Structure of PDB 7opd Chain A

Receptor sequence

>7opdA (length=1412) Species: 9823 (Sus scrofa)

SACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDP
RQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCV
CFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGCGR
YQPRIRRSGLELYAEWKILLSPERVHEIFKRISDEECFVLGMEPRYARPE
WMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQN
GAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGK
EGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTP
FNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKV
ERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADF
DGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR
KFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLII
PGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLG
TSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADS
KTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILN
DARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGK
RIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREG
LIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGL
AGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNA
HIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHI
NPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLR
STLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLG
EPATQMTLNAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERA
KDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDV
ARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEK
LVLRIRIMNMDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKK
IIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVL
GIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGV
NRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTG
CFDLLLDAEKCK

3D structure

• PDB: 7opd Structural basis of human transcription-DNA repair coupling.
• Chain: A
• Resolution: 3.0 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	K1133 H1417	K1079 H1348
BS02	rna	A	R67 F431 D497 D499	R57 F385 D451 D453
BS03	dna	A	P44 E45 M266 Q267 N272 K331 S332 K346 R358 Q461 T854 A855 Y859 R1416 E1433 E1434 D1437	P34 E35 M220 Q221 N226 K285 S286 K300 R312 Q415 T808 A809 Y813 R1347 E1364 E1365 D1368
BS04	ZN	A	C71 H84	C61 H74
BS05	ZN	A	C114 C154 C184	C104 C144 C148
BS06	MG	A	D495 D497 D499	D449 D451 D453

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:7opd, PDBe:7opd, PDBj:7opd
• PDBsum: 7opd
• PubMed: 34526721
• UniProt: P11414|RPB1_CRIGR DNA-directed RNA polymerase II subunit RPB1 (Gene Name=POLR2A)