3E2U

Crystal structure of the zink-knuckle 2 domain of human CLIP-170 in complex with CAP-Gly domain of human dynactin-1 (p150-GLUED)

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3e2ua_	All beta proteins	SH3-like barrel	Cap-Gly domain	Cap-Gly domain	Dynactin 1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3e2ub_	All beta proteins	SH3-like barrel	Cap-Gly domain	Cap-Gly domain	Dynactin 1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3e2uc_	All beta proteins	SH3-like barrel	Cap-Gly domain	Cap-Gly domain	Dynactin 1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3e2ud_	All beta proteins	SH3-like barrel	Cap-Gly domain	Cap-Gly domain	Dynactin 1	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cap-Gly domain	8034244	3000882	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cap-Gly domain	8034244	3000882	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cap-Gly domain	8034244	3000882	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cap-Gly domain	8034244	3000882	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Retroviral zinc finger-like domains	8092361	3001193	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Retroviral zinc finger-like domains	8092361	3001193	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Retroviral zinc finger-like domains	8092361	3001193	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Retroviral zinc finger-like domains	8092361	3001193	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	CAP_GLY	e3e2uA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CAP_GLY	ECOD (1.6)
B	CAP_GLY	e3e2uB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CAP_GLY	ECOD (1.6)
C	CAP_GLY	e3e2uC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CAP_GLY	ECOD (1.6)
D	CAP_GLY	e3e2uD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CAP_GLY	ECOD (1.6)
E	CLIP1_ZNF	e3e2uE1	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains (From Topology)	T: Retrovirus zinc finger-related domains	F: CLIP1_ZNF	ECOD (1.6)
F	CLIP1_ZNF	e3e2uF1	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains (From Topology)	T: Retrovirus zinc finger-related domains	F: CLIP1_ZNF	ECOD (1.6)
G	CLIP1_ZNF	e3e2uG1	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains (From Topology)	T: Retrovirus zinc finger-related domains	F: CLIP1_ZNF	ECOD (1.6)
H	CLIP1_ZNF	e3e2uH1	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains (From Topology)	T: Retrovirus zinc finger-related domains	F: CLIP1_ZNF	ECOD (1.6)

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)
B	2.30.30.190	Mainly Beta	Roll	SH3 type barrels.	CAP Gly-rich-like domain	CATH (4.3.0)
C	2.30.30.190	Mainly Beta	Roll	SH3 type barrels.	CAP Gly-rich-like domain	CATH (4.3.0)
D	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, B, C, D	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
E, F, G, H	PF16641	CLIP1 zinc knuckle (CLIP1_ZNF)	CLIP1 zinc knuckle	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Dynactin subunit 1	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding tau protein binding kinase binding enzyme binding protein kinase binding	cellular process cell division establishment of organelle localization cellular localization transport nucleus localization intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear migration maintenance of synapse structure cellular component organization cellular process cell division establishment of organelle localization cellular localization transport nucleus localization intracellular transport establishment of localization localization organelle localization establishment of localization in cell nuclear migration maintenance of synapse structure cellular component organization cell junction maintenance cell junction organization cellular component maintenance synapse organization cellular component organization or biogenesis multicellular organismal process system process nervous system process neuromuscular process membrane organization cellular component disassembly nuclear membrane disassembly membrane disassembly nuclear membrane organization nucleus organization organelle organization nuclear envelope organization endomembrane system organization microtubule cytoskeleton organization spindle localization establishment or maintenance of cell polarity mitotic cell cycle establishment of mitotic spindle localization establishment of spindle localization establishment of spindle orientation cell cycle microtubule cytoskeleton organization involved in mitosis cell cycle process establishment of cell polarity mitotic cell cycle process establishment of mitotic spindle orientation microtubule-based process cytoskeleton organization developmental process multicellular organism development anatomical structure development nervous system development system development vesicle localization establishment of melanosome localization establishment of vesicle localization cellular pigmentation pigment granule transport establishment of pigment granule localization pigmentation pigment granule localization melanosome transport melanosome localization vesicle-mediated transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi positive regulation of organelle organization regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of biological process cellular component biogenesis regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly microtubule polymerization or depolymerization positive regulation of protein polymerization protein-containing complex assembly positive regulation of cellular process protein polymerization regulation of biological process positive regulation of microtubule polymerization or depolymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization biological regulation regulation of microtubule-based process microtubule polymerization positive regulation of supramolecular fiber organization regulation of cellular component biogenesis regulation of organelle organization positive regulation of microtubule polymerization regulation of protein polymerization regulation of microtubule polymerization regulation of supramolecular fiber organization supramolecular fiber organization regulation of microtubule cytoskeleton organization positive regulation of neuromuscular junction development regulation of synapse organization neuromuscular junction development regulation of synapse structure or activity regulation of biological quality regulation of neuromuscular junction development microtubule anchoring at microtubule organizing center microtubule anchoring at centrosome microtubule anchoring cellular homeostasis neuron cellular homeostasis homeostatic process positive regulation of microtubule nucleation regulation of microtubule nucleation microtubule nucleation organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cilium assembly non-motile cilium assembly cilium organization cell projection assembly regulation of mitotic spindle organization regulation of cell cycle spindle organization regulation of cell cycle process regulation of spindle organization mitotic spindle organization spinal cord development central nervous system development ventral spinal cord development behavior motor behavior microtubule organizing center organization centriole-centriole cohesion centrosome cycle neuron projection maintenance neuron projection organization	intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle intracellular non-membrane-bounded organelle spindle pole cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle membrane membrane-bounded organelle organelle envelope nuclear envelope intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle intracellular non-membrane-bounded organelle spindle pole cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle membrane membrane-bounded organelle organelle envelope nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol cell leading edge cell projection neuron projection plasma membrane bounded cell projection intercellular bridge somatodendritic compartment cell body neuronal cell body axon protein-containing complex microtubule associated complex cilium ciliary basal body microtubule organizing center polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex cell periphery cell cortex centrosome microtubule end microtubule plus-end centriole intracellular protein-containing complex centriolar subdistal appendage mitotic spindle cell cortex region cytoplasmic region chromosome chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region condensed chromosome catalytic complex dynein complex
E, F, G, H	CAP-Gly domain-containing linker protein 1	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding microtubule plus-end binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding	cellular process cell cycle mitotic cell cycle cellular component organization organelle organization microtubule cytoskeleton organization microtubule-based process cytoplasmic microtubule organization cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization microtubule bundle formation positive regulation of organelle organization regulation of cytoskeleton organization cellular process cell cycle mitotic cell cycle cellular component organization organelle organization microtubule cytoskeleton organization microtubule-based process cytoplasmic microtubule organization cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization microtubule bundle formation positive regulation of organelle organization regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of biological process cellular component biogenesis regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly microtubule polymerization or depolymerization positive regulation of protein polymerization protein-containing complex assembly positive regulation of cellular process protein polymerization regulation of biological process positive regulation of microtubule polymerization or depolymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization biological regulation regulation of microtubule-based process microtubule polymerization positive regulation of supramolecular fiber organization regulation of cellular component biogenesis regulation of organelle organization positive regulation of microtubule polymerization regulation of protein polymerization regulation of microtubule polymerization regulation of supramolecular fiber organization regulation of microtubule cytoskeleton organization	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane chromosome chromosomal region kinetochore intracellular non-membrane-bounded organelle chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome non-membrane-bounded organelle cell periphery cell cortex polymeric cytoskeletal fiber intermediate filament cytoskeleton cytoskeleton intermediate filament supramolecular fiber supramolecular polymer centrosome microtubule organizing center microtubule cytoskeleton ruffle cell projection cell leading edge plasma membrane bounded cell projection cytosol microtubule nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036859	CAP Gly-rich domain superfamily	Homologous Superfamily
A, B, C, D	IPR000938	CAP Gly-rich domain	Domain
A, B, C, D	IPR022157	Dynein associated protein	Domain
E, F, G, H	IPR036859	CAP Gly-rich domain superfamily	Homologous Superfamily
E, F, G, H	IPR032108	CLIP1, zinc knuckle	Domain
E, F, G, H	IPR000938	CAP Gly-rich domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q14203	Perry syndrome amyotrophic lateral sclerosis neuronopathy, distal hereditary motor, type 7B amyotrophic lateral sclerosis type 1 Charcot-Marie-Tooth disease Hypoventilation Parkinson disease intellectual disability mood disorder neurodegenerative disease parkinsonian disorder autosomal recessive juvenile Parkinson disease 2 malignant ependymoma peripheral neuropathy medulloblastoma Perry syndrome amyotrophic lateral sclerosis neuronopathy, distal hereditary motor, type 7B amyotrophic lateral sclerosis type 1 Charcot-Marie-Tooth disease Hypoventilation Parkinson disease intellectual disability mood disorder neurodegenerative disease parkinsonian disorder autosomal recessive juvenile Parkinson disease 2 malignant ependymoma peripheral neuropathy medulloblastoma motor peripheral neuropathy
E, F, G, H	Pharos: P30622	spina bifida adenoma esophageal adenocarcinoma hereditary spastic paraplegia malignant ependymoma medulloblastoma periodontitis psoriasis allergic rhinitis gastric carcinoma large cell medulloblastoma malignant glioma osteosarcoma Pick disease rheumatoid arthritis spina bifida adenoma esophageal adenocarcinoma hereditary spastic paraplegia malignant ependymoma medulloblastoma periodontitis psoriasis allergic rhinitis gastric carcinoma large cell medulloblastoma malignant glioma osteosarcoma Pick disease rheumatoid arthritis breast cancer glioblastoma lung cancer Malignant neoplasm of breast ovarian cancer progressive supranuclear palsy

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.