Structure of PDB 7mei Chain b

Receptor sequence

>7meib (length=1160) Species: 4932 (Saccharomyces cerevisiae)

DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARL
RNLTYSSGLFVDVKTYEAIDVPGRELKYEDSESGKVFIGRLPIMLRSKNC
YLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKA
APSPISHVAEIRSALEKGSRFISTLQVKLYGRSSARTIKATLPYIKQDIP
IVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETAL
DFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYM
INRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRY
MQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQ
VLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVK
NLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWH
GVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPL
FIVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAE
EEESILIAMQPEDLEPAAKRIRATTFTHCEIHPSMILGVAASIIPFPDHN
QSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYL
KFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQ
EKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVII
GKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLK
FVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLII
NPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREH
GYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQ
VLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHI
CGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNI
PRLYTDRSRD

3D structure

• PDB: 7mei Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
• Chain: b
• Resolution: 3.54 Å

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	dna	b	Y275 K277 K426 I502 Y866 G867 M868	Y244 K246 K395 I471 Y804 G805 M806
BS02	dna	b	R857 R1122 R1129	R795 R1060 R1067
BS03	rna	b	A477 Q481 E529 Q776 R884 K979 K987 H1097 P1110 R1124	A446 Q450 E492 Q714 R822 K917 K925 H1035 P1048 R1062
BS04	ZN	b	C1163 C1166 C1182 C1185	C1101 C1104 C1120 C1123

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

External links

• PDB: RCSB:7mei, PDBe:7mei, PDBj:7mei
• PDBsum: 7mei
• PubMed: 35051353
• UniProt: P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)