Structure of PDB 5c4j Chain A

Receptor sequence
>5c4jA (length=1432) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKRFPETMDEKIGGLNDPR
LGSIDRNLKCQTCQEGMNECPGHFGDLAKPVFHVGFIAKIKKVCECVCMH
CGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPT
QLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILN
IFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGE
DDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIA
GQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNL
ELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDS
GDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHR
VKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPL
QIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGV
IPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIID
GQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLH
NGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMT
LRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIA
QMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLT
PQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNS
LGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLD
PSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVN
IRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQN
AQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVH
PGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAK
NMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPR
STVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTM
GQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVEDHMLKKIENTMLENI
TLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPG
IDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALL
VDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDC
RGVSENVILGQMAPIGTGAFDVMIDEESLVKY
3D structure
PDB5c4j Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
ChainA
Resolution4.0 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) D472 D474 D476 H1076
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 W139 K143 R175 L315 K317 A1108 N1110 H1387 R1391 W130 K134 R166 L306 K308 A1099 N1101 H1366 R1370
BS02 dna A R189 A309 R326 K330 K332 Q447 A832 G835 Y836 R1386 E1403 R180 A300 R317 K321 K323 Q438 A823 G826 Y827 R1365 E1382
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:5c4j, PDBe:5c4j, PDBj:5c4j
PDBsum5c4j
PubMed26186291
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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