1WHH | pdb_00001whh

Solution structure of the 2nd CAP-Gly domain in mouse CLIP170-related 59kDa protein CLIPR-59

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1whha1	All beta proteins	SH3-like barrel	Cap-Gly domain	Cap-Gly domain	CLIP170-related 59kda protein CLIPR-59 (1500005P14Rik)	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1whha3	Artifacts	Tags	Tags	Tags	C-terminal Tags	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1whha2	Artifacts	Tags	Tags	Tags	N-terminal Tags	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Cap-Gly domain	8031172	4002146	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cap-Gly domain	8043550	3000882	SCOP2 (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	Terminase_2	e1whhA1	A: a/b three-layered sandwiches	X: small terminase oligomerization domain	H: small terminase oligomerization domain	T: small terminase oligomerization domain	F: Terminase_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.190	Mainly Beta	Roll	SH3 type barrels.	CAP Gly-rich-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01302	CAP-Gly domain (CAP_GLY)	CAP-Gly domain	Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP ...	Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein Swiss:Q20728 CAP-Gly domain was recently solved [2]. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CLIPR-59	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding glycosphingolipid binding ceramide binding ganglioside binding sphingolipid binding lipid binding glycolipid binding carbohydrate derivative binding microtubule plus-end binding	regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of cellular component organization regulation of cellular process microtubule cytoskeleton organization negative regulation of biological process cellular component organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly microtubule polymerization or depolymerization negative regulation of cellular process protein-containing complex assembly negative regulation of protein polymerization regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of cellular component organization regulation of cellular process microtubule cytoskeleton organization negative regulation of biological process cellular component organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly microtubule polymerization or depolymerization negative regulation of cellular process protein-containing complex assembly negative regulation of protein polymerization negative regulation of supramolecular fiber organization cellular component organization or biogenesis protein polymerization regulation of biological process negative regulation of cellular component organization negative regulation of microtubule polymerization or depolymerization protein-containing complex organization negative regulation of cytoskeleton organization biological regulation regulation of microtubule-based process negative regulation of microtubule polymerization microtubule polymerization regulation of cellular component biogenesis regulation of organelle organization negative regulation of protein-containing complex assembly organelle organization negative regulation of organelle organization regulation of protein polymerization regulation of microtubule polymerization regulation of supramolecular fiber organization cellular process microtubule-based process supramolecular fiber organization cytoskeleton organization regulation of microtubule cytoskeleton organization positive regulation of protein localization to plasma membrane regulation of localization cellular localization regulation of protein localization positive regulation of biological process localization intracellular protein localization regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of protein localization to plasma membrane positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death membrane biogenesis cytoplasmic microtubule organization establishment of protein localization transport protein transport along microtubule microtubule-based protein transport intracellular transport establishment of localization protein transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement intracellular protein transport developmental process fat cell differentiation cellular developmental process cell differentiation peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine peptidyl-cysteine modification lipoprotein biosynthetic process lipoprotein metabolic process primary metabolic process macromolecule biosynthetic process protein acylation protein lipidation protein palmitoylation biosynthetic process macromolecule modification peptidyl-amino acid modification peptidyl-L-cysteine S-palmitoylation metabolic process protein metabolic process macromolecule metabolic process protein modification process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of macromolecule metabolic process regulation of phosphorus metabolic process regulation of phosphorylation regulation of metabolic process hexose transmembrane transport regulation of transport carbohydrate transport positive regulation of D-glucose transmembrane transport transmembrane transport regulation of transmembrane transport positive regulation of transport D-glucose transmembrane transport positive regulation of transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport import into cell positive regulation of cellular component organization regulation of vesicle-mediated transport vesicle-mediated transport positive regulation of endocytosis endocytosis regulation of endocytosis	membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle Golgi stack cytoplasm cell periphery cell cortex membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure organelle Golgi stack cytoplasm cell periphery cell cortex polymeric cytoskeletal fiber microtubule end intracellular membraneless organelle cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule plus-end microtubule cytoskeleton plasma membrane membrane membrane microdomain membrane raft endosome membrane endosome intracellular vesicle recycling endosome cytoplasmic vesicle membrane bounding membrane of organelle recycling endosome membrane vesicle membrane cytoplasmic vesicle vesicle organelle membrane trans-Golgi network early endosome early endosome membrane trans-Golgi network membrane nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A	IPR000938	CAP Gly-rich domain	Domain
A	IPR002110	Ankyrin repeat	Repeat
A	IPR036859	CAP Gly-rich domain 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.