9EI1

Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide

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	0000974	cellular_component	Prp19 complex
A	0001172	biological_process	RNA-templated transcription
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003723	molecular_function	RNA binding
A	0003899	molecular_function	DNA-directed RNA polymerase activity
A	0003968	molecular_function	RNA-directed 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	0005730	cellular_component	nucleolus
A	0005737	cellular_component	cytoplasm
A	0006353	biological_process	DNA-templated transcription termination
A	0006355	biological_process	regulation of DNA-templated transcription
A	0006366	biological_process	transcription by RNA polymerase II
A	0006368	biological_process	transcription elongation by RNA polymerase II
A	0008270	molecular_function	zinc ion binding
A	0010628	biological_process	positive regulation of gene expression
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0019900	molecular_function	kinase binding
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0033120	biological_process	positive regulation of RNA splicing
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0042789	biological_process	mRNA transcription by RNA polymerase II
A	0046872	molecular_function	metal ion binding
A	0050436	molecular_function	microfibril binding
A	1990841	molecular_function	promoter-specific chromatin binding
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0000781	cellular_component	chromosome, telomeric region
B	0001172	biological_process	RNA-templated transcription
B	0003677	molecular_function	DNA binding
B	0003682	molecular_function	chromatin binding
B	0003723	molecular_function	RNA binding
B	0003899	molecular_function	DNA-directed RNA polymerase activity
B	0003968	molecular_function	RNA-directed 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	0006366	biological_process	transcription by RNA polymerase II
B	0008270	molecular_function	zinc ion binding
B	0016020	cellular_component	membrane
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0016787	molecular_function	hydrolase activity
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	0003899	molecular_function	DNA-directed RNA polymerase activity
C	0005515	molecular_function	protein binding
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	0006366	biological_process	transcription by RNA polymerase II
D	0000428	cellular_component	DNA-directed RNA polymerase complex
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005665	cellular_component	RNA polymerase II, core complex
D	0005829	cellular_component	cytosol
D	0006366	biological_process	transcription by RNA polymerase II
D	0006367	biological_process	transcription initiation at RNA polymerase II promoter
D	0016607	cellular_component	nuclear speck
D	0031369	molecular_function	translation initiation factor binding
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0003899	molecular_function	DNA-directed RNA polymerase activity
E	0005515	molecular_function	protein binding
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	0005730	cellular_component	nucleolus
E	0005736	cellular_component	RNA polymerase I complex
E	0005829	cellular_component	cytosol
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	0050821	biological_process	protein stabilization
E	1990062	cellular_component	RPAP3/R2TP/prefoldin-like complex
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0001650	cellular_component	fibrillar center
F	0003899	molecular_function	DNA-directed 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	0005730	cellular_component	nucleolus
F	0005736	cellular_component	RNA polymerase I complex
F	0005829	cellular_component	cytosol
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	0000428	cellular_component	DNA-directed RNA polymerase complex
G	0000932	cellular_component	P-body
G	0000956	biological_process	nuclear-transcribed mRNA catabolic process
G	0003697	molecular_function	single-stranded DNA binding
G	0003723	molecular_function	RNA binding
G	0003727	molecular_function	single-stranded RNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005665	cellular_component	RNA polymerase II, core complex
G	0006366	biological_process	transcription by RNA polymerase II
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	0003677	molecular_function	DNA binding
H	0003697	molecular_function	single-stranded DNA binding
H	0003899	molecular_function	DNA-directed RNA polymerase activity
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
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	0005829	cellular_component	cytosol
H	0006366	biological_process	transcription by RNA polymerase II
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	0003899	molecular_function	DNA-directed RNA polymerase activity
I	0005515	molecular_function	protein binding
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	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	0003899	molecular_function	DNA-directed RNA polymerase activity
J	0005515	molecular_function	protein binding
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	0005829	cellular_component	cytosol
J	0006356	biological_process	regulation of transcription by RNA polymerase I
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	0003899	molecular_function	DNA-directed RNA polymerase activity
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005665	cellular_component	RNA polymerase II, core complex
K	0006366	biological_process	transcription by RNA polymerase II
K	0030275	molecular_function	LRR domain binding
L	0000428	cellular_component	DNA-directed RNA polymerase complex
L	0003899	molecular_function	DNA-directed RNA polymerase activity
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
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	0005829	cellular_component	cytosol
L	0006356	biological_process	regulation of 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
U	0000166	molecular_function	nucleotide binding
U	0000278	biological_process	mitotic cell cycle
U	0000724	biological_process	double-strand break repair via homologous recombination
U	0000993	molecular_function	RNA polymerase II complex binding
U	0003677	molecular_function	DNA binding
U	0003678	molecular_function	DNA helicase activity
U	0004386	molecular_function	helicase activity
U	0005524	molecular_function	ATP binding
U	0005634	cellular_component	nucleus
U	0005654	cellular_component	nucleoplasm
U	0005657	cellular_component	replication fork
U	0005694	cellular_component	chromosome
U	0005737	cellular_component	cytoplasm
U	0005829	cellular_component	cytosol
U	0006259	biological_process	DNA metabolic process
U	0006260	biological_process	DNA replication
U	0006281	biological_process	DNA repair
U	0006974	biological_process	DNA damage response
U	0009378	molecular_function	four-way junction helicase activity
U	0010605	biological_process	negative regulation of macromolecule metabolic process
U	0016787	molecular_function	hydrolase activity
U	0016853	molecular_function	isomerase activity
U	0016887	molecular_function	ATP hydrolysis activity
U	0034244	biological_process	negative regulation of transcription elongation by RNA polymerase II
U	0043138	molecular_function	3'-5' DNA helicase activity
U	0045934	biological_process	negative regulation of nucleobase-containing compound metabolic process
U	0046872	molecular_function	metal ion binding
U	0051301	biological_process	cell division
U	0051304	biological_process	chromosome separation
U	0071466	biological_process	cellular response to xenobiotic stimulus
U	0072757	biological_process	cellular response to camptothecin
U	0097550	cellular_component	transcription preinitiation complex
U	0140097	molecular_function	catalytic activity, acting on DNA
U	1990414	biological_process	replication-born double-strand break repair via sister chromatid exchange
U	1990506	biological_process	mitotic DNA-templated DNA replication
U	2000042	biological_process	negative regulation of double-strand break repair via homologous recombination

Functional Information from PROSITE/UniProt

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	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	TYR1839-SER1845
A	TYR1853-LYS1859
A	TYR1860-LYS1866
A	TYR1867-LYS1873
A	TYR1874-THR1880
A	TYR1888-THR1894
A	TYR1902-LYS1908
A	TYR1909-THR1915
A	TYR1916-LYS1922
A	TYR1629-ASN1635
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	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	9
Details	BINDING: BINDING => ECO:0000305|PubMed:28100692, ECO:0007744|PDB:5LB3, ECO:0007744|PDB:5LB5, ECO:0007744|PDB:5LBA

Chain	Residue	Details
U	PHE26
U	SER28
U	LYS30
U	GLN34
U	GLY55
U	ALA56
U	GLY57
U	LYS58
U	SER59

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	BINDING: BINDING => ECO:0007744|PDB:5LB5

Chain	Residue	Details
U	PRO53
A	ASP495
B	ASP792
A	CYS81
A	HIS84
A	CYS111
A	CYS114
A	CYS154
A	CYS184
A	ASN493

---

site_id	SWS_FT_FI3
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269|PubMed:28100692, ECO:0007744|PDB:5LB3, ECO:0007744|PDB:5LB5, ECO:0007744|PDB:5LB8, ECO:0007744|PDB:5LBA

Chain	Residue	Details
U	CYS411
U	CYS431
U	CYS434
I	CYS42
B	LYS942
B	ARG1078
B	ARG1085

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269|PubMed:28100692, ECO:0007744|PDB:5LB3, ECO:0007744|PDB:5LB5, ECO:0007744|PDB:5LBA

Chain	Residue	Details
U	CYS427
I	CYS89
I	CYS114
I	CYS119

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:D4ACP5

Chain	Residue	Details
U	SER488
A	SER217
A	SER1868

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
U	SER491

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	MOD_RES: Phosphoserine; by CDK1 => ECO:0000269|PubMed:28575661, ECO:0007744|PubMed:23186163

Chain	Residue	Details
U	SER727

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569

Chain	Residue	Details
U	SER815

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
U	THR839
A	THR1933
A	THR1863
A	THR1870
A	THR1877
A	THR1912
A	THR1915
A	THR1919
A	THR1926
A	THR1929

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:19690332

Chain	Residue	Details
A	SER1843

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685

Chain	Residue	Details
A	SER1845
A	SER1857
A	SER1861
A	SER1875

---

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	1
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:18669648

Chain	Residue	Details
A	SER1849

---

site_id	SWS_FT_FI14
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER1850
A	SER1864

---

site_id	SWS_FT_FI15
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332

Chain	Residue	Details
A	THR1854

---

site_id	SWS_FT_FI16
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:26566685

Chain	Residue	Details
A	LYS1859
A	LYS1866
A	LYS1873
A	LYS1887

---

site_id	SWS_FT_FI17
Number of Residues	5
Details	MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:26566685

Chain	Residue	Details
A	TYR1860
A	TYR1867
A	TYR1881
A	TYR1916
A	TYR1930

---

site_id	SWS_FT_FI18
Number of Residues	1
Details	MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:24275569

Chain	Residue	Details
A	TYR1874

---

site_id	SWS_FT_FI19
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER1878
A	SER1882

---

site_id	SWS_FT_FI20
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	THR1885

---

site_id	SWS_FT_FI21
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P08775

Chain	Residue	Details
A	THR1894

---

site_id	SWS_FT_FI22
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648

Chain	Residue	Details
A	SER1896

---

site_id	SWS_FT_FI23
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER1899

---

site_id	SWS_FT_FI24
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
A	SER1906

---

site_id	SWS_FT_FI25
Number of Residues	1
Details	MOD_RES: N6,N6-dimethyllysine => ECO:0000250|UniProtKB:P08775

Chain	Residue	Details
A	LYS1908

---

site_id	SWS_FT_FI26
Number of Residues	2
Details	MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:24275569

Chain	Residue	Details
A	TYR1909
A	TYR1923

---

site_id	SWS_FT_FI27
Number of Residues	3
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER1913
A	SER1920
A	SER1927

---

site_id	SWS_FT_FI28
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:21406692

Chain	Residue	Details
A	SER1917
A	SER1931

---

site_id	SWS_FT_FI29
Number of Residues	2
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000305|PubMed:26566685

Chain	Residue	Details
A	LYS1922
A	LYS1936

---

site_id	SWS_FT_FI30
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER1934

---

site_id	SWS_FT_FI31
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); by NEDD4 => ECO:0000269|PubMed:32142649, ECO:0000305|PubMed:32142654

Chain	Residue	Details
A	LYS1268

---