5WP9 | pdb_00005wp9

Structural Basis of Mitochondrial Receptor Binding and Constriction by Dynamin-Related Protein 1

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8054357	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Dynamin stalk-like	8054358	3002023	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8054357	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Dynamin stalk-like	8054358	3002023	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Dynamin stalk-like	8054358	3002023	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ras-like P-loop GTPases	8054357	3002022	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ras-like P-loop GTPases	8054357	3002022	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Dynamin stalk-like	8054358	3002023	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Dynamin stalk-like	8054358	3002023	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ras-like P-loop GTPases	8054357	3002022	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ras-like P-loop GTPases	8054357	3002022	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Dynamin stalk-like	8054358	3002023	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Ras-like P-loop GTPases	8054357	3002022	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Dynamin stalk-like	8054358	3002023	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Dynamin stalk-like	8054358	3002023	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Ras-like P-loop GTPases	8054357	3002022	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	bZIP_1	e5wp9A1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: bZIP_1	ECOD (develop294)
C	Chlorophyllase2	e5wp9C1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
E	Chlorophyllase2	e5wp9E1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
G	Chlorophyllase2	e5wp9G1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
I	Chlorophyllase2	e5wp9I1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
K	Chlorophyllase2	e5wp9K1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
M	Chlorophyllase2	e5wp9M1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
O	Chlorophyllase2	e5wp9O1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
B	bZIP_1	e5wp9B1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: bZIP_1	ECOD (develop294)
D	Chlorophyllase2	e5wp9D1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
F	Chlorophyllase2	e5wp9F1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
H	Chlorophyllase2	e5wp9H1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
J	Chlorophyllase2	e5wp9J1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
L	Chlorophyllase2	e5wp9L1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
N	Chlorophyllase2	e5wp9N1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
P	Chlorophyllase2	e5wp9P1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K, M, O	PF01031	Dynamin central region (Dynamin_M)	Dynamin central region	-	Family
A, C, E, G, I A, C, E, G, I, K, M, O	PF00350	Dynamin family (Dynamin_N)	Dynamin family		Domain
A, C, E, G, I A, C, E, G, I, K, M, O	PF02212	Dynamin GTPase effector domain (GED)	Dynamin GTPase effector domain	-	Family
B, D, F, H, J B, D, F, H, J, L, N, P	PF20266	Mab-21 protein HhH/H2TH-like domain (Mab-21_C)	Mab-21 protein HhH/H2TH-like domain	This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development [2-3].	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	PF21297	Mitochondrial dynamics protein MID51-like, C-terminal domain (MID51-like_C)	Mitochondrial dynamics protein MID51-like, C-terminal domain	This domain is found in Mitochondrial dynamics protein MID51 from humans and similar proteins predominantly found in vertebrates. MID51 promotes the recruitment and association of the fission mediator dynamin-related protein 1 (DNM1L) to the mitochon ...	This domain is found in Mitochondrial dynamics protein MID51 from humans and similar proteins predominantly found in vertebrates. MID51 promotes the recruitment and association of the fission mediator dynamin-related protein 1 (DNM1L) to the mitochondrial surface to drive mitochondrial fission. This entry represents the C-terminal domain of this protein, which adopts a nucleotidyltransferase fold with a mixed alpha-beta topology configured into two lobes separated by a deep cleft [1-4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K, M, O	Dynamin-1-like protein	small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity cytoskeletal protein binding microtubule binding small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity cytoskeletal protein binding microtubule binding tubulin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding pyrophosphatase activity GTPase 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 identical protein binding GTP-dependent protein binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein homodimerization activity protein dimerization activity lipid 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 regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression 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 regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process ribose phosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process regulation of ATP metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process regulation of small molecule metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process phosphorus metabolic process nucleoside phosphate metabolic process purine nucleoside triphosphate metabolic process primary metabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process purine-containing compound metabolic process organophosphate metabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process catabolic process macroautophagy autophagy regulation of mitophagy regulation of catabolic process regulation of autophagy regulation of macroautophagy mitophagy regulation of autophagy of mitochondrion process utilizing autophagic mechanism autophagy of mitochondrion regulation of cellular component organization regulation of organelle organization peroxisome organization regulation of peroxisome organization organelle organization mitochondrion distribution localization mitochondrion localization organelle localization intracellular distribution of mitochondria import into cell transport endocytosis establishment of localization vesicle-mediated transport establishment of organelle localization mitocytosis establishment of mitochondrion localization export from cell migracytosis peroxisome fission organelle fission cellular response to stimulus positive regulation of locomotion regulation of cell motility response to stimulus positive regulation of chemotaxis positive regulation of cell migration positive regulation of neutrophil chemotaxis taxis cell migration regulation of immune system process positive regulation of immune system process chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration response to external stimulus positive regulation of leukocyte chemotaxis neutrophil migration granulocyte migration leukocyte migration positive regulation of granulocyte chemotaxis regulation of response to stimulus response to chemical regulation of locomotion regulation of neutrophil chemotaxis regulation of neutrophil migration regulation of response to external stimulus positive regulation of biological process neutrophil chemotaxis positive regulation of response to stimulus regulation of granulocyte chemotaxis positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration myeloid leukocyte migration cell motility locomotion positive regulation of cellular process cell chemotaxis positive regulation of leukocyte migration positive regulation of neutrophil migration regulation of chemotaxis cellular response to chemical stimulus immune system process granulocyte chemotaxis leukocyte chemotaxis heart process multicellular organismal process system process circulatory system process heart contraction blood circulation mitochondrial fragmentation involved in apoptotic process apoptotic mitochondrial changes apoptotic process cell death programmed cell death mitochondrion organization regulation of localization establishment of protein localization regulation of protein localization positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport regulation of secretion by cell secretion by cell positive regulation of secretion intracellular protein localization regulation of transport secretion regulation of establishment of protein localization establishment of protein localization to extracellular region regulation of protein transport protein secretion positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport macromolecule localization positive regulation of protein localization rhythmic process positive regulation of organelle organization positive regulation of cellular component organization regulation of developmental process positive regulation of developmental process anatomical structure development regulation of anatomical structure morphogenesis developmental process mitochondrial fission anatomical structure morphogenesis regulation of mitochondrial fission regulation of mitochondrion organization positive regulation of mitochondrial fission protein localization to organelle protein localization to mitochondrion monoatomic ion transport monoatomic cation transport calcium ion transport metal ion transport mitochondrial membrane fission membrane organization membrane fission	cellular anatomical structure clathrin-coated pit membrane endomembrane system intracellular anatomical structure cytoplasm cytosol apical part of cell cluster of actin-based cell projections brush border membrane-bounded organelle intracellular organelle Golgi apparatus organelle cellular anatomical structure clathrin-coated pit membrane endomembrane system intracellular anatomical structure cytoplasm cytosol apical part of cell cluster of actin-based cell projections brush border membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle peroxisome microbody perinuclear region of cytoplasm mitochondrial membrane mitochondrion organelle outer membrane organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane synapse intracellular vesicle transport vesicle membrane presynapse cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane cell junction vesicle transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle exocytic vesicle polymeric cytoskeletal fiber intracellular membraneless organelle cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton protein-containing complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B, D, F, H, J B, D, F, H, J, L, N, P	Mitochondrial dynamics protein MID49	-	regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation regulation of organelle organization cellular component organization organelle organization regulation of mitochondrion organization cellular process cellular component organization or biogenesis mitochondrion organization positive regulation of organelle organization positive regulation of cellular component organization regulation of developmental process regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation regulation of organelle organization cellular component organization organelle organization regulation of mitochondrion organization cellular process cellular component organization or biogenesis mitochondrion organization positive regulation of organelle organization positive regulation of cellular component organization regulation of developmental process positive regulation of biological process positive regulation of developmental process anatomical structure development positive regulation of cellular process regulation of anatomical structure morphogenesis developmental process organelle fission mitochondrial fission anatomical structure morphogenesis regulation of mitochondrial fission positive regulation of mitochondrial fission regulation of localization cellular localization establishment of protein localization regulation of protein localization protein targeting positive regulation of establishment of protein localization localization regulation of protein targeting to membrane intracellular protein localization establishment of protein localization to membrane regulation of establishment of protein localization localization within membrane establishment of localization protein targeting to membrane regulation of cellular localization regulation of protein targeting macromolecule localization positive regulation of protein targeting to membrane	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane membrane organelle outer membrane organelle envelope bounding membrane of organelle mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane membrane organelle outer membrane organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR020850	GTPase effector domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR001401	Dynamin, GTPase domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR045063	Dynamin, N-terminal	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR019762	Dynamin, GTPase region, conserved site	Conserved Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR030381	Dynamin-type guanine nucleotide-binding (G) domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR003130	Dynamin GTPase effector	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR000375	Dynamin stalk domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR022812	Dynamin	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR024810	MAB21L/Cyclic GMP-AMP synthase-like receptor	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR045909	Mitochondrial dynamics protein MID49/MID51	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR046906	Mab-21-like, HhH/H2TH-like domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR049097	Mitochondrial dynamics protein MID51-like, C-terminal domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K, M, O	Pharos: O00429	encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1 microcephaly mitochondrial encephalomyopathy optic atrophy 5 acquired lactic acidosis optic atrophy coronary artery disease hereditary spastic paraplegia Severe Congenital Microcephaly atrial fibrillation lactic acidosis microlissencephaly myocardial ischemia autosomal dominant optic atrophy lung cancer encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1 microcephaly mitochondrial encephalomyopathy optic atrophy 5 acquired lactic acidosis optic atrophy coronary artery disease hereditary spastic paraplegia Severe Congenital Microcephaly atrial fibrillation lactic acidosis microlissencephaly myocardial ischemia autosomal dominant optic atrophy lung cancer neurodegenerative disease peroxisomal disease
B, D, F, H, J B, D, F, H, J, L, N, P	Pharos: Q96C03	attention deficit hyperactivity disorder, inattentive type osteosarcoma spina bifida

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.