Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8P4B

Structural insights into human co-transcriptional capping - structure 2

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0001055	molecular_function	RNA polymerase II activity
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
A	0005634	cellular_component	nucleus
A	0005665	cellular_component	RNA polymerase II, core complex
A	0006351	biological_process	DNA-templated transcription
A	0006366	biological_process	transcription by RNA polymerase II
A	0016779	molecular_function	nucleotidyltransferase activity
A	0031981	cellular_component	nuclear lumen
A	0032991	cellular_component	protein-containing complex
A	0046872	molecular_function	metal ion binding
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0000781	cellular_component	chromosome, telomeric region
B	0001055	molecular_function	RNA polymerase II activity
B	0001172	biological_process	RNA-templated transcription
B	0003677	molecular_function	DNA binding
B	0003682	molecular_function	chromatin binding
B	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
B	0003968	molecular_function	RNA-dependent RNA polymerase activity
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005665	cellular_component	RNA polymerase II, core complex
B	0006351	biological_process	DNA-templated transcription
B	0006366	biological_process	transcription by RNA polymerase II
B	0016779	molecular_function	nucleotidyltransferase activity
B	0032549	molecular_function	ribonucleoside binding
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0046872	molecular_function	metal ion binding
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005665	cellular_component	RNA polymerase II, core complex
C	0005829	cellular_component	cytosol
C	0006351	biological_process	DNA-templated transcription
C	0006366	biological_process	transcription by RNA polymerase II
C	0046983	molecular_function	protein dimerization activity
D	0000166	molecular_function	nucleotide binding
D	0000428	cellular_component	DNA-directed RNA polymerase complex
D	0005634	cellular_component	nucleus
D	0005665	cellular_component	RNA polymerase II, core complex
D	0006352	biological_process	DNA-templated transcription initiation
D	0006367	biological_process	transcription initiation at RNA polymerase II promoter
D	0030880	cellular_component	RNA polymerase complex
D	0031369	molecular_function	translation initiation factor binding
D	0044237	biological_process	cellular metabolic process
E	0001054	molecular_function	RNA polymerase I activity
E	0001055	molecular_function	RNA polymerase II activity
E	0001056	molecular_function	RNA polymerase III activity
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005665	cellular_component	RNA polymerase II, core complex
E	0005666	cellular_component	RNA polymerase III complex
E	0005736	cellular_component	RNA polymerase I complex
E	0006351	biological_process	DNA-templated transcription
E	0006362	biological_process	transcription elongation by RNA polymerase I
E	0006366	biological_process	transcription by RNA polymerase II
E	0042797	biological_process	tRNA transcription by RNA polymerase III
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0001650	cellular_component	fibrillar center
F	0003677	molecular_function	DNA binding
F	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005665	cellular_component	RNA polymerase II, core complex
F	0005666	cellular_component	RNA polymerase III complex
F	0005736	cellular_component	RNA polymerase I complex
F	0006351	biological_process	DNA-templated transcription
F	0006366	biological_process	transcription by RNA polymerase II
G	0000428	cellular_component	DNA-directed RNA polymerase complex
G	0000932	cellular_component	P-body
G	0003676	molecular_function	nucleic acid binding
G	0003697	molecular_function	single-stranded DNA binding
G	0003727	molecular_function	single-stranded RNA binding
G	0005634	cellular_component	nucleus
G	0005665	cellular_component	RNA polymerase II, core complex
G	0006351	biological_process	DNA-templated transcription
G	0006352	biological_process	DNA-templated transcription initiation
G	0006367	biological_process	transcription initiation at RNA polymerase II promoter
G	0031369	molecular_function	translation initiation factor binding
G	0045948	biological_process	positive regulation of translational initiation
G	0060213	biological_process	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
H	0000428	cellular_component	DNA-directed RNA polymerase complex
H	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
H	0005634	cellular_component	nucleus
H	0005665	cellular_component	RNA polymerase II, core complex
H	0006351	biological_process	DNA-templated transcription
I	0000428	cellular_component	DNA-directed RNA polymerase complex
I	0001193	biological_process	maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II
I	0003676	molecular_function	nucleic acid binding
I	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005665	cellular_component	RNA polymerase II, core complex
I	0005730	cellular_component	nucleolus
I	0006283	biological_process	transcription-coupled nucleotide-excision repair
I	0006351	biological_process	DNA-templated transcription
I	0006366	biological_process	transcription by RNA polymerase II
I	0006367	biological_process	transcription initiation at RNA polymerase II promoter
I	0008270	molecular_function	zinc ion binding
I	0046872	molecular_function	metal ion binding
J	0000428	cellular_component	DNA-directed RNA polymerase complex
J	0003677	molecular_function	DNA binding
J	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
J	0006351	biological_process	DNA-templated transcription
J	0008270	molecular_function	zinc ion binding
J	0046872	molecular_function	metal ion binding
K	0000428	cellular_component	DNA-directed RNA polymerase complex
K	0001055	molecular_function	RNA polymerase II activity
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
K	0005634	cellular_component	nucleus
K	0005665	cellular_component	RNA polymerase II, core complex
K	0006351	biological_process	DNA-templated transcription
K	0006366	biological_process	transcription by RNA polymerase II
K	0046983	molecular_function	protein dimerization activity
L	0003677	molecular_function	DNA binding
L	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
L	0005634	cellular_component	nucleus
L	0005665	cellular_component	RNA polymerase II, core complex
L	0005666	cellular_component	RNA polymerase III complex
L	0005736	cellular_component	RNA polymerase I complex
L	0006351	biological_process	DNA-templated transcription
L	0006366	biological_process	transcription by RNA polymerase II
L	0008270	molecular_function	zinc ion binding
L	0046872	molecular_function	metal ion binding
M	0003824	molecular_function	catalytic activity
M	0004484	molecular_function	mRNA guanylyltransferase activity
M	0004651	molecular_function	polynucleotide 5'-phosphatase activity
M	0004721	molecular_function	phosphoprotein phosphatase activity
M	0005515	molecular_function	protein binding
M	0005524	molecular_function	ATP binding
M	0005525	molecular_function	GTP binding
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0006139	biological_process	nucleobase-containing compound metabolic process
M	0006370	biological_process	7-methylguanosine mRNA capping
M	0006396	biological_process	RNA processing
M	0006470	biological_process	protein dephosphorylation
M	0008192	molecular_function	RNA guanylyltransferase activity
M	0016311	biological_process	dephosphorylation
M	0016779	molecular_function	nucleotidyltransferase activity
M	0050355	molecular_function	inorganic triphosphate phosphatase activity
M	0140818	molecular_function	mRNA 5'-triphosphate monophosphatase activity

Functional Information from PROSITE/UniProt

site_id	PS00018
Number of Residues	13
Details	EF_HAND_1 EF-hand calcium-binding domain. DNDPSDYVEqdDI

Chain	Residue	Details
C	ASP136-ILE148

site_id	PS00115
Number of Residues	7
Details	RNA_POL_II_REPEAT Eukaryotic RNA polymerase II heptapeptide repeat. YSPTSPA

Chain	Residue	Details
A	TYR1593-ALA1599
A	TYR1671-SER1677
A	TYR1678-SER1684
A	TYR1685-SER1691
A	TYR1692-SER1698
A	TYR1699-SER1705
A	TYR1706-SER1712
A	TYR1713-SER1719
A	TYR1720-SER1726
A	TYR1727-SER1733
A	TYR1734-SER1740
A	TYR1615-SER1621
A	TYR1741-ASN1747
A	TYR1748-ASN1754
A	TYR1755-SER1761
A	TYR1762-SER1768
A	TYR1769-ASN1775
A	TYR1776-ASN1782
A	TYR1783-SER1789
A	TYR1790-SER1796
A	TYR1797-SER1803
A	TYR1818-SER1824
A	TYR1622-SER1628
A	TYR1825-SER1831
A	TYR1832-LYS1838
A	TYR1839-SER1845
A	TYR1853-LYS1859
A	TYR1860-LYS1866
A	TYR1867-LYS1873
A	TYR1874-THR1880
A	TYR1888-THR1894
A	TYR1902-LYS1908
A	TYR1909-THR1915
A	TYR1629-ASN1635
A	TYR1916-LYS1922
A	TYR1923-THR1929
A	TYR1930-LYS1936
A	TYR1947-THR1953
A	TYR1636-SER1642
A	TYR1643-SER1649
A	TYR1650-SER1656
A	TYR1657-SER1663
A	TYR1664-SER1670

site_id	PS00290
Number of Residues	7
Details	IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YVCTAPH

Chain	Residue	Details
I	TYR112-HIS118

site_id	PS00383
Number of Residues	11
Details	TYR_PHOSPHATASE_1 Tyrosine specific protein phosphatases active site. VHCthGfnRTG

Chain	Residue	Details
M	VAL124-GLY134

site_id	PS00446
Number of Residues	41
Details	RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSIRRvfiaevpiiAidwVqidaNsSvlhDEfIAhRLGLIP

Chain	Residue	Details
C	ASN32-PRO72

site_id	PS00466
Number of Residues	38
Details	ZF_TFIIS_1 Zinc finger TFIIS-type signature. CqkCghkeavffqSHSARaEDAmrlyyvCtaph.CghrW

Chain	Residue	Details
I	CYS86-TRP123

site_id	PS01030
Number of Residues	27
Details	RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCQECNNMLypkedkenrillyaCrnC

Chain	Residue	Details
I	PHE16-CYS42

site_id	PS01110
Number of Residues	14
Details	RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPEHvvMtkEE

Chain	Residue	Details
E	HIS142-GLU155

site_id	PS01111
Number of Residues	15
Details	RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARvLGtRAlQ

Chain	Residue	Details
F	THR58-GLN72

site_id	PS01112
Number of Residues	10
Details	RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IIPVrCFTCG

Chain	Residue	Details
J	ILE2-GLY11

site_id	PS01154
Number of Residues	32
Details	RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. InkEdHTLgNiIksqLlkdpqVlfagYkvpHP

Chain	Residue	Details
K	ILE35-PRO66

site_id	PS01166
Number of Residues	13
Details	RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT

Chain	Residue	Details
B	GLY932-THR944

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	ACT_SITE: Phosphocysteine intermediate => ECO:0000255\|PROSITE-ProRule:PRU00160

Chain	Residue	Details
M	CYS126
A	LYS346
A	ARG358
A	ARG460
A	ASP499
A	ARG1416
A	ARG1421

site_id	SWS_FT_FI2
Number of Residues	1
Details	ACT_SITE: N6-GMP-lysine intermediate => ECO:0000269\|PubMed:21636784

Chain	Residue	Details
M	LYS294
A	ASP495
A	CYS74
A	CYS81
A	HIS84
A	CYS111
A	CYS114
A	CYS154
A	CYS184
A	ASN493

site_id	SWS_FT_FI3
Number of Residues	1
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
M	ARG299
I	CYS20
I	CYS39
I	CYS42

site_id	SWS_FT_FI4
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255

Chain	Residue	Details
M	ARG315
M	ASP343
M	LYS458
M	ARG528

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: N-acetylmethionine => ECO:0000250\|UniProtKB:P36954

Chain	Residue	Details
I	MET1
A	SER1868
A	SER1875
A	SER1878
A	SER1882
A	SER1896
A	SER1899
A	SER1906
A	SER1913
A	SER1917
A	SER1920
A	SER217
A	SER1927
A	SER1931
A	SER1934
A	SER1843
A	SER1845
A	SER1849
A	SER1850
A	SER1857
A	SER1861
A	SER1864

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: Omega-N-methylated arginine; by CARM1; in vitro => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	ARG1603

site_id	SWS_FT_FI7
Number of Residues	1
Details	MOD_RES: Symmetric dimethylarginine; alternate; by PRMT5 => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	ARG1810

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250\|UniProtKB:P08775

Chain	Residue	Details
A	LYS1838

site_id	SWS_FT_FI9
Number of Residues	12
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	THR1840
A	THR1926
A	THR1929
A	THR1933
A	THR1854
A	THR1863
A	THR1870
A	THR1877
A	THR1885
A	THR1912
A	THR1915
A	THR1919

site_id	SWS_FT_FI10
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P08775

Chain	Residue	Details
A	SER1847

site_id	SWS_FT_FI11
Number of Residues	6
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	LYS1859
A	LYS1866
A	LYS1873
A	LYS1887
A	LYS1922
A	LYS1936

site_id	SWS_FT_FI12
Number of Residues	8
Details	MOD_RES: Phosphotyrosine => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	TYR1860
A	TYR1867
A	TYR1874
A	TYR1881
A	TYR1909
A	TYR1916
A	TYR1923
A	TYR1930

site_id	SWS_FT_FI13
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:P08775

Chain	Residue	Details
A	THR1894

site_id	SWS_FT_FI14
Number of Residues	1
Details	MOD_RES: N6,N6-dimethyllysine => ECO:0000250\|UniProtKB:P08775

Chain	Residue	Details
A	LYS1908

site_id	SWS_FT_FI15
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); by NEDD4 => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	LYS1268

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)