Structure of PDB 7rix Chain A

Receptor sequence
>7rixA (length=1384) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PLVSRGGCGNTQPTIRKDGLKLVGSWKLRVLSTEEILNIFKHISVKDFTS
LGFNEVFSRPEWMILTCLPVPPPPVRPSRGEDDLTFKLADILKANISLET
LEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRAR
LKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPE
VVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQY
GWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPY
NADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTL
CGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQIL
SVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGG
LIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMRE
ITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDK
AGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFG
FVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTA
VKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHI
EKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVL
LDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKP
SDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLAT
RRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQ
MTLKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAI
EHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLQSPWLLRLELDR
AAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVDHMLKK
IENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVN
LSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSY
VNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEA
GASAELDDCRGVSENVILGQMAPIGTGAFDVMID
3D structure
PDB7rix RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
ChainA
Resolution3.4 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 rna A N479 D483 D485 N451 D455 D457
BS02 dna A K332 R344 R350 Q447 T831 A832 G835 R1386 E1403 K304 R316 R322 Q419 T803 A804 G807 R1324 E1341
BS03 MG A D483 D485 D455 D457
BS04 ZN A C107 C110 C167 C105 C108 C158
BS05 ZN A C67 C70 C77 H80 C65 C68 C75 H78
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006368 transcription elongation by RNA polymerase II
GO:0019985 translesion synthesis
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005665 RNA polymerase II, core complex
GO:0005739 mitochondrion
GO:0010494 cytoplasmic stress granule

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7rix, PDBe:7rix, PDBj:7rix
PDBsum7rix
PubMed35022237
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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