3MUD

Structure of the Tropomyosin Overlap Complex from Chicken Smooth Muscle

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8036633	3001319	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	XRCC4 N-terminal domain-like	8036633	3001319	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	XRCC4_1st	e3mudA3	A: beta barrels	X: XRCC4, N-terminal domain-like	H: XRCC4, N-terminal domain (From Topology)	T: XRCC4, N-terminal domain	F: XRCC4_1st	ECOD (1.6)
A	XRCC4_2nd	e3mudA1	A: alpha arrays	X: HTH	H: HTH	T: HTH motif inserted in other structures	F: XRCC4_2nd	ECOD (1.6)
A	XRCC4_3rd_2,Tropomyosin_2	e3mudA2	A: alpha duplicates or obligate multimers	X: XRCC4 C-terminal oligomerization domain (From Topology)	H: XRCC4 C-terminal oligomerization domain (From Topology)	T: XRCC4 C-terminal oligomerization domain	F: XRCC4_3rd_2,Tropomyosin_2	ECOD (1.6)
B	XRCC4_1st	e3mudB2	A: beta barrels	X: XRCC4, N-terminal domain-like	H: XRCC4, N-terminal domain (From Topology)	T: XRCC4, N-terminal domain	F: XRCC4_1st	ECOD (1.6)
B	XRCC4_2nd	e3mudB3	A: alpha arrays	X: HTH	H: HTH	T: HTH motif inserted in other structures	F: XRCC4_2nd	ECOD (1.6)
B	XRCC4_3rd_2,Tropomyosin_2	e3mudB1	A: alpha duplicates or obligate multimers	X: XRCC4 C-terminal oligomerization domain (From Topology)	H: XRCC4 C-terminal oligomerization domain (From Topology)	T: XRCC4 C-terminal oligomerization domain	F: XRCC4_3rd_2,Tropomyosin_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	CATH (4.3.0)
A	1.20.5.370	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	2.170.210.10	Mainly Beta	Beta Complex	Dna Repair Protein Xrcc4	Chain: A, domain 1	CATH (4.3.0)
B	1.20.5.370	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	1.20.5.1160	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Vasodilator-stimulated phosphoprotein	CATH (4.3.0)
D	1.20.5.1160	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Vasodilator-stimulated phosphoprotein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF06632	XRCC4 N-terminal domain (XRCC4)	XRCC4 N-terminal domain	This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalysed by a complex of XRC ...	This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalysed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks [1]. This entry represents the N-terminal beta sandwich domain.	Domain
C, D	PF03271	EB1-like C-terminal motif (EB1)	EB1-like C-terminal motif	-	Family
C, D	PF00261	Tropomyosin (Tropomyosin)	Tropomyosin	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA repair protein XRCC4,Tropomyosin alpha-1 chain	protein heterodimerization activity protein binding binding protein dimerization activity cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding identical protein binding protein homodimerization activity FHA domain binding protein domain specific binding	cellular component organization organelle organization actin cytoskeleton organization actin filament organization actin filament-based process cellular process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization heart process multicellular organismal process system process circulatory system process cardiac muscle contraction cellular component organization organelle organization actin cytoskeleton organization actin filament organization actin filament-based process cellular process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization heart process multicellular organismal process system process circulatory system process cardiac muscle contraction heart contraction muscle contraction muscle system process blood circulation striated muscle contraction cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to lithium ion cellular response to lithium ion response to stimulus response to metal ion response to chemical positive regulation of molecular function regulation of molecular function regulation of ligase activity regulation of catalytic activity biological regulation positive regulation of catalytic activity positive regulation of ligase activity response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus DNA ligation involved in DNA repair primary metabolic process DNA metabolic process nucleic acid metabolic process DNA ligation nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair protein localization localization cellular localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to site of double-strand break double-strand break repair immune system development immunoglobulin production cellular biosynthetic process somatic cell DNA recombination multicellular organism development V(D)J recombination somatic recombination of immunoglobulin gene segments anatomical structure development somatic diversification of immune receptors system development developmental process production of molecular mediator of immune response DNA recombination cellular metabolic process gene expression macromolecule biosynthetic process somatic diversification of immunoglobulins immunoglobulin V(D)J recombination biosynthetic process immune system process somatic diversification of immune receptors via germline recombination within a single locus double-strand break repair via nonhomologous end joining	polymeric cytoskeletal fiber intracellular anatomical structure actin filament cellular anatomical entity actin cytoskeleton intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle supramolecular fiber supramolecular polymer supramolecular complex non-membrane-bounded organelle cell periphery polymeric cytoskeletal fiber intracellular anatomical structure actin filament cellular anatomical entity actin cytoskeleton intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle supramolecular fiber supramolecular polymer supramolecular complex non-membrane-bounded organelle cell periphery plasma membrane membrane cytoplasm protein-containing complex nonhomologous end joining complex catalytic complex intracellular protein-containing complex DNA repair complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle DNA-dependent protein kinase-DNA ligase 4 complex cytosol DNA ligase IV complex site of double-strand break site of DNA damage chromosome membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, D	Tropomyosin alpha-1 chain,Microtubule-associated protein RP/EB family member 1	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding structural molecule activity structural constituent of muscle protein heterodimerization activity protein dimerization activity identical protein binding protein homodimerization activity structural constituent of cytoskeleton RNA binding cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding structural molecule activity structural constituent of muscle protein heterodimerization activity protein dimerization activity identical protein binding protein homodimerization activity structural constituent of cytoskeleton RNA binding organic cyclic compound binding nucleic acid binding kinase binding enzyme binding protein kinase binding cell adhesion molecule binding cadherin binding microtubule plus-end binding microtubule binding tubulin binding	heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation regulation of multicellular organismal process heart contraction blood circulation regulation of muscle contraction muscle contraction heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation regulation of multicellular organismal process heart contraction blood circulation regulation of muscle contraction muscle contraction regulation of muscle system process muscle system process regulation of vascular associated smooth muscle cell migration negative regulation of locomotion vascular associated smooth muscle cell migration regulation of cell motility regulation of cellular process negative regulation of vascular associated smooth muscle cell migration regulation of smooth muscle cell migration negative regulation of biological process smooth muscle cell migration muscle cell migration negative regulation of smooth muscle cell migration regulation of locomotion regulation of cell migration negative regulation of cellular process negative regulation of cell motility cell migration cellular process cell motility locomotion negative regulation of cell migration muscle filament sliding actin filament-based process actin-mediated cell contraction actin filament-based movement actin-myosin filament sliding developmental process regulation of developmental process regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cell adhesion positive regulation of cell adhesion regulation of cell adhesion positive regulation of biological process positive regulation of cellular process cellular component organization organelle organization cellular component organization or biogenesis cytoskeleton organization cellular response to stimulus response to stimulus cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound response to reactive oxygen species cellular response to reactive oxygen species response to oxidative stress cellular response to chemical stimulus cellular response to stress response to stress response to chemical wound healing response to wounding plasma membrane bounded cell projection organization ruffle organization cell projection organization cardiac muscle contraction striated muscle contraction actin cytoskeleton organization actin filament organization supramolecular fiber organization ventricular cardiac muscle tissue morphogenesis heart morphogenesis striated muscle tissue development muscle structure development multicellular organism development ventricular cardiac muscle tissue development cardiac chamber development animal organ morphogenesis muscle tissue development muscle organ development system development heart development cardiac chamber morphogenesis cardiac muscle tissue development animal organ development tissue development muscle tissue morphogenesis circulatory system development tissue morphogenesis cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis cardiac ventricle development muscle organ morphogenesis positive regulation of molecular function regulation of molecular function regulation of ATP-dependent activity positive regulation of ATP-dependent activity positive regulation of organelle organization regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process positive regulation of cellular component organization regulation of actin filament bundle assembly cellular component biogenesis cellular component assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly stress fiber assembly regulation of actin filament organization actomyosin structure organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of organelle organization regulation of stress fiber assembly contractile actin filament bundle assembly regulation of actomyosin structure organization actin filament bundle assembly regulation of actin cytoskeleton organization regulation of supramolecular fiber organization cellular developmental process cellular component assembly involved in morphogenesis non-membrane-bounded organelle assembly cell development muscle cell differentiation striated muscle cell development cellular anatomical entity morphogenesis muscle cell development cell differentiation sarcomere organization organelle assembly myofibril assembly anatomical structure formation involved in morphogenesis striated muscle cell differentiation regulation of vascular associated smooth muscle cell proliferation negative regulation of cell population proliferation cell population proliferation regulation of smooth muscle cell proliferation negative regulation of vascular associated smooth muscle cell proliferation smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation regulation of systemic arterial blood pressure mediated by a chemical signal positive regulation of blood pressure positive regulation of blood circulation regulation of systemic arterial blood pressure by norepinephrine-epinephrine positive regulation of blood pressure by epinephrine-norepinephrine regulation of heart rate regulation of heart rate by chemical signal regulation of blood pressure positive regulation of heart rate positive regulation of heart rate by epinephrine-norepinephrine positive regulation of heart contraction regulation of systemic arterial blood pressure positive regulation of heart rate by epinephrine positive regulation of multicellular organismal process microtubule bundle formation microtubule cytoskeleton organization microtubule-based process protein localization localization cellular localization cellular macromolecule localization macromolecule localization protein localization to microtubule cytoskeleton protein localization to microtubule organizing center protein localization to cytoskeleton protein localization to organelle protein localization to centrosome regulation of microtubule polymerization or depolymerization regulation of protein-containing complex assembly microtubule polymerization or depolymerization protein-containing complex assembly negative regulation of protein polymerization negative regulation of supramolecular fiber organization protein polymerization negative regulation of cellular component organization negative regulation of microtubule polymerization or depolymerization protein-containing complex organization negative regulation of cytoskeleton organization regulation of microtubule-based process negative regulation of microtubule polymerization microtubule polymerization negative regulation of protein-containing complex assembly negative regulation of organelle organization regulation of protein polymerization regulation of microtubule polymerization regulation of microtubule cytoskeleton organization establishment of organelle localization mitotic metaphase chromosome alignment mitotic cell cycle metaphase chromosome alignment chromosome localization organelle localization establishment of localization in cell 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 establishment of localization nuclear division mitotic cell cycle process nuclear chromosome segregation establishment of chromosome localization cell division spindle assembly spindle 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 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 positive regulation of protein-containing complex assembly positive regulation of protein polymerization positive regulation of microtubule polymerization or depolymerization positive regulation of microtubule polymerization	ruffle cell leading edge plasma membrane membrane leading edge membrane cellular anatomical entity plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane intracellular organelle intracellular anatomical structure ruffle cell leading edge plasma membrane membrane leading edge membrane cellular anatomical entity plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cytoplasm cytosol striated muscle thin filament protein-containing complex myofilament muscle thin filament tropomyosin sarcomere contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex bleb actin filament bundle actomyosin stress fiber contractile actin filament bundle polymeric cytoskeletal fiber actin filament anchoring junction cell junction focal adhesion cell-substrate junction spindle spindle midzone microtubule cytoskeleton centrosome microtubule organizing center mitotic spindle aster spindle microtubule cytoplasmic microtubule mitotic spindle astral microtubule end microtubule end mitotic spindle astral microtubule astral microtubule microtubule microtubule plus-end 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000533	Tropomyosin	Family
A, B	IPR014751	DNA repair protein XRCC4-like, C-terminal	Homologous Superfamily
A, B	IPR010585	DNA repair protein XRCC4	Family
A, B	IPR038051	XRCC4-like, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR009089	XRCC4, N-terminal domain superfamily	Homologous Superfamily
C, D	IPR000533	Tropomyosin	Family
C, D	IPR001715	Calponin homology domain	Domain
C, D	IPR004953	EB1, C-terminal	Domain
C, D	IPR027328	Microtubule-associated protein RP/EB	Family
C, D	IPR036133	EB1, C-terminal domain superfamily	Homologous Superfamily
C, D	IPR036872	CH domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q13426	short stature, microcephaly, and endocrine dysfunction DNA ligase IV deficiency Chromosome Aberrations pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia astrocytic tumor congestive heart failure isolated growth hormone deficiency type IA malignant mesothelioma microcephalic primordial dwarfism-insulin resistance syndrome pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma primitive neuroectodermal tumor malignant colon neoplasm malignant pancreatic neoplasm short stature, microcephaly, and endocrine dysfunction DNA ligase IV deficiency Chromosome Aberrations pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia astrocytic tumor congestive heart failure isolated growth hormone deficiency type IA malignant mesothelioma microcephalic primordial dwarfism-insulin resistance syndrome pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma primitive neuroectodermal tumor malignant colon neoplasm malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm pituitary cancer psoriasis tuberculosis intellectual disability malignant ependymoma medulloblastoma osteosarcoma
C, D	Pharos: Q15691	hypertrophic cardiomyopathy 3 left ventricular noncompaction hypertrophic cardiomyopathy dilated cardiomyopathy dilated cardiomyopathy 1Y esophageal squamous cell carcinoma keloid Liver Cirrhosis, Experimental esophageal cancer hypertensive disorder cardiomyopathy familial hypertrophic cardiomyopathy gastric carcinoma acute myeloid leukemia breast cancer hypertrophic cardiomyopathy 3 left ventricular noncompaction hypertrophic cardiomyopathy dilated cardiomyopathy dilated cardiomyopathy 1Y esophageal squamous cell carcinoma keloid Liver Cirrhosis, Experimental esophageal cancer hypertensive disorder cardiomyopathy familial hypertrophic cardiomyopathy gastric carcinoma acute myeloid leukemia breast cancer malignant mesothelioma myopathy ovarian cancer psoriasis Emery-Dreifuss muscular dystrophy exocrine pancreatic carcinoma familial isolated dilated cardiomyopathy glioblastoma large cell medulloblastoma atopic eczema breast fibroadenoma malignant pancreatic neoplasm neoplasm of esophagus pancreatic ductal adenocarcinoma cystic fibrosis familial dilated cardiomyopathy gastric cancer atypical teratoid rhabdoid tumor malignant colon neoplasm medulloblastoma Charcot-Marie-Tooth disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia dermatomyositis Duchenne muscular dystrophy 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 R01GM133198.