Structure of PDB 7b0y Chain A

Receptor sequence

>7b0yA (length=1422) Species: 9825 (Sus scrofa domesticus)

SACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDP
RQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCV
CFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGCGR
YQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVL
GMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKI
NNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPL
KSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAA
NMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPS
DLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNL
SVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMG
IVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLW
TGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELI
MGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHT
IGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQT
FENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIA
VVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEF
FFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQV
VQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQE
DLVKDVLSNAHIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLLRM
IWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQEN
ATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEM
VGALAAQSLGEPATQMTLNAKNVTLGVPRLKELINISKKPKTPSLTVFLL
GQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVN
VYYEMPDFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLN
CIFNDDNAEKLVLRIRIMNMDDDVFLRCIESNMLTDMTLQGIEQISKVYM
HLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTS
NDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRG
HLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIM
LGQLAPAGTGCFDLLLDAEKCK

3D structure

• PDB: 7b0y Structure of a transcribing RNA polymerase II-U1 snRNP complex.
• Chain: A
• Resolution: 3.6 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.6: DNA-directed RNA polymerase.
  3.1.13.-

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	A	R108 Y145 H1417	R98 Y135 H1358
BS02	rna	A	R67 V264 M266 Q267 F431 D499	R57 V228 M230 Q231 F395 D463
BS03	dna	A	P323 K331 S332 K346 R351 R358 Q461 T854 A855 R1416 E1433	P287 K295 S296 K310 R315 R322 Q425 T818 A819 R1357 E1374
BS04	ZN	A	C71 C74 H84	C61 C64 H74
BS05	ZN	A	C111 C114 C154 C184	C101 C104 C144 C148
BS06	MG	A	D495 D497 D499	D459 D461 D463

Gene Ontology

Molecular Function

• GO:0001055 RNA polymerase II activity
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0016787 hydrolase activity
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding
• GO:1990841 promoter-specific chromatin binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0006366 transcription by RNA polymerase II
• GO:0033120 positive regulation of RNA splicing

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0000974 Prp19 complex
• GO:0005634 nucleus
• GO:0005665 RNA polymerase II, core complex
• GO:0005694 chromosome
• GO:0005737 cytoplasm
• GO:0031981 nuclear lumen
• GO:0032991 protein-containing complex

External links

• PDB: RCSB:7b0y, PDBe:7b0y, PDBj:7b0y
• PDBsum: 7b0y
• PubMed: 33446560
• UniProt: P11414|RPB1_CRIGR DNA-directed RNA polymerase II subunit RPB1 (Gene Name=POLR2A)