Structure of PDB 6o6c Chain A

Receptor sequence
>6o6cA (length=1446) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
SAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPR
LGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVC
MHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDD
PTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEI
LNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQR
GEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDND
IAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDP
NLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIR
DSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMA
HRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAV
PLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWD
GVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLI
IDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWL
LHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHG
MTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFIN
IAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRG
LTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTR
NSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHT
LDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLP
VNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEII
QNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSV
VHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNV
AKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYPDI
HDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDE
KLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVM
MKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFID
IMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSV
TRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMA
PIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLV
3D structure
PDB6o6c 3.1 angstrom structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids.
ChainA
Resolution3.1 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485 H1085
Catalytic site (residue number reindexed from 1) D474 D476 D478 H1078
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 dna A K101 K143 K1109 H1387 R1391 K94 K136 K1102 H1353 R1357
BS02 dna A K145 K332 R337 P448 G835 Y836 E1403 K138 K325 R330 P441 G828 Y829 E1369
BS03 ZN A C107 M108 C148 C167 C100 M101 C141 C160
BS04 ZN A C67 H80 C60 H73
BS05 MG A D481 D483 D485 D474 D476 D478
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:6o6c, PDBe:6o6c, PDBj:6o6c
PDBsum6o6c
PubMed31200019
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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