Structure of PDB 5c3e Chain A

Receptor sequence
>5c3eA (length=1430) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDEQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVL
STEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISF
NESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVAT
YMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTV
ISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGA
KYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHK
MSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELS
QLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYW
VPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKD
NGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKV
VNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLL
TAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSK
GSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVEN
SYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHY
DNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLL
NTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEA
NWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRG
KNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQ
FLRSVVHPGEMVGVLAAQSIGEPATQMTLNTVASKKVTSGVPRLKEILNV
AKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPD
PRSTVIPEDEEIIQLHFSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERI
KQTFKNDLFVIWSEDNDEKLIIRCRVVRPAEEDHMLKKIENTMLENITLR
GVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDP
TRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDV
MTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGV
SENVILGQMAPIGTGAFDVMIDEESLVKYM
3D structure
PDB5c3e Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
ChainA
Resolution3.7 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
Catalytic site (residue number reindexed from 1) D479 D481 D483
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 R320 D483 D485 R318 D481 D483
BS02 dna A K1109 N1110 K1102 N1103
BS03 dna A S318 R326 K330 K332 R337 R344 R350 Q447 P448 A832 G835 Y836 R1386 E1403 E1407 S316 R324 K328 K330 R335 R342 R348 Q445 P446 A830 G833 Y834 R1362 E1379 E1383
BS04 ZN A C110 C148 C167 C108 C146 C165
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:5c3e, PDBe:5c3e, PDBj:5c3e
PDBsum5c3e
PubMed26186291
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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