Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6B6H

The cryo-EM structure of a bacterial class I transcription activation complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006351	biological_process	DNA-templated transcription
A	0006352	biological_process	DNA-templated transcription initiation
A	0006879	biological_process	intracellular iron ion homeostasis
A	0008023	cellular_component	transcription elongation factor complex
A	0009408	biological_process	response to heat
A	0016020	cellular_component	membrane
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0031564	biological_process	transcription antitermination
A	0032784	biological_process	regulation of DNA-templated transcription elongation
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0036460	biological_process	cellular response to cell envelope stress
A	0042128	biological_process	nitrate assimilation
A	0044780	biological_process	bacterial-type flagellum assembly
A	0046983	molecular_function	protein dimerization activity
A	0048870	biological_process	cell motility
A	0071973	biological_process	bacterial-type flagellum-dependent cell motility
A	0090605	biological_process	submerged biofilm formation
A	2000142	biological_process	regulation of DNA-templated transcription initiation
B	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0003677	molecular_function	DNA binding
B	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006351	biological_process	DNA-templated transcription
B	0006352	biological_process	DNA-templated transcription initiation
B	0006879	biological_process	intracellular iron ion homeostasis
B	0008023	cellular_component	transcription elongation factor complex
B	0009408	biological_process	response to heat
B	0016020	cellular_component	membrane
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0031564	biological_process	transcription antitermination
B	0032784	biological_process	regulation of DNA-templated transcription elongation
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0036460	biological_process	cellular response to cell envelope stress
B	0042128	biological_process	nitrate assimilation
B	0044780	biological_process	bacterial-type flagellum assembly
B	0046983	molecular_function	protein dimerization activity
B	0048870	biological_process	cell motility
B	0071973	biological_process	bacterial-type flagellum-dependent cell motility
B	0090605	biological_process	submerged biofilm formation
B	2000142	biological_process	regulation of DNA-templated transcription initiation
C	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
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	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006351	biological_process	DNA-templated transcription
C	0006352	biological_process	DNA-templated transcription initiation
C	0006879	biological_process	intracellular iron ion homeostasis
C	0008023	cellular_component	transcription elongation factor complex
C	0009408	biological_process	response to heat
C	0016020	cellular_component	membrane
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0031564	biological_process	transcription antitermination
C	0032549	molecular_function	ribonucleoside binding
C	0032784	biological_process	regulation of DNA-templated transcription elongation
C	0034062	molecular_function	5'-3' RNA polymerase activity
C	0036460	biological_process	cellular response to cell envelope stress
C	0042128	biological_process	nitrate assimilation
C	0044780	biological_process	bacterial-type flagellum assembly
C	0046677	biological_process	response to antibiotic
C	0048870	biological_process	cell motility
C	0071973	biological_process	bacterial-type flagellum-dependent cell motility
C	0090605	biological_process	submerged biofilm formation
C	2000142	biological_process	regulation of DNA-templated transcription initiation
D	0000287	molecular_function	magnesium ion binding
D	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
D	0000428	cellular_component	DNA-directed RNA polymerase complex
D	0003677	molecular_function	DNA binding
D	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
D	0005515	molecular_function	protein binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006351	biological_process	DNA-templated transcription
D	0006352	biological_process	DNA-templated transcription initiation
D	0006879	biological_process	intracellular iron ion homeostasis
D	0008023	cellular_component	transcription elongation factor complex
D	0008270	molecular_function	zinc ion binding
D	0009408	biological_process	response to heat
D	0016020	cellular_component	membrane
D	0016740	molecular_function	transferase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0031564	biological_process	transcription antitermination
D	0032784	biological_process	regulation of DNA-templated transcription elongation
D	0034062	molecular_function	5'-3' RNA polymerase activity
D	0036460	biological_process	cellular response to cell envelope stress
D	0042128	biological_process	nitrate assimilation
D	0044780	biological_process	bacterial-type flagellum assembly
D	0046677	biological_process	response to antibiotic
D	0046872	molecular_function	metal ion binding
D	0048870	biological_process	cell motility
D	0071973	biological_process	bacterial-type flagellum-dependent cell motility
D	0090605	biological_process	submerged biofilm formation
D	2000142	biological_process	regulation of DNA-templated transcription initiation
E	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
E	0005829	cellular_component	cytosol
E	0006351	biological_process	DNA-templated transcription
E	0006352	biological_process	DNA-templated transcription initiation
E	0006879	biological_process	intracellular iron ion homeostasis
E	0008023	cellular_component	transcription elongation factor complex
E	0009408	biological_process	response to heat
E	0016740	molecular_function	transferase activity
E	0016779	molecular_function	nucleotidyltransferase activity
E	0030880	cellular_component	RNA polymerase complex
E	0031564	biological_process	transcription antitermination
E	0032784	biological_process	regulation of DNA-templated transcription elongation
E	0034062	molecular_function	5'-3' RNA polymerase activity
E	0036460	biological_process	cellular response to cell envelope stress
E	0042128	biological_process	nitrate assimilation
E	0044780	biological_process	bacterial-type flagellum assembly
E	0048870	biological_process	cell motility
E	0065003	biological_process	protein-containing complex assembly
E	0071973	biological_process	bacterial-type flagellum-dependent cell motility
E	0090605	biological_process	submerged biofilm formation
E	2000142	biological_process	regulation of DNA-templated transcription initiation
F	0000345	cellular_component	cytosolic DNA-directed RNA polymerase complex
F	0003677	molecular_function	DNA binding
F	0003700	molecular_function	DNA-binding transcription factor 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	0000166	molecular_function	nucleotide binding
G	0003677	molecular_function	DNA binding
G	0003680	molecular_function	minor groove of adenine-thymine-rich DNA binding
G	0003700	molecular_function	DNA-binding transcription factor activity
G	0005515	molecular_function	protein binding
G	0005829	cellular_component	cytosol
G	0006351	biological_process	DNA-templated transcription
G	0006355	biological_process	regulation of DNA-templated transcription
G	0008301	molecular_function	DNA binding, bending
G	0030552	molecular_function	cAMP binding
G	0032993	cellular_component	protein-DNA complex
G	0042802	molecular_function	identical protein binding
G	0043565	molecular_function	sequence-specific DNA binding
G	0045013	biological_process	carbon catabolite repression of transcription
G	0045892	biological_process	negative regulation of DNA-templated transcription
G	0045893	biological_process	positive regulation of DNA-templated transcription
H	0000166	molecular_function	nucleotide binding
H	0003677	molecular_function	DNA binding
H	0003680	molecular_function	minor groove of adenine-thymine-rich DNA binding
H	0003700	molecular_function	DNA-binding transcription factor activity
H	0005515	molecular_function	protein binding
H	0005829	cellular_component	cytosol
H	0006351	biological_process	DNA-templated transcription
H	0006355	biological_process	regulation of DNA-templated transcription
H	0008301	molecular_function	DNA binding, bending
H	0030552	molecular_function	cAMP binding
H	0032993	cellular_component	protein-DNA complex
H	0042802	molecular_function	identical protein binding
H	0043565	molecular_function	sequence-specific DNA binding
H	0045013	biological_process	carbon catabolite repression of transcription
H	0045892	biological_process	negative regulation of DNA-templated transcription
H	0045893	biological_process	positive regulation of DNA-templated transcription
I	0003677	molecular_function	DNA binding
I	0003899	molecular_function	DNA-directed 5'-3' RNA polymerase activity
I	0006351	biological_process	DNA-templated transcription

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue ZN D 1501

Chain	Residue
D	CYS70
D	LEU71
D	CYS72
D	CYS85
D	CYS88

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

Chain	Residue
D	CYS898
D	CYS814
D	THR816
D	CYS888
D	CYS895

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

Chain	Residue
3	G3
D	ASP460
D	ASP462
D	ASP464

site_id	AC4
Number of Residues	12
Details	binding site for residue CMP G 301

Chain	Residue
G	VAL49
G	LEU61
G	ILE70
G	GLY71
G	GLU72
G	LEU73
G	ARG82
G	SER83
G	ALA84
G	VAL86
G	ARG123
H	SER128

site_id	AC5
Number of Residues	12
Details	binding site for residue CMP H 301

Chain	Residue
G	LEU124
G	GLN125
G	SER128
H	LEU61
H	GLY71
H	GLU72
H	LEU73
H	GLY74
H	ARG82
H	SER83
H	ALA84
H	THR127

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
C	GLY1063-VAL1075

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	PS00042
Number of Residues	24
Details	HTH_CRP_1 Crp-type HTH domain signature. ITRqeIGqIVGcSreTv.GRiLkmL

Chain	Residue	Details
G	ILE167-LEU190

site_id	PS00888
Number of Residues	17
Details	CNMP_BINDING_1 Cyclic nucleotide-binding domain signature 1. LIhQGEkAEtLYYIvkG

Chain	Residue	Details
G	LEU29-GLY45

site_id	PS00889
Number of Residues	19
Details	CNMP_BINDING_2 Cyclic nucleotide-binding domain signature 2. IGElGLfeegqe.....RSAwVrA

Chain	Residue	Details
G	ILE70-ALA88

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	MOD_RES: ADP-ribosylarginine => ECO:0000269\|PubMed:4371081

Chain	Residue	Details
I	ARG265
D	CYS895
D	CYS898
H	SER179-ARG185
D	CYS85
D	CYS88
D	ASP460
D	ASP462
D	ASP464
D	CYS814
D	CYS888

site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:21696463

Chain	Residue	Details
I	LYS297
H	THR127
H	ALA135
H	GLN170
G	GLY71
G	ARG82
G	THR127
G	ALA135
G	GLN170
H	GLY56
H	GLY71
H	ARG82

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: N6-acetyllysine; by PatZ => ECO:0000269\|PubMed:21696463

Chain	Residue	Details
I	LYS298
H	GLU96

site_id	SWS_FT_FI4
Number of Residues	2
Details	SITE: Activating region 2 (AR2); probably contacts the N-terminus of RpoA => ECO:0000269\|PubMed:15520470, ECO:0000269\|PubMed:8978616

Chain	Residue	Details
G	LYS101
H	LYS101

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:18723842

Chain	Residue	Details
G	LYS100
H	LYS100

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