2HL5 | pdb_00002hl5

Crystal structure of the C-terminal domain of human EB1 in complex with the A49M mutant 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)
D	d2hl5d_	All beta proteins	SH3-like barrel	Cap-Gly domain	Cap-Gly domain	Dynactin 1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d2hl5c_	All beta proteins	SH3-like barrel	Cap-Gly domain	Cap-Gly domain	Dynactin 1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d2hl5b_	All alpha proteins	EB1 dimerisation domain-like	EB1 dimerisation domain-like	EB1 dimerisation domain-like	Microtubule-associated protein EB1, C-terminal dimerization domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2hl5a_	All alpha proteins	EB1 dimerisation domain-like	EB1 dimerisation domain-like	EB1 dimerisation domain-like	Microtubule-associated protein EB1, C-terminal dimerization domain	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)
D	SCOP2B Superfamily	Cap-Gly domain	8034244	3000882	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Cap-Gly domain	8034244	3000882	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	EB1 dimerisation domain-like	8054350	3001381	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EB1 dimerisation domain-like	8054350	3001381	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)
D		e2hl5D1	A: HTH	X: HTH	H: winged helix domain	T: MarR	F:	ECOD (20:10:01)
B [auth C]		e2hl5C1	A: HTH	X: HTH	H: winged helix domain	T: MarR	F:	ECOD (20:10:01)
C [auth B]		e2hl5B1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Tryp_alpha_amyl	F:	ECOD (20:10:01)
A		e2hl5A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Tryp_alpha_amyl	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.30.190	Mainly Beta	Roll	SH3 type barrels.	CAP Gly-rich-like domain	CATH (4.3.0)
B [auth C]	2.30.30.190	Mainly Beta	Roll	SH3 type barrels.	CAP Gly-rich-like domain	CATH (4.3.0)
C [auth B]	1.20.5.1430	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	1.20.5.1430	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth 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
A, C [auth B]	PF03271	EB1-like C-terminal motif (EB1)	EB1-like C-terminal motif	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], D	Dynactin-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 membrane organization cellular component disassembly 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 membrane organization cellular component disassembly nuclear membrane disassembly mitotic cell cycle membrane disassembly nuclear membrane organization cellular component organization mitotic nuclear membrane disassembly nucleus organization organelle organization mitotic cell cycle process nuclear envelope organization cell cycle cellular component organization or biogenesis endomembrane system organization cell cycle process maintenance of synapse structure cell junction maintenance cell junction organization cellular component maintenance synapse organization multicellular organismal process system process nervous system process neuromuscular process microtubule cytoskeleton organization spindle localization establishment or maintenance of cell polarity establishment of mitotic spindle localization establishment of spindle localization establishment of spindle orientation microtubule cytoskeleton organization involved in mitosis establishment of cell polarity 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 cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane membrane-bounded organelle organelle envelope nuclear envelope intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane membrane-bounded organelle organelle envelope nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm cytosol cell leading edge perinuclear theca perinuclear region of cytoplasm 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 acrosomal vesicle intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle vesicle 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
A, C [auth B]	Microtubule-associated protein RP/EB family member 1	RNA binding binding nucleic acid binding protein binding protein serine/threonine kinase binding kinase binding enzyme binding protein kinase binding cell adhesion molecule binding cadherin binding cytoskeletal protein binding microtubule plus-end binding microtubule binding tubulin binding RNA binding binding nucleic acid binding protein binding protein serine/threonine kinase binding kinase binding enzyme binding protein kinase binding cell adhesion molecule binding cadherin binding cytoskeletal protein binding microtubule plus-end binding microtubule binding tubulin binding identical protein binding	cellular component organization microtubule bundle formation organelle organization microtubule cytoskeleton organization cellular process microtubule-based process cellular component organization or biogenesis cytoskeleton organization protein localization to microtubule cytoskeleton localization protein localization to cytoskeleton protein localization to organelle macromolecule localization protein localization to microtubule organizing center cellular component organization microtubule bundle formation organelle organization microtubule cytoskeleton organization cellular process microtubule-based process cellular component organization or biogenesis cytoskeleton organization protein localization to microtubule cytoskeleton localization protein localization to cytoskeleton protein localization to organelle macromolecule localization protein localization to microtubule organizing center intracellular protein localization protein localization to centrosome regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of cellular component organization regulation of cellular process negative regulation of biological process 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 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 negative regulation of organelle organization regulation of protein polymerization regulation of microtubule polymerization regulation of supramolecular fiber organization supramolecular fiber organization regulation of microtubule cytoskeleton organization mitotic metaphase chromosome alignment mitotic cell cycle metaphase chromosome alignment chromosome localization organelle localization mitotic sister chromatid segregation cell cycle chromosome segregation cell cycle process mitotic nuclear division attachment of spindle microtubules to kinetochore organelle fission attachment of mitotic spindle microtubules to kinetochore chromosome organization sister chromatid segregation nuclear division mitotic cell cycle process nuclear chromosome segregation cell division cell migration cell motility organelle assembly membraneless organelle assembly spindle assembly spindle organization 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 protein localization to astral microtubule protein localization to microtubule protein localization to cytoplasmic microtubule protein localization to spindle microtubule protein localization to mitotic spindle establishment of organelle localization cellular localization spindle localization establishment or maintenance of cell polarity establishment of mitotic spindle localization establishment of spindle localization establishment of spindle orientation establishment of localization in cell microtubule cytoskeleton organization involved in mitosis establishment of localization establishment of cell polarity establishment of mitotic spindle orientation positive regulation of organelle organization positive regulation of cellular component organization positive regulation of biological process positive regulation of protein-containing complex assembly positive regulation of protein polymerization positive regulation of cellular process positive regulation of microtubule polymerization or depolymerization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization positive regulation of supramolecular fiber organization positive regulation of microtubule polymerization	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle midzone microtubule cytoskeleton cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle midzone microtubule cytoskeleton centrosome microtubule organizing center polymeric cytoskeletal fiber mitotic spindle aster spindle microtubule cytoplasmic microtubule mitotic spindle astral microtubule end supramolecular polymer supramolecular complex microtubule end mitotic spindle astral microtubule astral microtubule supramolecular fiber cytoplasm microtubule microtubule plus-end cytosol cell periphery cell projection membrane plasma membrane plasma membrane region cell projection membrane plasma membrane bounded cell projection membrane-bounded organelle Golgi apparatus intracellular membrane-bounded organelle endomembrane system cell cortex cortical cytoskeleton cortical microtubule cytoskeleton mitotic spindle pole spindle pole cilium ciliary basal body mitotic spindle microtubule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR036859	CAP Gly-rich domain superfamily	Homologous Superfamily
B [auth C], D	IPR000938	CAP Gly-rich domain	Domain
B [auth C], D	IPR022157	Dynein associated protein	Domain
A, C [auth B]	IPR001715	Calponin homology domain	Domain
A, C [auth B]	IPR004953	EB1, C-terminal	Domain
A, C [auth B]	IPR027328	Microtubule-associated protein RP/EB	Family
A, C [auth B]	IPR036133	EB1, C-terminal domain superfamily	Homologous Superfamily
A, C [auth B]	IPR036872	CH domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth 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
A, C [auth B]	Pharos: Q15691	Weight Gain primitive neuroectodermal tumor astrocytic tumor coronary artery disease inflammatory bowel disease lymphoplasmacytic lymphoma medulloblastoma oligodendroglioma plasma cell myeloma atypical teratoid rhabdoid tumor dermatomyositis juvenile dermatomyositis malignant ependymoma myocardial ischemia osteosarcoma Weight Gain primitive neuroectodermal tumor astrocytic tumor coronary artery disease inflammatory bowel disease lymphoplasmacytic lymphoma medulloblastoma oligodendroglioma plasma cell myeloma atypical teratoid rhabdoid tumor dermatomyositis juvenile dermatomyositis malignant ependymoma myocardial ischemia osteosarcoma polycystic ovary syndrome breast carcinoma glioblastoma large cell medulloblastoma malignant glioma nicotine dependence ovarian cancer

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.