Structure of PDB 5c4j Chain B

Receptor sequence

>5c4jB (length=1157) Species: 559292 (Saccharomyces cerevisiae S288C)

DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARL
RNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESGKVFIGRLPIMLR
SKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQV
FKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPY
IKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQ
DRETALDFIIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCA
LDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEA
HDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYS
STLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNL
SLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGV
HRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFI
VEDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLNEGLVEYIDAEEEE
SILIAMQPEDLEPAEAKRIRATTFTHCEIHPSMILGVAASIIPFPDHNQS
PRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKF
RELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEK
KYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGK
TTPISPDEEELTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVR
VRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAI
PSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSR
GFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQ
PVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICG
LMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLY
TDRSRDF

3D structure

• PDB: 5c4j Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
• Chain: B
• Resolution: 4.0 Å

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	Q481 Q776 K979 H1097	Q442 Q712 K912 H1030
BS02	dna	B	S248 F250 I251 S252 P274 E359 K471 G503 R504 D505 M868	S223 F225 I226 S227 P249 E320 K432 G464 R465 D466 M804
BS03	dna	B	R430 R434 Y459 K470 R942 G1121 R1122 L1128 R1129	R391 R395 Y420 K431 R875 G1054 R1055 L1061 R1062
BS04	ZN	B	C1163 C1185	C1096 C1118

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:5c4j, PDBe:5c4j, PDBj:5c4j
• PDBsum: 5c4j
• PubMed: 26186291
• UniProt: P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)