Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5FLM

Structure of transcribing mammalian RNA polymerase II

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0000791	cellular_component	euchromatin
A	0001046	molecular_function	core promoter sequence-specific DNA binding
A	0001055	molecular_function	RNA polymerase II activity
A	0001172	biological_process	RNA-templated transcription
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
A	0003968	molecular_function	RNA-dependent RNA polymerase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005665	cellular_component	RNA polymerase II, core complex
A	0005694	cellular_component	chromosome
A	0005737	cellular_component	cytoplasm
A	0006351	biological_process	DNA-templated transcription
A	0006366	biological_process	transcription by RNA polymerase II
A	0008270	molecular_function	zinc ion binding
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0031981	cellular_component	nuclear lumen
A	0046872	molecular_function	metal ion binding
A	0071667	molecular_function	DNA/RNA hybrid 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	0005515	molecular_function	protein binding
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	0008270	molecular_function	zinc ion binding
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0016787	molecular_function	hydrolase activity
B	0032549	molecular_function	ribonucleoside binding
B	0046872	molecular_function	metal ion binding
B	0071667	molecular_function	DNA/RNA hybrid binding
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0001055	molecular_function	RNA polymerase II activity
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	0008270	molecular_function	zinc ion binding
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	0006366	biological_process	transcription by RNA polymerase II
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	0034402	biological_process	obsolete recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex
D	0044237	biological_process	cellular metabolic process
E	0000428	cellular_component	DNA-directed RNA polymerase complex
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	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005665	cellular_component	RNA polymerase II, core complex
E	0005666	cellular_component	RNA polymerase III complex
E	0005730	cellular_component	nucleolus
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
E	0055029	cellular_component	nuclear DNA-directed RNA polymerase complex
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0001054	molecular_function	RNA polymerase I activity
F	0001055	molecular_function	RNA polymerase II activity
F	0001056	molecular_function	RNA polymerase III activity
F	0003677	molecular_function	DNA binding
F	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
F	0005634	cellular_component	nucleus
F	0005665	cellular_component	RNA polymerase II, core complex
F	0005666	cellular_component	RNA polymerase III complex
F	0005730	cellular_component	nucleolus
F	0005736	cellular_component	RNA polymerase I complex
F	0006351	biological_process	DNA-templated transcription
F	0006360	biological_process	transcription by RNA polymerase I
F	0006366	biological_process	transcription by RNA polymerase II
F	0042797	biological_process	tRNA transcription by RNA polymerase III
G	0000291	biological_process	obsolete nuclear-transcribed mRNA catabolic process, exonucleolytic
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	0003723	molecular_function	RNA binding
G	0003727	molecular_function	single-stranded RNA binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
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	0006366	biological_process	transcription by RNA polymerase II
G	0006367	biological_process	transcription initiation at RNA polymerase II promoter
G	0031090	cellular_component	organelle membrane
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	0001054	molecular_function	RNA polymerase I activity
H	0001055	molecular_function	RNA polymerase II activity
H	0001056	molecular_function	RNA polymerase III activity
H	0003697	molecular_function	single-stranded DNA binding
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	0005666	cellular_component	RNA polymerase III complex
H	0005730	cellular_component	nucleolus
H	0005736	cellular_component	RNA polymerase I complex
H	0006351	biological_process	DNA-templated transcription
H	0006360	biological_process	transcription by RNA polymerase I
H	0006366	biological_process	transcription by RNA polymerase II
H	0006383	biological_process	transcription by RNA polymerase III
H	0031090	cellular_component	organelle membrane
H	0032993	cellular_component	protein-DNA complex
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	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	0001054	molecular_function	RNA polymerase I activity
J	0001055	molecular_function	RNA polymerase II activity
J	0001056	molecular_function	RNA polymerase III activity
J	0003677	molecular_function	DNA binding
J	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0005665	cellular_component	RNA polymerase II, core complex
J	0005666	cellular_component	RNA polymerase III complex
J	0005730	cellular_component	nucleolus
J	0005736	cellular_component	RNA polymerase I complex
J	0006351	biological_process	DNA-templated transcription
J	0006360	biological_process	transcription by RNA polymerase I
J	0006366	biological_process	transcription by RNA polymerase II
J	0008270	molecular_function	zinc ion binding
J	0042797	biological_process	tRNA transcription by RNA polymerase III
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	0000428	cellular_component	DNA-directed RNA polymerase complex
L	0001054	molecular_function	RNA polymerase I activity
L	0001055	molecular_function	RNA polymerase II activity
L	0001056	molecular_function	RNA polymerase III 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	0005730	cellular_component	nucleolus
L	0005736	cellular_component	RNA polymerase I complex
L	0006351	biological_process	DNA-templated transcription
L	0006360	biological_process	transcription by RNA polymerase I
L	0006366	biological_process	transcription by RNA polymerase II
L	0006383	biological_process	transcription by RNA polymerase III
L	0008270	molecular_function	zinc ion binding
L	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 2488

Chain	Residue
A	CYS71
A	THR73
A	CYS74
A	CYS81
A	HIS84

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN A 2489

Chain	Residue
A	CYS184
A	CYS111
A	CYS114
A	CYS154
A	GLY183

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 2490

Chain	Residue
A	ASP495
A	ASP497
A	ASP499
P	C20

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 2175

Chain	Residue
B	CYS1119
B	CYS1122
B	CYS1137
B	CYS1140

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 1272

Chain	Residue
C	CYS88
C	CYS90
C	CYS94
C	CYS97

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN I 1126

Chain	Residue
I	CYS17
I	CYS20
I	CYS39
I	CYS42

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN I 1127

Chain	Residue
I	CYS86
I	CYS89
I	CYS114
I	CYS119

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN J 1068

Chain	Residue
J	CYS7
J	CYS10
J	CYS44
J	CYS45

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN L 1059

Chain	Residue
L	CYS19
L	CYS22
L	THR24
L	CYS36
L	CYS39

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
C	ASP136-ILE148

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	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

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

Chain	Residue	Details
I	TYR112-HIS118

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

Chain	Residue	Details
J	ILE2-GLY11

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	MOD_RES: Phosphoserine; by CK2 => ECO:0000250\|UniProtKB:O88828

Chain	Residue	Details
F	SER2
A	CYS154
A	ARG1421
J	CYS45

site_id	SWS_FT_FI2
Number of Residues	11
Details	BINDING: BINDING => ECO:0000269\|PubMed:26789250, ECO:0000269\|PubMed:28892040, ECO:0007744\|PDB:5FLM, ECO:0007744\|PDB:5OIK

Chain	Residue	Details
A	CYS71
A	ASP499
A	ARG1416
A	CYS74
A	CYS81
A	HIS84
A	CYS111
A	CYS114
A	CYS184
A	LYS346
A	ARG460

site_id	SWS_FT_FI3
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:28892040, ECO:0007744\|PDB:5OIK

Chain	Residue	Details
A	ARG358
I	CYS20
I	CYS39
I	CYS42

site_id	SWS_FT_FI4
Number of Residues	2
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	ASN493
A	ASP495
I	CYS119
B	ARG1085
B	CYS1119
B	CYS1122
B	CYS1137
B	CYS1140

site_id	SWS_FT_FI5
Number of Residues	1
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P04050

Chain	Residue	Details
A	ASP497

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: N-acetylmethionine => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	MET1

site_id	SWS_FT_FI7
Number of Residues	22
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	SER27
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_FI8
Number of Residues	1
Details	MOD_RES: Omega-N-methylated arginine => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	ARG1603

site_id	SWS_FT_FI9
Number of Residues	1
Details	MOD_RES: Symmetric dimethylarginine; alternate => ECO:0000250\|UniProtKB:P24928

Chain	Residue	Details
A	ARG1810

site_id	SWS_FT_FI10
Number of Residues	1
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250\|UniProtKB:P08775

Chain	Residue	Details
A	LYS1838

site_id	SWS_FT_FI11
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_FI12
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P08775

Chain	Residue	Details
A	SER1847

site_id	SWS_FT_FI13
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_FI14
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_FI15
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:P08775

Chain	Residue	Details
A	THR1894

site_id	SWS_FT_FI16
Number of Residues	1
Details	MOD_RES: N6,N6-dimethyllysine => ECO:0000250\|UniProtKB:P08775

Chain	Residue	Details
A	LYS1908

site_id	SWS_FT_FI17
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)