1RIO

Structure of bacteriophage lambda cI-NTD in complex with sigma-region4 of Thermus aquaticus bound to DNA

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth H]	d1rioh_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma4 domain	Sigma70 (SigA, RpoD)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
D [auth A]	d1rioa1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Phage repressors	lambda C1 repressor, DNA-binding domain	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
D [auth A]	d1rioa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
E [auth B]	d1riob1	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	Phage repressors	lambda C1 repressor, DNA-binding domain	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
E [auth B]	d1riob2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth H]	SCOP2 Family	Sigma4 domain	8028300	4003503	SCOP2 (2022-06-29)
C [auth H]	SCOP2 Superfamily	Sigma factor domain-like	8040679	3000953	SCOP2 (2022-06-29)
D [auth A]	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8058183	3000119	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8058183	3000119	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth H]	PF04545	e1rioH1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF04545	ECOD (1.6)
D [auth A]	PF01381	e1rioA1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PF01381	ECOD (1.6)
E [auth B]	PF01381	e1rioB1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PF01381	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth H]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D [auth A]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
E [auth B]	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth H]	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
D [auth A], E [auth B]	PF01381	Helix-turn-helix (HTH_3)	Helix-turn-helix	This large family of DNA binding helix-turn helix proteins includes Cro Swiss:P03036 and CI Swiss:P03034. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be ...	This large family of DNA binding helix-turn helix proteins includes Cro Swiss:P03036 and CI Swiss:P03034. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth U]	27-MER	-	-	-
B [auth T]	27-MER	-	-	-
C [auth H]	sigma factor SigA	DNA binding binding organic cyclic compound binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	cellular biosynthetic process RNA metabolic process cellular nitrogen compound biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process nucleobase-containing compound biosynthetic process cellular biosynthetic process RNA metabolic process cellular nitrogen compound biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic substance metabolic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process cellular aromatic compound metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity
D [auth A], E [auth B]	Repressor protein CI	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding core promoter sequence-specific DNA binding nucleic acid binding transcription regulatory region nucleic acid binding identical protein binding protein binding	latent virus replication viral process viral latency release from viral latency latency-replication decision regulation of cellular process negative regulation of biological process negative regulation of nitrogen compound metabolic process cellular nitrogen compound biosynthetic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process latent virus replication viral process viral latency release from viral latency latency-replication decision regulation of cellular process negative regulation of biological process negative regulation of nitrogen compound metabolic process cellular nitrogen compound biosynthetic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process DNA-templated transcription regulation of RNA metabolic process heterocycle metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of transcription by competitive promoter binding aromatic compound biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process organic substance metabolic process negative regulation of cellular process nitrogen compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process cellular aromatic compound metabolic process maintenance of viral latency viral gene expression regulation of viral process regulation of viral transcription positive regulation of viral process positive regulation of biological process viral transcription positive regulation of viral transcription	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth H]	IPR007627	RNA polymerase sigma-70 region 2	Domain
C [auth H]	IPR000943	RNA polymerase sigma-70	Domain
C [auth H]	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
C [auth H]	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
C [auth H]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C [auth H]	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
C [auth H]	IPR014284	RNA polymerase sigma-70 like domain	Domain
C [auth H]	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
C [auth H]	IPR007630	RNA polymerase sigma-70 region 4	Domain
C [auth H]	IPR007624	RNA polymerase sigma-70 region 3	Domain
C [auth H]	IPR028630	RNA polymerase sigma factor RpoD	Family
D [auth A], E [auth B]	IPR015927	Peptidase S24/S26A/S26B/S26C	Domain
D [auth A], E [auth B]	IPR001387	Cro/C1-type helix-turn-helix domain	Domain
D [auth A], E [auth B]	IPR039418	LexA-like	Domain
D [auth A], E [auth B]	IPR036286	LexA/Signal peptidase-like superfamily	Homologous Superfamily
D [auth A], E [auth B]	IPR010982	Lambda repressor-like, DNA-binding domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.