Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4YLN

E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed RNA polymerase activity
A	0006351	biological_process	DNA-templated transcription
A	0046983	molecular_function	protein dimerization activity
B	0003677	molecular_function	DNA binding
B	0003899	molecular_function	DNA-directed RNA polymerase activity
B	0006351	biological_process	DNA-templated transcription
B	0046983	molecular_function	protein dimerization activity
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed RNA polymerase activity
C	0006351	biological_process	DNA-templated transcription
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0032549	molecular_function	ribonucleoside binding
C	0034062	molecular_function	5'-3' RNA polymerase activity
D	0000287	molecular_function	magnesium ion binding
D	0000428	cellular_component	DNA-directed RNA polymerase complex
D	0003677	molecular_function	DNA binding
D	0003899	molecular_function	DNA-directed RNA polymerase activity
D	0005829	cellular_component	cytosol
D	0006351	biological_process	DNA-templated transcription
D	0008270	molecular_function	zinc ion binding
D	0016740	molecular_function	transferase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0034062	molecular_function	5'-3' RNA polymerase activity
D	0046872	molecular_function	metal ion binding
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed RNA polymerase activity
E	0006351	biological_process	DNA-templated transcription
E	0016740	molecular_function	transferase activity
E	0016779	molecular_function	nucleotidyltransferase activity
E	0034062	molecular_function	5'-3' RNA polymerase activity
F	0000976	molecular_function	transcription cis-regulatory region binding
F	0003677	molecular_function	DNA binding
F	0003700	molecular_function	DNA-binding transcription factor activity
F	0003899	molecular_function	DNA-directed RNA polymerase activity
F	0005515	molecular_function	protein binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006351	biological_process	DNA-templated transcription
F	0006352	biological_process	DNA-templated transcription initiation
F	0006355	biological_process	regulation of DNA-templated transcription
F	0009408	biological_process	response to heat
F	0010468	biological_process	regulation of gene expression
F	0016987	molecular_function	sigma factor activity
F	0045892	biological_process	negative regulation of DNA-templated transcription
F	1903865	cellular_component	sigma factor antagonist complex
F	2000142	biological_process	regulation of DNA-templated transcription initiation
G	0003677	molecular_function	DNA binding
G	0003899	molecular_function	DNA-directed RNA polymerase activity
G	0006351	biological_process	DNA-templated transcription
G	0046983	molecular_function	protein dimerization activity
H	0003677	molecular_function	DNA binding
H	0003899	molecular_function	DNA-directed RNA polymerase activity
H	0006351	biological_process	DNA-templated transcription
H	0046983	molecular_function	protein dimerization activity
I	0000428	cellular_component	DNA-directed RNA polymerase complex
I	0003677	molecular_function	DNA binding
I	0003899	molecular_function	DNA-directed RNA polymerase activity
I	0006351	biological_process	DNA-templated transcription
I	0016740	molecular_function	transferase activity
I	0016779	molecular_function	nucleotidyltransferase activity
I	0032549	molecular_function	ribonucleoside binding
I	0034062	molecular_function	5'-3' RNA polymerase activity
J	0000287	molecular_function	magnesium 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	0005829	cellular_component	cytosol
J	0006351	biological_process	DNA-templated transcription
J	0008270	molecular_function	zinc ion binding
J	0016740	molecular_function	transferase activity
J	0016779	molecular_function	nucleotidyltransferase activity
J	0034062	molecular_function	5'-3' RNA polymerase activity
J	0046872	molecular_function	metal ion binding
K	0000428	cellular_component	DNA-directed RNA polymerase complex
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed RNA polymerase activity
K	0006351	biological_process	DNA-templated transcription
K	0016740	molecular_function	transferase activity
K	0016779	molecular_function	nucleotidyltransferase activity
K	0034062	molecular_function	5'-3' RNA polymerase activity
L	0000976	molecular_function	transcription cis-regulatory region binding
L	0003677	molecular_function	DNA binding
L	0003700	molecular_function	DNA-binding transcription factor activity
L	0003899	molecular_function	DNA-directed RNA polymerase activity
L	0005515	molecular_function	protein binding
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0006351	biological_process	DNA-templated transcription
L	0006352	biological_process	DNA-templated transcription initiation
L	0006355	biological_process	regulation of DNA-templated transcription
L	0009408	biological_process	response to heat
L	0010468	biological_process	regulation of gene expression
L	0016987	molecular_function	sigma factor activity
L	0045892	biological_process	negative regulation of DNA-templated transcription
L	1903865	cellular_component	sigma factor antagonist complex
L	2000142	biological_process	regulation of DNA-templated transcription initiation
M	0003677	molecular_function	DNA binding
M	0003899	molecular_function	DNA-directed RNA polymerase activity
M	0006351	biological_process	DNA-templated transcription
M	0046983	molecular_function	protein dimerization activity
N	0003677	molecular_function	DNA binding
N	0003899	molecular_function	DNA-directed RNA polymerase activity
N	0006351	biological_process	DNA-templated transcription
N	0046983	molecular_function	protein dimerization activity
O	0000428	cellular_component	DNA-directed RNA polymerase complex
O	0003677	molecular_function	DNA binding
O	0003899	molecular_function	DNA-directed RNA polymerase activity
O	0006351	biological_process	DNA-templated transcription
O	0016740	molecular_function	transferase activity
O	0016779	molecular_function	nucleotidyltransferase activity
O	0032549	molecular_function	ribonucleoside binding
O	0034062	molecular_function	5'-3' RNA polymerase activity
P	0000287	molecular_function	magnesium ion binding
P	0000428	cellular_component	DNA-directed RNA polymerase complex
P	0003677	molecular_function	DNA binding
P	0003899	molecular_function	DNA-directed RNA polymerase activity
P	0005829	cellular_component	cytosol
P	0006351	biological_process	DNA-templated transcription
P	0008270	molecular_function	zinc ion binding
P	0016740	molecular_function	transferase activity
P	0016779	molecular_function	nucleotidyltransferase activity
P	0034062	molecular_function	5'-3' RNA polymerase activity
P	0046872	molecular_function	metal ion binding
Q	0000428	cellular_component	DNA-directed RNA polymerase complex
Q	0003677	molecular_function	DNA binding
Q	0003899	molecular_function	DNA-directed RNA polymerase activity
Q	0006351	biological_process	DNA-templated transcription
Q	0016740	molecular_function	transferase activity
Q	0016779	molecular_function	nucleotidyltransferase activity
Q	0034062	molecular_function	5'-3' RNA polymerase activity
R	0000976	molecular_function	transcription cis-regulatory region binding
R	0003677	molecular_function	DNA binding
R	0003700	molecular_function	DNA-binding transcription factor activity
R	0003899	molecular_function	DNA-directed RNA polymerase activity
R	0005515	molecular_function	protein binding
R	0005737	cellular_component	cytoplasm
R	0005829	cellular_component	cytosol
R	0006351	biological_process	DNA-templated transcription
R	0006352	biological_process	DNA-templated transcription initiation
R	0006355	biological_process	regulation of DNA-templated transcription
R	0009408	biological_process	response to heat
R	0010468	biological_process	regulation of gene expression
R	0016987	molecular_function	sigma factor activity
R	0045892	biological_process	negative regulation of DNA-templated transcription
R	1903865	cellular_component	sigma factor antagonist complex
R	2000142	biological_process	regulation of DNA-templated transcription initiation

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN D 1501

Chain	Residue
D	CYS70
D	CYS72
D	CYS85
D	CYS88

site_id	AC2
Number of Residues	5
Details	binding site for residue ZN D 1502

Chain	Residue
D	CYS814
D	ARG883
D	CYS888
D	CYS895
D	CYS898

site_id	AC3
Number of Residues	4
Details	binding site for residue MG D 1503

Chain	Residue
3	G15
D	ASP460
D	ASP462
D	ASP464

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN J 1501

Chain	Residue
J	CYS70
J	CYS72
J	CYS85
J	CYS88

site_id	AC5
Number of Residues	6
Details	binding site for residue ZN J 1502

Chain	Residue
J	CYS814
J	ARG883
J	CYS888
J	THR890
J	CYS895
J	CYS898

site_id	AC6
Number of Residues	2
Details	binding site for residue MG 6 101

Chain	Residue
6	U16
I	GLU565

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN P 1501

Chain	Residue
P	CYS70
P	CYS72
P	CYS85
P	CYS88

site_id	AC8
Number of Residues	5
Details	binding site for residue ZN P 1502

Chain	Residue
P	CYS814
P	ARG883
P	CYS888
P	CYS895
P	CYS898

site_id	AC9
Number of Residues	4
Details	binding site for residue MG P 1503

Chain	Residue
9	G15
P	ASP460
P	ASP462
P	ASP464

site_id	AD1
Number of Residues	8
Details	binding site for nucleotide GTP 3 13

Chain	Residue
2	DT15
2	DC16
2	DG17
3	G15
C	ARG529
C	ASN684
C	GLN688
C	LYS1065

site_id	AD2
Number of Residues	12
Details	binding site for nucleotide GTP 6 13

Chain	Residue
5	DC16
5	DG17
6	G15
I	GLN513
I	ARG529
I	PRO564
I	ASN568
I	ILE572
I	ASN684
I	GLN688
I	LYS1065
I	HIS1237

site_id	AD3
Number of Residues	11
Details	binding site for nucleotide GTP 9 13

Chain	Residue
8	DT15
8	DC16
8	DG17
9	G15
O	GLN513
O	ARG529
O	PRO564
O	ASN568
O	ASN684
O	GLN688
O	LYS1065

Functional Information from PROSITE/UniProt

site_id	PS00715
Number of Residues	14
Details	SIGMA70_1 Sigma-70 factors family signature 1. DLIQeGnIGLMkAV

Chain	Residue	Details
F	ASP403-VAL416

site_id	PS00716
Number of Residues	27
Details	SIGMA70_2 Sigma-70 factors family signature 2. TleEVGkqfdVTrerIrQIEakaLrkL

Chain	Residue	Details
F	THR572-LEU598

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

Chain	Residue	Details
C	GLY1063-VAL1075

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"HAMAP-Rule","id":"MF_01321","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	33
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01322","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"HAMAP-Rule","id":"MF_01322","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	57
Details	DNA binding: {"description":"H-T-H motif","evidences":[{"source":"HAMAP-Rule","id":"MF_00963","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	210
Details	Region: {"description":"Sigma-70 factor domain-2"}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	228
Details	Region: {"description":"Sigma-70 factor domain-3"}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	159
Details	Region: {"description":"Sigma-70 factor domain-4"}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	45
Details	Region: {"description":"Interaction with anti-sigma factors"}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	9
Details	Motif: {"description":"Interaction with polymerase core subunit RpoC"}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	3
Details	Site: {"description":"Interaction with anti-sigma factors"}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)