3GEF | pdb_00003gef

Crystal structure of the R482W mutant of lamin A/C

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3gefd1	All beta proteins	Immunoglobulin-like beta-sandwich	Lamin A/C globular tail domain	Lamin A/C globular tail domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3gefd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3gefc1	All beta proteins	Immunoglobulin-like beta-sandwich	Lamin A/C globular tail domain	Lamin A/C globular tail domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3gefc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3gefb1	All beta proteins	Immunoglobulin-like beta-sandwich	Lamin A/C globular tail domain	Lamin A/C globular tail domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3gefb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3gefa1	All beta proteins	Immunoglobulin-like beta-sandwich	Lamin A/C globular tail domain	Lamin A/C globular tail domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3gefa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	Lamin A/C globular tail domain	8055285	3002064	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lamin A/C globular tail domain	8055285	3002064	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lamin A/C globular tail domain	8055285	3002064	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lamin A/C globular tail domain	8055285	3002064	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	Ribosomal_L36	e3gefD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (v294.1)
C	Ribosomal_L36	e3gefC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (v294.1)
B	Ribosomal_L36	e3gefB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (v294.1)
A	TGF_beta	e3gefA1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: HMA-related	T: HMA, heavy metal-associated domain	F: TGF_beta	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.40.1260	Mainly Beta	Sandwich	Immunoglobulin-like	Lamin Tail domain	CATH (4.3.0)
C	2.60.40.1260	Mainly Beta	Sandwich	Immunoglobulin-like	Lamin Tail domain	CATH (4.3.0)
B	2.60.40.1260	Mainly Beta	Sandwich	Immunoglobulin-like	Lamin Tail domain	CATH (4.3.0)
A	2.60.40.1260	Mainly Beta	Sandwich	Immunoglobulin-like	Lamin Tail domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00932	Lamin Tail Domain (LTD)	Lamin Tail Domain	The lamin-tail domain (LTD), which has an immunoglobulin (Ig) fold, is found in Nuclear Lamins, Chlo1887 from Chloroflexus, and several bacterial proteins where it occurs with membrane associated hydrolases of the metallo-beta-lactamase,synaptojanin ...	The lamin-tail domain (LTD), which has an immunoglobulin (Ig) fold, is found in Nuclear Lamins, Chlo1887 from Chloroflexus, and several bacterial proteins where it occurs with membrane associated hydrolases of the metallo-beta-lactamase,synaptojanin, and calcineurin-like phosphoesterase superfamilies [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Lamin-A/C	structural molecule activity structural constituent of nuclear lamina structural constituent of cytoskeleton identical protein binding protein binding binding	nuclear pore localization cellular localization localization within membrane protein-containing complex localization cellular component organization localization nucleus organization organelle organization macromolecule localization cellular process cellular component organization or biogenesis membrane organization nuclear envelope organization endomembrane system organization nuclear pore localization cellular localization localization within membrane protein-containing complex localization cellular component organization localization nucleus organization organelle organization macromolecule localization cellular process cellular component organization or biogenesis membrane organization nuclear envelope organization endomembrane system organization regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus establishment of organelle localization transport nucleus localization intracellular transport establishment of localization organelle localization establishment of localization in cell nuclear migration developmental process muscle structure development animal organ development anatomical structure development muscle organ development protein localization to organelle protein localization to nucleus intracellular protein localization protein localization to nuclear envelope establishment of protein localization nucleocytoplasmic transport nuclear transport intercellular transport import into nucleus establishment of protein localization to organelle protein transport protein import into nucleus intracellular protein transport regulation of telomere maintenance regulation of cellular component organization telomere organization regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process chromosome organization primary metabolic process regulation of chromosome organization DNA metabolic process regulation of organelle organization nucleic acid metabolic process telomere maintenance regulation of DNA metabolic process regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion cellular senescence negative regulation of cell population proliferation cell population proliferation negative regulation of biological process regulation of mesenchymal cell proliferation regulation of cell population proliferation mesenchymal cell proliferation negative regulation of cellular process negative regulation of mesenchymal cell proliferation regulation of localization regulation of protein localization regulation of protein localization to nucleus DNA double-strand break attachment to nuclear envelope chromosome localization chromosome attachment to the nuclear envelope cell cycle cell cycle process regulation of protein stability regulation of biological quality ventricular cardiac muscle cell differentiation multicellular organismal process cellular developmental process cardiac muscle cell development cell development muscle cell differentiation striated muscle tissue development multicellular organism development striated muscle cell development muscle cell development cell differentiation muscle tissue development cardiac cell development system development heart development cardiac muscle tissue development cardiac muscle cell differentiation tissue development ventricular cardiac muscle cell development cardiocyte differentiation circulatory system development striated muscle cell differentiation signaling negative regulation of signaling apoptotic mitochondrial changes regulation of signal transduction regulation of release of cytochrome c from mitochondria regulation of programmed cell death negative regulation of cell communication cell communication negative regulation of release of cytochrome c from mitochondria negative regulation of apoptotic signaling pathway signal transduction mitochondrion organization regulation of signaling negative regulation of cellular component organization negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction apoptotic signaling pathway release of cytochrome c from mitochondria negative regulation of apoptotic process negative regulation of organelle organization regulation of response to stimulus regulation of mitochondrion organization regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway establishment or maintenance of microtubule cytoskeleton polarity establishment or maintenance of cytoskeleton polarity microtubule cytoskeleton organization microtubule-based process establishment or maintenance of cell polarity cytoskeleton organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling negative regulation of macromolecule metabolic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic negative regulation of muscle adaptation system process striated muscle adaptation negative regulation of muscle hypertrophy regulation of system process regulation of muscle hypertrophy regulation of cardiac muscle hypertrophy in response to stress muscle adaptation cardiac muscle adaptation regulation of response to stress cardiac muscle hypertrophy regulation of multicellular organismal process cardiac muscle hypertrophy in response to stress muscle hypertrophy regulation of muscle adaptation negative regulation of cardiac muscle hypertrophy in response to stress striated muscle hypertrophy regulation of muscle system process muscle system process regulation of cardiac muscle hypertrophy negative regulation of cardiac muscle adaptation negative regulation of multicellular organismal process regulation of cardiac muscle adaptation negative regulation of cardiac muscle hypertrophy muscle hypertrophy in response to stress extrinsic apoptotic signaling pathway negative regulation of extrinsic apoptotic signaling pathway cell surface receptor signaling pathway regulation of extrinsic apoptotic signaling pathway double-strand break repair double-strand break repair via nonhomologous end joining DNA damage response DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix organelle envelope nuclear envelope membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix organelle envelope nuclear envelope endomembrane system intracellular membraneless organelle nuclear speck ribonucleoprotein granule nuclear body nucleoplasm membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear membrane membrane organelle membrane polymeric cytoskeletal fiber intermediate filament cytoskeleton cytoskeleton intermediate filament supramolecular fiber supramolecular polymer cytoplasm cytosol lamin filament nuclear lamina nuclear periphery perinuclear region of cytoplasm site of double-strand break site of DNA damage chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018039	Intermediate filament protein, conserved site	Conserved Site
A, B, C, D	IPR036415	Lamin tail domain superfamily	Homologous Superfamily
A, B, C, D	IPR039008	Intermediate filament, rod domain	Domain
A, B, C, D	IPR001322	Lamin tail domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P02545	Hutchinson-Gilford progeria syndrome limb-girdle muscular dystrophy Emery-Dreifuss muscular dystrophy congenital muscular dystrophy due to LMNA mutation dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Charcot-Marie-Tooth disease dilated cardiomyopathy heart-hand syndrome, Slovenian type Charcot-Marie-Tooth disease type 2B1 left ventricular noncompaction familial partial lipodystrophy lethal restrictive dermopathy localized scleroderma Emery-Dreifuss muscular dystrophy 3, autosomal recessive mandibuloacral dysplasia with type A lipodystrophy Hutchinson-Gilford progeria syndrome limb-girdle muscular dystrophy Emery-Dreifuss muscular dystrophy congenital muscular dystrophy due to LMNA mutation dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome Charcot-Marie-Tooth disease dilated cardiomyopathy heart-hand syndrome, Slovenian type Charcot-Marie-Tooth disease type 2B1 left ventricular noncompaction familial partial lipodystrophy lethal restrictive dermopathy localized scleroderma Emery-Dreifuss muscular dystrophy 3, autosomal recessive mandibuloacral dysplasia with type A lipodystrophy myopathy congenital muscular dystrophy ventricular tachycardia arrhythmogenic right ventricular cardiomyopathy polycystic ovary syndrome sinoatrial block dilated cardiomyopathy 1A Emery-Dreifuss muscular dystrophy 2, autosomal dominant familial partial lipodystrophy, Dunnigan type atrioventricular block atypical Werner syndrome scleroderma Craniofacial Abnormalities cardiomyopathy peripheral neuropathy Werner syndrome linear scleroderma Sjogren syndrome diabetes mellitus lung carcinoma tuberculosis malignant pancreatic neoplasm X-linked Emery-Dreifuss muscular dystrophy muscle tissue disease glioblastoma autosomal recessive Emery-Dreifuss muscular dystrophy heart disease osteosarcoma peripheral nervous system disease plasma cell myeloma laminopathy type Decaudain-Vigouroux psoriasis lipodystrophy subependymal giant cell astrocytoma lung adenocarcinoma testicular cancer malignant ependymoma familial atrial fibrillation MALT lymphoma atrioventricular dissociation muscular disease neurodegenerative disease ovarian cancer hypertrophic cardiomyopathy sarcoidosis LMNA-related cardiocutaneous progeria syndrome sudden cardiac arrest lung cancer testicular germ cell tumor malignant glioma arthrogryposis motor peripheral neuropathy atypical teratoid rhabdoid tumor gastric carcinoma muscular dystrophy osteogenesis imperfecta cerebrovascular disorder pancreatic ductal adenocarcinoma pilocytic astrocytoma chronic obstructive pulmonary disease intellectual disability

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

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.