLISTMQIKLYGREDKGTGRTIKATLPYVKQDIPIVIVFRALGVVPDGEILQHICYDENDWQMLEMLKPCIEEGFVIQDKEVALDFIGRRGSAALGIRREKRIQYAKDILQKELLPHITQEEGFETRKTFFLGYMVNRLLLCALERKDQDDRDHFGKKRLDLAGPLLANLFRILFRKLTREIYRYMQRCIETDRDFNLNLAVKSTTITSGLKYSLATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLLSGISIGSPSEPIINFLEEWGMEPLEDYDPAQHTKSTRIFVNGVWTGIHRDPSMLVSTMRDLRRSGAISPEVSIIRDIREREFKIFTDVGRVYRPLFIVEDDESKDNKGELRITKEHIRKIQQGYDDDAMNDDSEEQEQDVYGWSSLVTSGVIEYVDGEEEETIMIAMTPEDLQTRSLEQKEIDLNDTAKRIKPEMSTSSHHTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLAKTQAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKRFGISIVEEFEKPTRATTLRLKHGTYEKLDEDGLIAPGVRVSGDDIIIGKTTPIPPDTEELGQRTKYHTKRDASTPLRSTENGIVDQVLLTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFSAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVGSIRGYEGDATPFTDLTVDAVSNLLRDNGYQSRGFEVMYNGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAAGFLKERLMEASDAFRVHVCGICGLMSVIANLKKNQFECRSCKNKTNIYQLHIPYAAKLLFQELMAMNIAPRLYTERSGVSMRS |
| RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III | F | 155 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MSEDEAFNEQTENFENFEDEHFSDDNFEDRSTQPEDYAVGVTADGRQIINGDGIQEVNGTIKAHRKRSNKELAILKEERTTTPYLTKYERARILGTRALQISMNAPVLVDIEGETDPLQIAMKELSQRKIPLVIRRYLPDGSYEDWGCDELIVDN |
| RNA polymerase II third largest subunit B44, part of central core | C | 304 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MSKEPKVNIINAQDDEVELMLSDVNLSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMKYSRDCTCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILLCKLRNHQELNIRCIAKKGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDSKYATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKANQVFSRGIKTLQEKLANVLFELENSRPANTTAYGGATAYGGQTVYGRETSYGGNTNYGDYNAPY |
| RNA polymerase II subunit | G | 171 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MFFLKDLSLILTLHPSYFGPQMNQYLREKLLTDVEGTCTGQFGYIVTVLDGMNIDVGKGRIIPGSGSAEFEVKYRAVVWKPFKGEVVDAIVSNVSPIGFFADVGPLNVFVSTRLIPDNLVYNPSNSPPAYMSNDELITKGSKVRLKVVGTRTDVNEIYAIGSIKEDFLGAI |
| RNA polymerase II subunit B32 | D | 186 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MNVSTSTVGARRRRAKQQVDDEENATLLRLGPEFALKQYDHDGNEHDLIALSLSESRLLIREALKARSRARNGGVDIESSNGEIDDDELAKVTSGAVANGVVKKTLDYLNTFARFKDEETCTAVDQLLHNSSDCSVLHPFEIAQLSSLGCEDVDEAITLIPSLAAKKEVNLQRILDELNRLEDPYK |
| DNA-directed RNA polymerases I, II, and III subunit RPABC3 | H | 145 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MSSALFDDIFTVQTVDNGRYNKVSRIIGISTTNSAIKLTLDINNEMFPVSQDDSLTVTLANSLSLDGEDESANFSKSWRPPKPTDKSLADDYDYVMFGTVYKFEEGDEDKIKVYVSFGGLLMCLEGGYKSLASLKQDNLYILIRR |
| DNA-directed RNA polymerase subunit | I | 115 | Homo Sapiens , Komagataella Phaffii (Strain Gs115 / Atcc 20864) , Synthetic Construct | MASFRFCLECNNMLYPKEDKENQRLLYSCRNCDYTELAEDPKVYRHELITNIGETAGIVDDIGQDPTLPRSDKECPECHSRDCVFFQSQQRRKDTNMTLFYVCLNCKKTFRDESE |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| RNA (5'-R(P*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3') | p | 11 | NA | GUGUCUUGGGU |
| DNA (198-MER) | t | 198 | NA | ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACACCCAAGACACCAGGCACGAGACAGAAAAAAACAACGAAAACGGCCACCACCCAAACACACCAAACACAAGAGCTAATTGACTGACGTAAGC |
| DNA (198-MER) | n | 198 | NA | GCTTACGTCAGTCTGGCCATCTTTGTGTTTGGTGTGTTTGGGTGGTGGCCGTTTTCGTTGTTTTTTTCTGTCTCGTGCCTGGTGTCTTGGGTGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT |
| DNA (31-MER) | 0 | 31 | NA | CCAAGACACCAGGCACGAGACAGAAAAAAAC |
| DNA (31-MER) | 1 | 31 | NA | GTTTTTTTCTGTCTCGTGCCTGGTGTCTTGG |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2018-10-26 Deposition Author(s): Ehara, H. , Fujino, Y. , Kujirai, T. , Kurumizaka, H. , Sekine, S. , Shirouzu, M.