Structure of PDB 5c3e Chain B

Receptor sequence
>5c3eB (length=1157) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILEQISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLF
VDVKKRTYEAIDVPGRELKYELIASESGKVFIGRLPIMLRSKNCYLSEAT
ESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPIS
HVAEIRSALEKGSRFISTLQVKLYGRSSARTIKATLPYIKQDIPIVIIFR
ALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRR
GTALGIKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCAL
DRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAH
DFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSS
TLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLS
LMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVH
RNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIV
EDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEE
SILIAMQPEDLEPAEAKRIRATTFTHCEIHPSMILGVAASIIPFPDHNQS
PRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKF
RELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEK
KYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGK
TTPISEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVR
VRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAI
PSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSR
GFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQ
PVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICG
LMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLY
TDRSRDF
3D structure
PDB5c3e Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
ChainB
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) D837
Catalytic site (residue number reindexed from 1) D773
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 B A477 Q481 Q776 K979 K987 H1097 V1113 A437 Q441 Q712 K912 K920 H1030 V1046
BS02 dna B K210 T791 R857 R1122 S1123 R1129 M1133 K175 T727 R793 R1055 S1056 R1062 M1066
BS03 ZN B C1163 C1166 C1096 C1099
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003729 mRNA 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:0032549 ribonucleoside binding
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
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
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
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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