Structure of PDB 7rim Chain B

Receptor sequence
>7rimB (length=1129) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILEQLARKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLF
VDVKKRTYESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGY
FIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFIS
TLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHIC
YDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRKEKRIQYAKDILQKE
FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLA
GPLLAQLFKTLFKKLTKDIFRYMQRTVEELAINAKTITSGLKYALATGNW
GEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHN
THWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPL
EDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMI
RDIREKELKIFTDAGRVYRPLFIVEDDGHKELKVRKGHIAKLMATEYQDV
EEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAELDVDPAKRIRVS
HHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFL
TNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSG
YNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNT
LRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISAYHSKRDASTPLR
STENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGI
TYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEG
DASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYY
QRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHG
AASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIY
QIHIPYAAKLLFQELMAMNITPRLYTDRS
3D structure
PDB7rim RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
ChainB
Resolution2.9 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 B Q776 K987 H1097 Q1112 Q694 K895 H1005 Q1020
BS02 dna B S208 D505 T791 M792 R857 R942 L1128 R1129 S156 D439 T709 M710 R775 R850 L1036 R1037
BS03 dna B I502 L508 I436 L442
BS04 ZN B C1163 C1166 C1185 C1071 C1074 C1093
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
View graph for
Cellular Component
External links
PDB RCSB:7rim, PDBe:7rim, PDBj:7rim
PDBsum7rim
PubMed35022237
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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