MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
2.7.7.48	Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases; RNA-directed RNA polymerase
2.7.7.6	Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases; DNA-directed RNA polymerase

Structure

PDB	Resolution (Å)	PDB name
2GHQ	2.05	CTD-specific phosphatase Scp1 in complex with peptide C-terminal domain of RNA polymerase II
2GHT	1.8	CTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA polymerase II
2LTO		TDRD3 complex
3D9K	2.2	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3D9L	2.2	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3D9M	1.75	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3D9N	1.6	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3D9O	2.0	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3D9P	2.1	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
4JXT	1.9	CID of human RPRD1A in complex with a phosphorylated peptide from RPB1-CTD
5IY6	7.2	Human holo-PIC in the closed state
5IY7	8.6	Human holo-PIC in the open state
5IY8	7.9	Human holo-PIC in the initial transcribing state
5IY9	6.3	Human holo-PIC in the initial transcribing state (no IIS)
5IYA	5.4	Human core-PIC in the closed state
5IYB	3.9	Human core-PIC in the open state
5IYC	3.9	Human core-PIC in the initial transcribing state
5IYD	3.9	Human core-PIC in the initial transcribing state (no IIS)
5M3H	2.5	Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD
5M3J	3.5	Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD
6DRD	3.9	RNA Pol II(G)
6F5P	4.14	A mechanism for the activation of the influenza virus transcriptase
6G0R	1.25	Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated POLR2A peptide (K775ac/K778ac)
6IC8	1.929	Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD diheptapeptide phosphorylated on Ser2
6IC9	1.748	Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD diheptapeptide phosphorylated on Ser2Ser7
6O9L	7.2	Human holo-PIC in the closed state
6Q5Y	2.85	Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD diheptapeptide phosphorylated on Ser2Ser5
6XKB	1.6	Crystal structure of SR-related and CTD-associated factor 4(SCAF4-CID)with peptide S2,S5p-CTD
6XRE	4.6	Structure of the p53/RNA polymerase II assembly
7EGB	3.3	TFIID-based holo PIC on SCP promoter
7EGC	3.9	p53-bound TFIID-based holo PIC on HDM2 promoter
7LBM	4.8	Structure of the human Mediator-bound transcription pre-initiation complex
7YCX	4.18	The structure of INTAC-PEC complex
7Z42	2.418	Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B

GO term

GO ontology	GO term	GO description
Biological Process	GO:0006353	DNA-templated transcription termination
Biological Process	GO:0033120	positive regulation of RNA splicing
Biological Process	GO:0006355	regulation of DNA-templated transcription
Biological Process	GO:0006366	transcription by RNA polymerase II
Molecular Function	GO:0003677	DNA binding
Molecular Function	GO:0003899	DNA-directed 5'-3' RNA polymerase activity
Molecular Function	GO:0003723	RNA binding
Molecular Function	GO:0001055	RNA polymerase II activity
Molecular Function	GO:0003968	RNA-dependent RNA polymerase activity
Molecular Function	GO:0019900	kinase binding
Molecular Function	GO:0046872	metal ion binding
Molecular Function	GO:1990841	promoter-specific chromatin binding
Molecular Function	GO:0031625	ubiquitin protein ligase binding
Cellular Component	GO:0005665	RNA polymerase II, core complex
Cellular Component	GO:0005694	chromosome
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus

InterPro / Pfam

InterPro	InterPro name
IPR000684	RNA polymerase II, heptapeptide repeat, eukaryotic
IPR000722	RNA polymerase, alpha subunit
IPR006592	RNA polymerase, N-terminal
IPR007066	RNA polymerase Rpb1, domain 3
IPR007073	RNA polymerase Rpb1, domain 7
IPR007075	RNA polymerase Rpb1, domain 6
IPR007080	RNA polymerase Rpb1, domain 1
IPR007081	RNA polymerase Rpb1, domain 5
IPR007083	RNA polymerase Rpb1, domain 4
IPR038120	RNA polymerase Rpb1, funnel domain superfamily
IPR038593	RNA polymerase Rpb1, domain 7 superfamily
IPR042102	RNA polymerase Rpb1, domain 3 superfamily
IPR044893	RNA polymerase Rpb1, clamp domain superfamily
IPR045867	DNA-directed RNA polymerase, subunit beta-prime

Pfam	Pfam name
PF00623	RNA polymerase Rpb1, domain 2
PF04983	RNA polymerase Rpb1, domain 3
PF04990	RNA polymerase Rpb1, domain 7
PF04992	RNA polymerase Rpb1, domain 6
PF04997	RNA polymerase Rpb1, domain 1
PF04998	RNA polymerase Rpb1, domain 5
PF05000	RNA polymerase Rpb1, domain 4
PF05001	RNA polymerase Rpb1 C-terminal repeat

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-112382	Formation of RNA Pol II elongation complex	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-113418	Formation of the Early Elongation Complex	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-167152	Formation of HIV elongation complex in the absence of HIV Tat	Leaf	R-HSA-1643685	Disease
R-HSA-167158	Formation of the HIV-1 Early Elongation Complex	Leaf	R-HSA-1643685	Disease
R-HSA-167160	RNA Pol II CTD phosphorylation and interaction with CE during HIV infection	Leaf	R-HSA-1643685	Disease
R-HSA-167161	HIV Transcription Initiation	Leaf	R-HSA-1643685	Disease
R-HSA-167162	RNA Polymerase II HIV Promoter Escape	Leaf	R-HSA-1643685	Disease
R-HSA-167172	Transcription of the HIV genome	Internal node	R-HSA-1643685	Disease
R-HSA-167200	Formation of HIV-1 elongation complex containing HIV-1 Tat	Leaf	R-HSA-1643685	Disease
R-HSA-167238	Pausing and recovery of Tat-mediated HIV elongation	Leaf	R-HSA-1643685	Disease
R-HSA-167242	Abortive elongation of HIV-1 transcript in the absence of Tat	Leaf	R-HSA-1643685	Disease
R-HSA-167243	Tat-mediated HIV elongation arrest and recovery	Leaf	R-HSA-1643685	Disease
R-HSA-167246	Tat-mediated elongation of the HIV-1 transcript	Internal node	R-HSA-1643685	Disease
R-HSA-167287	HIV elongation arrest and recovery	Leaf	R-HSA-1643685	Disease
R-HSA-167290	Pausing and recovery of HIV elongation	Leaf	R-HSA-1643685	Disease
R-HSA-168325	Viral Messenger RNA Synthesis	Leaf	R-HSA-1643685	Disease
R-HSA-203927	MicroRNA (miRNA) biogenesis	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-5578749	Transcriptional regulation by small RNAs	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-5601884	PIWI-interacting RNA (piRNA) biogenesis	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-5617472	Activation of anterior HOX genes in hindbrain development during early embryogenesis	Leaf	R-HSA-1266738	Developmental Biology
R-HSA-674695	RNA Polymerase II Pre-transcription Events	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-6781823	Formation of TC-NER Pre-Incision Complex	Leaf	R-HSA-73894	DNA Repair
R-HSA-6781827	Transcription-Coupled Nucleotide Excision Repair (TC-NER)	Internal node	R-HSA-73894	DNA Repair
R-HSA-6782135	Dual incision in TC-NER	Leaf	R-HSA-73894	DNA Repair
R-HSA-6782210	Gap-filling DNA repair synthesis and ligation in TC-NER	Leaf	R-HSA-73894	DNA Repair
R-HSA-6796648	TP53 Regulates Transcription of DNA Repair Genes	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-6803529	FGFR2 alternative splicing	Leaf	R-HSA-162582	Signal Transduction
R-HSA-6807505	RNA polymerase II transcribes snRNA genes	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-72086	mRNA Capping	Leaf	R-HSA-8953854	Metabolism of RNA
R-HSA-72163	mRNA Splicing - Major Pathway	Leaf	R-HSA-8953854	Metabolism of RNA
R-HSA-72165	mRNA Splicing - Minor Pathway	Leaf	R-HSA-8953854	Metabolism of RNA
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA	Internal node	R-HSA-8953854	Metabolism of RNA
R-HSA-73776	RNA Polymerase II Promoter Escape	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-73779	RNA Polymerase II Transcription Pre-Initiation And Promoter Opening	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-75953	RNA Polymerase II Transcription Initiation	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-75955	RNA Polymerase II Transcription Elongation	Internal node	R-HSA-74160	Gene expression (Transcription)
R-HSA-76042	RNA Polymerase II Transcription Initiation And Promoter Clearance	Internal node	R-HSA-74160	Gene expression (Transcription)
R-HSA-77075	RNA Pol II CTD phosphorylation and interaction with CE	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-8851708	Signaling by FGFR2 IIIa TM	Leaf	R-HSA-1643685	Disease
R-HSA-9018519	Estrogen-dependent gene expression	Leaf	R-HSA-162582	Signal Transduction
R-HSA-9670095	Inhibition of DNA recombination at telomere	Leaf	R-HSA-1640170	Cell Cycle

Subcellular location

Location	ECO term	Pubmed
Chromosome	ECO:0000269	PubMed:28076779
Cytoplasm	ECO:0000269	PubMed:26566685
Nucleus	ECO:0000269	PubMed:26566685
Nucleus	ECO:0000269	PubMed:28076779
Nucleus	ECO:0000269	PubMed:9852112

Interactor | Variant | Drug

Phenotype

HPO ID	HPO name
HP:0000006	Autosomal dominant inheritance
HP:0000023	Inguinal hernia
HP:0000175	Cleft palate
HP:0000218	High palate
HP:0000248	Brachycephaly
HP:0000252	Microcephaly
HP:0000316	Hypertelorism
HP:0000348	High forehead
HP:0000486	Strabismus
HP:0000505	Visual impairment
HP:0000692	Tooth malposition
HP:0000729	Autistic behavior
HP:0000767	Pectus excavatum
HP:0001250	Seizure
HP:0001274	Agenesis of corpus callosum
HP:0001290	Generalized hypotonia
HP:0001357	Plagiocephaly
HP:0001508	Failure to thrive
HP:0001558	Decreased fetal movement
HP:0002020	Gastroesophageal reflux
HP:0002079	Hypoplasia of the corpus callosum
HP:0002119	Ventriculomegaly
HP:0002188	Delayed CNS myelination
HP:0002205	Recurrent respiratory infections
HP:0002280	Enlarged cisterna magna
HP:0002360	Sleep disturbance
HP:0002453	Abnormal globus pallidus morphology
HP:0003202	Skeletal muscle atrophy
HP:0003546	Exercise intolerance
HP:0007281	Developmental stagnation
HP:0011968	Feeding difficulties
HP:0025336	Delayed ability to sit
HP:0025352	Typically de novo
HP:0031139	Frog-leg posture
HP:0031936	Delayed ability to walk

Tissue and cell type

Disease

Disease name	MONDO ID	ICD10	ICD10 chapter	OMIM	Orphanet
neurodevelopmental disorder with hypotonia and variable intellectual and behavioral abnormalities	MONDO:0032829	G00	chapter6, Diseases of the nervous system	OMIM:618603
neurodevelopmental disorder with hypotonia and variable intellectual and behavioral abnormalities	MONDO:0032829	G98	chapter6, Diseases of the nervous system	OMIM:618603

Summary of P24928

Gene: POLR2A, POLR2
Protein: DNA-directed RNA polymerase II subunit RPB1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of P24928

Gene: POLR2A, POLR2 Protein: DNA-directed RNA polymerase II subunit RPB1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: POLR2A, POLR2
Protein: DNA-directed RNA polymerase II subunit RPB1