1RP3 | pdb_00001rp3

Cocrystal structure of the flagellar sigma/anti-sigma complex, Sigma-28/FlgM

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d1rp3h_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Anti-sigma factor FlgM	Anti-sigma factor FlgM	Anti-sigma factor FlgM	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
F	d1rp3f_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Anti-sigma factor FlgM	Anti-sigma factor FlgM	Anti-sigma factor FlgM	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
D	d1rp3d_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Anti-sigma factor FlgM	Anti-sigma factor FlgM	Anti-sigma factor FlgM	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d1rp3b_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Anti-sigma factor FlgM	Anti-sigma factor FlgM	Anti-sigma factor FlgM	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
G	d1rp3g1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma3 domain	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
G	d1rp3g2	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma4 domain	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
G	d1rp3g3	All alpha proteins	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
E	d1rp3e1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma3 domain	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
E	d1rp3e2	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma4 domain	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
E	d1rp3e3	All alpha proteins	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
C	d1rp3c1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma3 domain	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
C	d1rp3c2	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma4 domain	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
C	d1rp3c3	All alpha proteins	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1rp3a1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma3 domain	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1rp3a2	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma4 domain	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1rp3a3	All alpha proteins	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma factor sigma-28 (FliA)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1rp3a4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Anti-sigma factor FlgM	8040794	3001384	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Anti-sigma factor FlgM	8040794	3001384	SCOP2B (2022-06-29)
B	SCOP2 Family	Anti-sigma factor FlgM	8028415	4000792	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Anti-sigma factor FlgM	8040794	3001384	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	Sigma factor domain-like	8040789	3000953	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8040791	3001393	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sigma factor domain-like	8040792	3000953	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sigma factor domain-like	8040789	3000953	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8040791	3001393	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sigma factor domain-like	8040792	3000953	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8040791	3001393	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sigma factor domain-like	8040789	3000953	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sigma factor domain-like	8040792	3000953	SCOP2B (2022-06-29)
A	SCOP2 Family	Sigma3 domain	8028410	4003497	SCOP2 (2022-06-29)
A	SCOP2 Family	Sigma2 domain of RNA polymerase sigma factors	8028412	4003741	SCOP2 (2022-06-29)
A	SCOP2 Family	Sigma4 domain	8028413	4003503	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sigma factor domain-like	8040789	3000953	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sigma2 domain of RNA polymerase sigma factors	8040791	3001393	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sigma factor domain-like	8040792	3000953	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	SRP_SPB	e1rp3H2	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: SRP_SPB	ECOD (develop294)
F	Stathmin	e1rp3F1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Stathmin	ECOD (develop294)
D	Stathmin	e1rp3D1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Stathmin	ECOD (develop294)
B	FlgM	e1rp3B1	A: extended segments	X: Anti-sigma factor FlgM	H: Anti-sigma factor FlgM	T: Anti-sigma factor FlgM	F: FlgM	ECOD (develop294)
G	Homeodomain	e1rp3G1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Homeodomain	ECOD (develop294)
G	Ion_trans_2	e1rp3G3	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (develop294)
E	Homeodomain	e1rp3E1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Homeodomain	ECOD (develop294)
E	Ion_trans_2	e1rp3E3	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (develop294)
C	Homeodomain	e1rp3C1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Homeodomain	ECOD (develop294)
C	Ion_trans_2	e1rp3C3	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (develop294)
A	Sigma70_r3	e1rp3A1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Sigma70_r3	ECOD (develop294)
A	Sigma70_r4	e1rp3A2	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Sigma70_r4	ECOD (develop294)
A	Sigma70_r2	e1rp3A3	A: a+b two layers	X: Sigma2 domain-like	H: Sigma2 domain of RNA polymerase sigma factors	T: Sigma2 domain of RNA polymerase sigma factors	F: Sigma70_r2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	6.10.140.150	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
H	6.10.140.30	Special	Helix non-globular	Helix Hairpins	Anti-sigma-28 factor FlgM	CATH (4.3.0)
F	6.10.140.150	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
F	6.10.140.30	Special	Helix non-globular	Helix Hairpins	Anti-sigma-28 factor FlgM	CATH (4.3.0)
D	6.10.140.150	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
D	6.10.140.30	Special	Helix non-globular	Helix Hairpins	Anti-sigma-28 factor FlgM	CATH (4.3.0)
B	6.10.140.150	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	6.10.140.30	Special	Helix non-globular	Helix Hairpins	Anti-sigma-28 factor FlgM	CATH (4.3.0)
G	1.10.1740.10	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)
G	1.20.140.160	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
E	1.10.1740.10	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)
E	1.20.140.160	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
C	1.10.1740.10	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)
C	1.20.140.160	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
A	1.10.1740.10	Mainly Alpha	Orthogonal Bundle	Rna Polymerase Sigma Factor	Chain: A	CATH (4.3.0)
A	1.20.140.160	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF04316	Anti-sigma-28 factor, FlgM (FlgM)	Anti-sigma-28 factor, FlgM	-	Family
A, C, E, G	PF04539	Sigma-70 region 3 (Sigma70_r3)	Sigma-70 region 3	-	Family
A, C, E, G	PF04542	Sigma-70 region 2 (Sigma70_r2)	Sigma-70 region 2	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA ...	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2].	Domain
A, C, E, G	PF04545	Sigma-70, region 4 (Sigma70_r4)	Sigma-70, region 4	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix fami ...	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	anti sigma factor FlgM	transcription factor binding transcription coregulator binding protein binding binding sigma factor antagonist activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	-	protein-containing complex sigma factor antagonist complex transcription regulator complex
A, C, E, G	RNA polymerase sigma factor SIGMA-28 (FliA)	DNA binding binding nucleic acid binding protein binding antisigma factor binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding protein binding antisigma factor binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups transcription regulator activity DNA-binding transcription factor activity sigma factor activity disordered domain specific binding protein domain specific binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process DNA-templated transcription initiation	protein-containing complex sigma factor antagonist complex transcription regulator complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR035890	Anti-sigma-28 factor FlgM superfamily	Homologous Superfamily
B, D, F, H	IPR031316	Anti-sigma-28 factor FlgM, C-terminal	Domain
A, C, E, G	IPR007627	RNA polymerase sigma-70 region 2	Domain
A, C, E, G	IPR000943	RNA polymerase sigma-70	Domain
A, C, E, G	IPR012845	RNA polymerase sigma factor, FliA/WhiG	Family
A, C, E, G	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
A, C, E, G	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
A, C, E, G	IPR007630	RNA polymerase sigma-70 region 4	Domain
A, C, E, G	IPR014284	RNA polymerase sigma-70-like domain	Domain
A, C, E, G	IPR007624	RNA polymerase sigma-70 region 3	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.