8ET3

Cryo-EM structure of a delivery complex containing the SspB adaptor, an ssrA-tagged substrate, and the AAA+ ClpXP protease

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)
G [auth H]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
H [auth I]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
I [auth J]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
J [auth K]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
K [auth L]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
L [auth M]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
M [auth N]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
O [auth Y]	SCOP2B Superfamily	SspB-like	8034381	3001811	SCOP2B (2022-06-29)
P [auth Z]	SCOP2B Superfamily	SspB-like	8034381	3001811	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	PF10431	e8et3A1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
A	PF07724	e8et3A2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
B	PF10431	e8et3B1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
B	PF07724	e8et3B2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
C	PF10431	e8et3C1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
C	PF07724	e8et3C2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
D	PF10431	e8et3D2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
D	PF07724	e8et3D1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
E	PF10431	e8et3E2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
E	PF07724	e8et3E1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
F	PF10431	e8et3F2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
F	PF07724	e8et3F1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
G [auth H]	PF00574	e8et3H1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
H [auth I]	PF00574	e8et3I1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
I [auth J]	PF00574	e8et3J1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
J [auth K]	PF00574	e8et3K1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
K [auth L]	PF00574	e8et3L1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
L [auth M]	PF00574	e8et3M1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
M [auth N]	PF00574	e8et3N1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: PF00574	ECOD (1.6)
O [auth Y]	PF04386	e8et3Y1	A: beta barrels	X: SH3	H: SH3	T: Stringent starvation protein B, SspB	F: PF04386	ECOD (1.6)
P [auth Z]	PF04386	e8et3Z1	A: beta barrels	X: SH3	H: SH3	T: Stringent starvation protein B, SspB	F: PF04386	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF10431	C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small)	C-terminal, D2-small domain, of ClpB protein	This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 ...	This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly [1]. The domain is associated with two Clp_N, Pfam:PF02861, at the N-terminus as well as AAA, Pfam:PF00004 and AAA_2, Pfam:PF07724.	Domain
A, B, C, D, E A, B, C, D, E, F	PF07724	AAA domain (Cdc48 subfamily) (AAA_2)	AAA domain (Cdc48 subfamily)	This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model.	Domain
G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N]	PF00574	Clp protease (CLP_protease)	Clp protease	The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large in ...	The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large insertions, Swiss:P42380 contains one large insertion.	Domain
O [auth Y], P [auth Z]	PF04386	Stringent starvation protein B (SspB)	Stringent starvation protein B	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
N [auth S]	Green fluorescent protein	-	bioluminescence cellular metabolic process metabolic process cellular process generation of precursor metabolites and energy	-
A, B, C, D, E A, B, C, D, E, F	ATP-dependent Clp protease ATP-binding subunit ClpX	protein binding binding enzyme binding protease binding ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding protein binding binding enzyme binding protease binding ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding unfolded protein binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity cation binding transition metal ion binding zinc ion binding metal ion binding ATP-dependent peptidase activity peptidase activity catalytic activity, acting on a protein protein dimerization activity disordered domain specific binding protein domain specific binding identical protein binding	cellular process cell division organonitrogen compound catabolic process protein denaturation organonitrogen compound metabolic process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process cellular process cell division organonitrogen compound catabolic process protein denaturation organonitrogen compound metabolic process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process proteolysis involved in protein catabolic process proteolysis protein unfolding	protein-containing complex intracellular anatomical structure catalytic complex peptidase complex cellular anatomical entity cytosolic proteasome complex HslUV protease complex proteasome complex endopeptidase complex cytoplasm cytosol intracellular protein-containing complex endopeptidase Clp complex
G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N]	ATP-dependent Clp protease proteolytic subunit	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity ATP-dependent peptidase activity ATP-dependent activity ATPase binding protein binding binding enzyme binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity ATP-dependent peptidase activity ATP-dependent activity ATPase binding protein binding binding enzyme binding identical protein binding	regulation of biological process positive regulation of programmed cell death regulation of cellular process biological regulation positive regulation of biological process cellular process regulation of programmed cell death cell death programmed cell death positive regulation of cellular process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process regulation of biological process positive regulation of programmed cell death regulation of cellular process biological regulation positive regulation of biological process cellular process regulation of programmed cell death cell death programmed cell death positive regulation of cellular process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process response to stimulus response to radiation response to abiotic stimulus response to stress response to heat response to temperature stimulus protein quality control for misfolded or incompletely synthesized proteins	membrane cellular anatomical entity protein-containing complex intracellular anatomical structure catalytic complex peptidase complex cytosolic proteasome complex HslUV protease complex proteasome complex endopeptidase complex cytoplasm cytosol intracellular protein-containing complex endopeptidase Clp complex
O [auth Y], P [auth Z]	Stringent starvation protein B	molecular adaptor activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity RNA binding organic cyclic compound binding nucleic acid binding ATPase binding enzyme binding	catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process organic substance metabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process organonitrogen compound catabolic process catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process organic substance metabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process organonitrogen compound catabolic process regulation of biological process organonitrogen compound metabolic process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of proteolysis metabolic process macromolecule metabolic process regulation of metabolic process organic substance catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process positive regulation of molecular function regulation of molecular function regulation of ATP-dependent activity positive regulation of ATP-dependent activity	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex catalytic complex peptidase complex cytosolic proteasome complex HslUV protease complex proteasome complex endopeptidase complex intracellular protein-containing complex intracellular organelle organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex catalytic complex peptidase complex cytosolic proteasome complex HslUV protease complex proteasome complex endopeptidase complex intracellular protein-containing complex intracellular organelle organelle intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
N [auth S]	IPR000786	Green fluorescent protein, GFP	Family
N [auth S]	IPR011584	Green fluorescent protein-related	Family
N [auth S]	IPR009017	Green fluorescent protein	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR046425	Clp protease, ATP-binding subunit ClpX, bacteria	Family
A, B, C, D, E A, B, C, D, E, F	IPR004487	Clp protease, ATP-binding subunit ClpX	Family
A, B, C, D, E A, B, C, D, E, F	IPR010603	Zinc finger, ClpX C4-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003959	ATPase, AAA-type, core	Domain
A, B, C, D, E A, B, C, D, E, F	IPR019489	Clp ATPase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR038366	Zinc finger, ClpX C4-type superfamily	Homologous Superfamily
G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N]	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N]	IPR018215	ClpP, Ser active site	Active Site
G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N]	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], L [auth M], M [auth N]	IPR033135	ClpP, histidine active site	Active Site
O [auth Y], P [auth Z]	IPR007481	Stringent starvation protein B	Family
O [auth Y], P [auth Z]	IPR036760	SspB-like superfamily	Homologous Superfamily