8B0J | pdb_00008b0j

CryoEM structure of bacterial RNaseE.RapZ.GlmZ complex central to the control of cell envelope biogenesis

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth L]	SCOP2B Superfamily	Ribonuclease H-like	8102251	3000143	SCOP2B (2022-06-29)
E [auth L]	SCOP2B Superfamily	MK0968-like	8102253	3002481	SCOP2B (2022-06-29)
E [auth L]	SCOP2B Superfamily	Nucleic acid-binding proteins	8039601	3000135	SCOP2B (2022-06-29)
E [auth L]	SCOP2B Superfamily	DnaJ/Hsp40 cysteine-rich domain-like	8102255	3001550	SCOP2B (2022-06-29)
E [auth L]	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8102249	3000100	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	Ribonuclease H-like	8102251	3000143	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	Type III KH-domain	8102257	3002727	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	MK0968-like	8102253	3002481	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)
A	SKI	e8b0jA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SKI	ECOD (1.6)
A	F_UNCLASSIFIED	e8b0jA1	A: a/b three-layered sandwiches	X: Phosphofructokinase C-terminal domain (From Topology)	H: Phosphofructokinase C-terminal domain (From Topology)	T: Phosphofructokinase C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
B	SKI	e8b0jB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SKI	ECOD (1.6)
B	F_UNCLASSIFIED	e8b0jB1	A: a/b three-layered sandwiches	X: Phosphofructokinase C-terminal domain (From Topology)	H: Phosphofructokinase C-terminal domain (From Topology)	T: Phosphofructokinase C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth D]	SKI	e8b0jD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SKI	ECOD (1.6)
C [auth D]	F_UNCLASSIFIED	e8b0jD2	A: a/b three-layered sandwiches	X: Phosphofructokinase C-terminal domain (From Topology)	H: Phosphofructokinase C-terminal domain (From Topology)	T: Phosphofructokinase C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth C]	SKI	e8b0jC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SKI	ECOD (1.6)
D [auth C]	F_UNCLASSIFIED	e8b0jC1	A: a/b three-layered sandwiches	X: Phosphofructokinase C-terminal domain (From Topology)	H: Phosphofructokinase C-terminal domain (From Topology)	T: Phosphofructokinase C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
E [auth L]	S1_4	e8b0jL4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_4	ECOD (1.6)
E [auth L]	RNase_E_G_1st	e8b0jL1	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: RNase_E_G_1st	ECOD (1.6)
E [auth L]	rne	e8b0jL2	A: a+b three layers	X: Thioredoxin-like domain in RNase E (From Topology)	H: Thioredoxin-like domain in RNase E (From Topology)	T: Thioredoxin-like domain in RNase E	F: rne	ECOD (1.6)
E [auth L]	RNase_E_G_3rd	e8b0jL5	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: RNase_E_G_3rd	ECOD (1.6)
E [auth L]	RNase_E_G_2nd	e8b0jL3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_E_G_2nd	ECOD (1.6)
F [auth N]	S1_4	e8b0jN4	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: S1_4	ECOD (1.6)
F [auth N]	rne	e8b0jN3	A: a+b three layers	X: Thioredoxin-like domain in RNase E (From Topology)	H: Thioredoxin-like domain in RNase E (From Topology)	T: Thioredoxin-like domain in RNase E	F: rne	ECOD (1.6)
F [auth N]	RNase_E_G_3rd	e8b0jN1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: RNase_E_G_3rd	ECOD (1.6)
F [auth N]	RNase_E_G_2nd	e8b0jN2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_E_G_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth D], D [auth C]	PF22740	RapZ C-terminal domain (PapZ_C)	RapZ C-terminal domain	This entry represents the C-terminal domain of RapZ which belongs to the Rhodanese-Phosphatase superfamily. It has been shown to bind multiple ligands as part of the regulation of glucosamine-6-phosphate (GlcN6P) levels, which is a precursor to the b ...	This entry represents the C-terminal domain of RapZ which belongs to the Rhodanese-Phosphatase superfamily. It has been shown to bind multiple ligands as part of the regulation of glucosamine-6-phosphate (GlcN6P) levels, which is a precursor to the bacterial cell wall polymer peptidoglycan. Assignment to the greater Rhodanese-Phosphatase superfamily has led to the prediction that, as part of this regulation, it functions as a sugar phosphorylation-dephosphorylation switch [1].	Domain
A, B, C [auth D], D [auth C]	PF03668	RapZ-like N-terminal domain (RapZ-like_N)	RapZ-like N-terminal domain	This entry represents the N-terminal P-loop kinase domain of RNase adapter protein RapZ and related proteins. RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism [1-3]. It is a RNA-binding protein that recruits the major en ...	This entry represents the N-terminal P-loop kinase domain of RNase adapter protein RapZ and related proteins. RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism [1-3]. It is a RNA-binding protein that recruits the major endoribonuclease RNase E to sRNAs GlmZ [1,2].	Domain
E [auth L], F [auth N]	PF20833	RNase E/G, Thioredoxin-like domain (RNase_E_G_Thio)	RNase E/G, Thioredoxin-like domain	Both RNase E and its homologue RNase G are endoribonucleases that play central roles in RNA processing. RNase E shows two globular domains. This entry represents the smaller domain, which shows a thioredoxin-like fold [1-3].	Domain
E [auth L], F [auth N]	PF10150	Ribonuclease E/G family (RNase_E_G)	Ribonuclease E/G family	-	Family
E [auth L], F [auth N]	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth D], D [auth C]	RNase adapter protein RapZ	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding molecular adaptor activity RNA binding nucleic acid binding guanyl nucleotide binding GTP binding guanyl ribonucleotide binding identical protein binding protein binding	regulation of cellular process catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of cellular process regulation of cellular process catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of cellular process RNA catabolic process regulation of biosynthetic process RNA destabilization positive regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process positive regulation of catabolic process regulation of gene expression biosynthetic process regulation of RNA stability nucleic acid catabolic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis	protein-containing complex
E [auth L], F [auth N]	Ribonuclease E	RNA binding binding rRNA binding nucleic acid binding tRNA binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding 7S RNA binding ribonuclease E activity nuclease activity hydrolase activity, acting on ester bonds RNA binding binding rRNA binding nucleic acid binding tRNA binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding 7S RNA binding ribonuclease E activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity endonuclease activity RNA endonuclease activity protein binding enzyme binding DEAD/H-box RNA helicase binding molecular adaptor activity transition metal ion binding zinc ion binding identical protein binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein homotetramerization protein tetramerization protein homooligomerization ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein homotetramerization protein tetramerization protein homooligomerization ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process RNA processing rRNA metabolic process tRNA metabolic process tRNA processing catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process mRNA metabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process regulation of ATP-dependent activity regulation of molecular function regulation of RNA helicase activity regulation of catalytic activity rRNA 5'-end processing RNA 5'-end processing	cellular anatomical structure membrane bacterial degradosome exosome (RNase complex) protein-containing complex intracellular anatomical structure catalytic complex cytoplasm cytosol cytoplasmic exosome (RNase complex) exoribonuclease complex endoribonuclease complex intracellular protein-containing complex endonuclease complex cellular anatomical structure membrane bacterial degradosome exosome (RNase complex) protein-containing complex intracellular anatomical structure catalytic complex cytoplasm cytosol cytoplasmic exosome (RNase complex) exoribonuclease complex endoribonuclease complex intracellular protein-containing complex endonuclease complex cell periphery cytoplasmic side of plasma membrane cytoplasmic side of membrane plasma membrane side of membrane
G [auth K]	GlmZ small RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth D], D [auth C]	IPR053930	RapZ-like, N-terminal domain	Domain
A, B, C [auth D], D [auth C]	IPR053931	RapZ, C-terminal domain	Domain
A, B, C [auth D], D [auth C]	IPR005337	RapZ-like family	Family
A, B, C [auth D], D [auth C]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
E [auth L], F [auth N]	IPR028878	Ribonuclease E	Family
E [auth L], F [auth N]	IPR004659	Ribonuclease E/G	Family
E [auth L], F [auth N]	IPR019307	RNA-binding protein AU-1/Ribonuclease E/G	Domain
E [auth L], F [auth N]	IPR003029	S1 domain	Domain
E [auth L], F [auth N]	IPR021968	Polyribonucleotide phosphorylase C-terminal	Domain
E [auth L], F [auth N]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
E [auth L], F [auth N]	IPR048583	RNase E/G, thioredoxin-like domain	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.