8YFR

Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0000785	cellular_component	chromatin
A	0001172	biological_process	RNA-templated transcription
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed RNA polymerase activity
A	0003968	molecular_function	RNA-directed RNA polymerase activity
A	0005634	cellular_component	nucleus
A	0005665	cellular_component	RNA polymerase II, core complex
A	0006325	biological_process	chromatin organization
A	0006351	biological_process	DNA-templated transcription
A	0006366	biological_process	transcription by RNA polymerase II
A	0006367	biological_process	transcription initiation at RNA polymerase II promoter
A	0006368	biological_process	transcription elongation by RNA polymerase II
A	0006369	biological_process	termination of RNA polymerase II transcription
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0019985	biological_process	translesion synthesis
A	0030643	biological_process	intracellular phosphate ion homeostasis
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0046872	molecular_function	metal ion binding
A	0140463	molecular_function	chromatin-protein adaptor activity
A	0180034	biological_process	co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0001172	biological_process	RNA-templated transcription
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA 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	0005634	cellular_component	nucleus
B	0005665	cellular_component	RNA polymerase II, core complex
B	0005721	cellular_component	pericentric heterochromatin
B	0006351	biological_process	DNA-templated transcription
B	0006366	biological_process	transcription by RNA polymerase II
B	0006367	biological_process	transcription initiation at RNA polymerase II promoter
B	0006368	biological_process	transcription elongation by RNA polymerase II
B	0008270	molecular_function	zinc ion binding
B	0016740	molecular_function	transferase activity
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
B	0140727	biological_process	siRNA-mediated pericentric heterochromatin formation
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0001172	biological_process	RNA-templated transcription
C	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed RNA polymerase activity
C	0003968	molecular_function	RNA-directed RNA polymerase activity
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005665	cellular_component	RNA polymerase II, core complex
C	0006351	biological_process	DNA-templated transcription
C	0006366	biological_process	transcription by RNA polymerase II
C	0006367	biological_process	transcription initiation at RNA polymerase II promoter
C	0006368	biological_process	transcription elongation by RNA polymerase II
C	0006369	biological_process	termination of RNA polymerase II transcription
C	0046872	molecular_function	metal ion binding
C	0046983	molecular_function	protein dimerization activity
D	0000166	molecular_function	nucleotide binding
D	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
D	0000932	cellular_component	P-body
D	0001172	biological_process	RNA-templated transcription
D	0003697	molecular_function	single-stranded DNA binding
D	0003727	molecular_function	single-stranded RNA binding
D	0003899	molecular_function	DNA-directed RNA polymerase activity
D	0003968	molecular_function	RNA-directed RNA polymerase activity
D	0005634	cellular_component	nucleus
D	0005665	cellular_component	RNA polymerase II, core complex
D	0005737	cellular_component	cytoplasm
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	0006368	biological_process	transcription elongation by RNA polymerase II
D	0030880	cellular_component	RNA polymerase complex
D	0031369	molecular_function	translation initiation factor binding
D	0045948	biological_process	positive regulation of translational initiation
E	0001172	biological_process	RNA-templated transcription
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed RNA polymerase activity
E	0003968	molecular_function	RNA-directed RNA polymerase activity
E	0005634	cellular_component	nucleus
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	0006360	biological_process	transcription by RNA polymerase I
E	0006361	biological_process	transcription initiation at RNA polymerase I promoter
E	0006362	biological_process	transcription elongation by RNA polymerase I
E	0006363	biological_process	termination of RNA polymerase I transcription
E	0006366	biological_process	transcription by RNA polymerase II
E	0006367	biological_process	transcription initiation at RNA polymerase II promoter
E	0006368	biological_process	transcription elongation by RNA polymerase II
E	0006383	biological_process	transcription by RNA polymerase III
E	0006384	biological_process	transcription initiation at RNA polymerase III promoter
E	0006386	biological_process	termination of RNA polymerase III transcription
E	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
E	0042797	biological_process	tRNA transcription by RNA polymerase III
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0003677	molecular_function	DNA binding
F	0003899	molecular_function	DNA-directed 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	0005736	cellular_component	RNA polymerase I complex
F	0006351	biological_process	DNA-templated transcription
F	0006360	biological_process	transcription by RNA polymerase I
F	0006362	biological_process	transcription elongation 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	0001172	biological_process	RNA-templated transcription
G	0003676	molecular_function	nucleic acid binding
G	0003697	molecular_function	single-stranded DNA binding
G	0003727	molecular_function	single-stranded RNA binding
G	0003968	molecular_function	RNA-directed RNA polymerase activity
G	0005634	cellular_component	nucleus
G	0005665	cellular_component	RNA polymerase II, core complex
G	0005737	cellular_component	cytoplasm
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	0006368	biological_process	transcription elongation by RNA polymerase II
G	0010590	biological_process	regulation of septum digestion after cytokinesis
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	0001172	biological_process	RNA-templated transcription
H	0003899	molecular_function	DNA-directed RNA polymerase activity
H	0003968	molecular_function	RNA-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	0005736	cellular_component	RNA polymerase I complex
H	0006351	biological_process	DNA-templated transcription
H	0006360	biological_process	transcription by RNA polymerase I
H	0006361	biological_process	transcription initiation at RNA polymerase I promoter
H	0006362	biological_process	transcription elongation by RNA polymerase I
H	0006363	biological_process	termination of RNA polymerase I transcription
H	0006366	biological_process	transcription by RNA polymerase II
H	0006367	biological_process	transcription initiation at RNA polymerase II promoter
H	0006368	biological_process	transcription elongation by RNA polymerase II
H	0006383	biological_process	transcription by RNA polymerase III
H	0006384	biological_process	transcription initiation at RNA polymerase III promoter
H	0006386	biological_process	termination of RNA polymerase III transcription
H	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
H	0042797	biological_process	tRNA transcription by RNA polymerase III
I	0000428	cellular_component	DNA-directed RNA polymerase complex
I	0001172	biological_process	RNA-templated transcription
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 RNA polymerase activity
I	0003968	molecular_function	RNA-directed RNA polymerase activity
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	0006368	biological_process	transcription elongation by RNA polymerase II
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 RNA polymerase activity
J	0005634	cellular_component	nucleus
J	0005665	cellular_component	RNA polymerase II, core complex
J	0005666	cellular_component	RNA polymerase III complex
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	0001172	biological_process	RNA-templated transcription
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed RNA polymerase activity
K	0003968	molecular_function	RNA-directed 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	0006367	biological_process	transcription initiation at RNA polymerase II promoter
K	0006368	biological_process	transcription elongation by RNA polymerase II
K	0006369	biological_process	termination of RNA polymerase II transcription
K	0046983	molecular_function	protein dimerization activity
L	0001172	biological_process	RNA-templated transcription
L	0003677	molecular_function	DNA binding
L	0003899	molecular_function	DNA-directed RNA polymerase activity
L	0003968	molecular_function	RNA-directed 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	0005777	cellular_component	peroxisome
L	0006351	biological_process	DNA-templated transcription
L	0006360	biological_process	transcription by RNA polymerase I
L	0006361	biological_process	transcription initiation at RNA polymerase I promoter
L	0006362	biological_process	transcription elongation by RNA polymerase I
L	0006363	biological_process	termination of RNA polymerase I transcription
L	0006366	biological_process	transcription by RNA polymerase II
L	0006367	biological_process	transcription initiation at RNA polymerase II promoter
L	0006368	biological_process	transcription elongation by RNA polymerase II
L	0006383	biological_process	transcription by RNA polymerase III
L	0006384	biological_process	transcription initiation at RNA polymerase III promoter
L	0006386	biological_process	termination of RNA polymerase III transcription
L	0008270	molecular_function	zinc ion binding
L	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
L	0042797	biological_process	tRNA transcription by RNA polymerase III
L	0046872	molecular_function	metal ion binding
R	0000448	biological_process	cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
R	0000956	biological_process	nuclear-transcribed mRNA catabolic process
R	0003676	molecular_function	nucleic acid binding
R	0003723	molecular_function	RNA binding
R	0004518	molecular_function	nuclease activity
R	0004527	molecular_function	exonuclease activity
R	0004534	molecular_function	5'-3' RNA exonuclease activity
R	0005634	cellular_component	nucleus
R	0006139	biological_process	nucleobase-containing compound metabolic process
R	0006351	biological_process	DNA-templated transcription
R	0006353	biological_process	DNA-templated transcription termination
R	0006364	biological_process	rRNA processing
R	0006397	biological_process	mRNA processing
R	0016787	molecular_function	hydrolase activity
R	0019843	molecular_function	rRNA binding
R	0030846	biological_process	termination of RNA polymerase II transcription, poly(A)-coupled
R	0030847	biological_process	termination of RNA polymerase II transcription, exosome-dependent
R	0034244	biological_process	negative regulation of transcription elongation by RNA polymerase II
R	0043144	biological_process	sno(s)RNA processing
R	0071028	biological_process	nuclear mRNA surveillance
R	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
R	0110155	biological_process	NAD-cap decapping
R	1904595	biological_process	positive regulation of termination of RNA polymerase II transcription
S	0000166	molecular_function	nucleotide binding
S	0000448	biological_process	cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
S	0000463	biological_process	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
S	0000466	biological_process	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
S	0000956	biological_process	nuclear-transcribed mRNA catabolic process
S	0003723	molecular_function	RNA binding
S	0004518	molecular_function	nuclease activity
S	0005634	cellular_component	nucleus
S	0005829	cellular_component	cytosol
S	0016787	molecular_function	hydrolase activity
S	0030234	molecular_function	enzyme regulator activity
S	0030846	biological_process	termination of RNA polymerase II transcription, poly(A)-coupled
S	0031087	biological_process	deadenylation-independent decapping of nuclear-transcribed mRNA
S	0034353	molecular_function	mRNA 5'-diphosphatase activity
S	0046872	molecular_function	metal ion binding
S	0071035	biological_process	nuclear polyadenylation-dependent rRNA catabolic process
S	0110155	biological_process	NAD-cap decapping
S	1904595	biological_process	positive regulation of termination of RNA polymerase II transcription
S	1990174	molecular_function	phosphodiesterase decapping endonuclease activity

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	TYR1560-SER1566
A	TYR1567-SER1573
A	TYR1574-SER1580
A	TYR1581-SER1587
A	TYR1588-SER1594
A	TYR1595-SER1601
A	TYR1602-SER1608
A	TYR1609-SER1615
A	TYR1616-SER1622

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

Chain	Residue	Details
C	ASN30-PRO70

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

Chain	Residue	Details
I	PHE6-CYS32

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

Chain	Residue	Details
E	HIS146-GLU159

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

Chain	Residue	Details
F	THR86-GLN100

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

Chain	Residue	Details
J	ILE2-GLY11

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

Chain	Residue	Details
K	PHE35-PRO66

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

Chain	Residue	Details
B	GLY977-THR989

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