9C88 | pdb_00009c88

Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Translocating a Portion of a Branched-Degron DHFR Substrate

External Resource: Annotation

Domain Annotation: SCOP2 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)
K [auth k]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
M [auth m]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
R [auth s]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
U [auth v]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
T [auth u]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
S [auth t]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
Q [auth r]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
P [auth q]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
O [auth p]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
N [auth n]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
L [auth l]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
J [auth j]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
I [auth i]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)
H [auth h]	SCOP2B Superfamily	ClpP/crotonase	8034397	3000033	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth 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
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	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 catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process primary metabolic 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 catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic 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	cellular anatomical structure membrane 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
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth 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 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 protein denaturation catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process proteolysis involved in protein catabolic process proteolysis protein unfolding	protein-containing complex intracellular anatomical structure catalytic complex peptidase complex cytosolic proteasome complex HslUV protease complex cellular anatomical structure proteasome complex endopeptidase complex cytoplasm cytosol intracellular protein-containing complex endopeptidase Clp complex
A [auth S]	Branched-Degron DHFR	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	IPR018215	ClpP, Ser active site	Active Site
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family
H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], H [auth h], I [auth i], J [auth j], K [auth k], L [auth l], M [auth m], N [auth n], O [auth p], P [auth q], Q [auth r], R [auth s], S [auth t], T [auth u], U [auth v]	IPR033135	ClpP, histidine active site	Active Site
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR046425	Clp protease, ATP-binding subunit ClpX, bacteria	Family
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR004487	Clp protease, ATP-binding subunit ClpX	Family
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR003593	AAA+ ATPase domain	Domain
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR010603	ATP-dependent Clp protease ATP-binding subunit ClpX, zinc ribbon domain	Domain
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR003959	ATPase, AAA-type, core	Domain
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR019489	Clp ATPase, C-terminal	Domain
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR050052	ATP-dependent Clp protease ATP-binding subunit ClpX	Family
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR038366	Zinc finger, ClpX C4-type superfamily	Homologous Superfamily

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.