Structure of PDB 7ycx Chain 1

Receptor sequence
>7ycx1 (length=1451) Species: 9606 (Homo sapiens) [Search protein sequence]
SACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDP
RQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCV
CFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEHGGCG
RYQPRIRRSGLELYAEWKKKILLSPERVHEIFKRISDEECFVLGMEPRYA
RPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRN
EQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRL
KGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEI
VTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTG
YKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYN
ADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLT
AVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFS
LIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKK
SLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSI
ADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNR
ILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNV
EGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGG
REGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGE
DGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVL
SNAHIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKI
FHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNI
HLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQ
SLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFL
LGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWV
NVISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEK
LVLRIRIMNDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKI
IITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLG
IEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVN
RQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGC
FDLLLDAEKCKYGMEIPAAAATSPSYSPTSPSYSPTSPSYSPTAAAAAAA
A
3D structure
PDB7ycx Structural basis of INTAC-regulated transcription.
Chain1
Resolution4.18 Å
3D
structure
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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 1 R108 K1132 H1417 R98 K1089 H1347
BS02 rna 1 R334 F431 D499 R291 F388 D456
BS03 dna 1 K331 S332 K344 R351 R364 T854 R1416 E1433 K288 S289 K301 R308 R321 T811 R1346 E1363
BS04 MG 1 D495 D497 D499 D452 D454 D456
BS05 ZN 1 C111 C184 C101 C149
BS06 ZN 1 C71 H84 C61 H74
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003723 RNA 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:0016787 hydrolase activity
GO:0019900 kinase binding
GO:0031625 ubiquitin protein ligase binding
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
GO:0050436 microfibril binding
GO:1990841 promoter-specific chromatin binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006353 DNA-templated transcription termination
GO:0006355 regulation of 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:0005654 nucleoplasm
GO:0005665 RNA polymerase II, core complex
GO:0005694 chromosome
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0031981 nuclear lumen
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7ycx, PDBe:7ycx, PDBj:7ycx
PDBsum7ycx
PubMed36869814
UniProtP24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 (Gene Name=POLR2A)

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