8DMK | pdb_00008dmk

Cryo-EM reveals the molecular basis of laminin polymerization and LN-lamininopathies

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Laminin_N	e8dmkA2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Laminin_N	ECOD (1.6)
A	Laminin_EGF_2	e8dmkA1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_2	ECOD (1.6)
C [auth G]	Laminin_N	e8dmkG2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Laminin_N	ECOD (1.6)
C [auth G]	Laminin_EGF_2	e8dmkG1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_2	ECOD (1.6)
B	Laminin_N	e8dmkB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: Laminin_N	ECOD (1.6)
B	Laminin_EGF_2	e8dmkB2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: Laminin_EGF_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (utative)
C [auth G]	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (utative)
B	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00053	Laminin EGF domain (EGF_laminin)	Laminin EGF domain	This family is like Pfam:PF00008 but has 8 conserved cysteines instead of six.	Domain
A	PF00055	Laminin N-terminal (Domain VI) (Laminin_N)	Laminin N-terminal (Domain VI)		Domain
C [auth G]	PF24973	Laminin/attractin EGF domain (EGF_LMN_ATRN)	Laminin/attractin EGF domain	This entry represents the EGF-like domains found in laminin subunits (alpha, beta, gamma), attractin (ATRN), netrin, among others. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activi ...	This entry represents the EGF-like domains found in laminin subunits (alpha, beta, gamma), attractin (ATRN), netrin, among others. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activity of chemokines. It may play a role in melanocortin signaling pathways that regulate energy homeostasis and hair color [1]. It was thought to have dipeptidase activity but it was shown later to lack that activity [2]. Laminins are crucial for the formation of stable basement membranes and organising receptor complexes and cytoskeletal components. Netrins control guidance of central nervous system commissural axons and peripheral motor axons, serving as survival factors and regulating apoptosis.	Domain
C [auth G]	PF00055	Laminin N-terminal (Domain VI) (Laminin_N)	Laminin N-terminal (Domain VI)		Domain
B	PF00053	Laminin EGF domain (EGF_laminin)	Laminin EGF domain	This family is like Pfam:PF00008 but has 8 conserved cysteines instead of six.	Domain
B	PF00055	Laminin N-terminal (Domain VI) (Laminin_N)	Laminin N-terminal (Domain VI)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Laminin subunit alpha-1	glycosphingolipid binding binding sphingolipid binding lipid binding glycolipid binding carbohydrate derivative binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity structural molecule activity extracellular matrix structural constituent	cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling Rac protein signal transduction biological regulation positive regulation of intracellular signal transduction regulation of Rac protein signal transduction positive regulation of Rac protein signal transduction regulation of response to stimulus regulation of cell communication cellular process positive regulation of small GTPase mediated signal transduction positive regulation of signaling regulation of localization cellular localization regulation of protein localization cellular component organization localization neuromuscular junction development receptor clustering synapse organization cellular component organization or biogenesis intracellular protein localization regulation of skeletal muscle acetylcholine-gated channel clustering regulation of receptor clustering postsynaptic membrane organization regulation of protein localization to membrane membrane organization postsynapse organization positive regulation of receptor clustering skeletal muscle acetylcholine-gated channel clustering positive regulation of protein localization to membrane localization within membrane protein localization to membrane positive regulation of skeletal muscle acetylcholine-gated channel clustering cell junction organization regulation of cellular localization macromolecule localization positive regulation of protein localization developmental process anatomical structure development tissue development anatomical structure morphogenesis animal organ development animal organ morphogenesis tissue morphogenesis epithelium development morphogenesis of an epithelium morphogenesis of an epithelial sheet regulation of developmental process cellular developmental process regulation of cell differentiation muscle cell differentiation positive regulation of muscle cell differentiation muscle structure development positive regulation of developmental process regulation of muscle cell differentiation positive regulation of cell differentiation cell differentiation multicellular organismal process sensory organ development eye development visual system development multicellular organism development camera-type eye development sensory system development system development retina development in camera-type eye branching morphogenesis of an epithelial tube respiratory tube development tube morphogenesis lung morphogenesis lung development respiratory system development epithelial tube morphogenesis tube development morphogenesis of a branching structure epithelial tube branching involved in lung morphogenesis morphogenesis of a branching epithelium regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction polarized epithelial cell differentiation establishment of monopolar cell polarity establishment or maintenance of monopolar cell polarity establishment or maintenance of cell polarity epithelial cell differentiation morphogenesis of a polarized epithelium establishment or maintenance of apical/basal cell polarity establishment or maintenance of bipolar cell polarity establishment of epithelial cell apical/basal polarity establishment of cell polarity establishment or maintenance of epithelial cell apical/basal polarity establishment of apical/basal cell polarity establishment of epithelial cell polarity regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion cell adhesion positive regulation of cell adhesion regulation of cell adhesion regulation of integrin-mediated signaling pathway positive regulation of integrin-mediated signaling pathway integrin-mediated signaling pathway cell surface receptor signaling pathway axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis plasma membrane bounded cell projection organization axon guidance nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron projection guidance neuron development regulation of embryonic development regulation of multicellular organismal development embryo development regulation of multicellular organismal process regulation of cellular component organization extracellular matrix organization regulation of basement membrane organization regulation of extracellular matrix organization extracellular structure organization external encapsulating structure organization basement membrane organization gland development branching involved in salivary gland morphogenesis salivary gland development gland morphogenesis salivary gland morphogenesis exocrine system development blood vessel morphogenesis retina vasculature development in camera-type eye retina vasculature morphogenesis in camera-type eye vasculature development circulatory system development retinal blood vessel morphogenesis blood vessel development	basement membrane protein-containing complex extracellular matrix solid phase of basement membrane laminin-111 trimer laminin trimer laminin network cell periphery cellular anatomical structure external encapsulating structure non-collagenous component of basement membrane supramolecular complex membrane cell-cell junction basement membrane protein-containing complex extracellular matrix solid phase of basement membrane laminin-111 trimer laminin trimer laminin network cell periphery cellular anatomical structure external encapsulating structure non-collagenous component of basement membrane supramolecular complex membrane cell-cell junction anchoring junction cell junction extracellular region protein complex involved in cell-matrix adhesion protein complex involved in cell adhesion extracellular space laminin-121 trimer
C [auth G]	Laminin subunit gamma-1	structural molecule activity extracellular matrix structural constituent	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation developmental process regulation of developmental process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation developmental process regulation of developmental process cellular developmental process positive regulation of biological process regulation of cell differentiation muscle cell differentiation positive regulation of muscle cell differentiation muscle structure development positive regulation of developmental process regulation of muscle cell differentiation positive regulation of cell differentiation cell differentiation anatomical structure development positive regulation of cellular process substrate adhesion-dependent cell spreading cell-substrate adhesion endoderm development tissue development cell population proliferation positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation cell junction organization cell junction assembly cell-substrate junction assembly cell-substrate junction organization hemidesmosome assembly cellular component disassembly extracellular matrix disassembly extracellular matrix organization extracellular structure organization external encapsulating structure organization cell migration cell motility regulation of cell motility regulation of locomotion regulation of cell migration locomotion cellular response to stimulus response to stimulus signaling signal transduction cell communication positive regulation of cell adhesion positive regulation of cell communication regulation of integrin-mediated signaling pathway positive regulation of signal transduction regulation of signal transduction positive regulation of response to stimulus positive regulation of integrin-mediated signaling pathway regulation of signaling integrin-mediated signaling pathway cell surface receptor signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling multicellular organismal process maintenance of blood-brain barrier multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis regulation of embryonic development regulation of multicellular organismal development embryo development multicellular organism development regulation of multicellular organismal process regulation of cellular component organization regulation of basement membrane organization regulation of extracellular matrix organization basement membrane organization	basement membrane protein-containing complex extracellular matrix solid phase of basement membrane laminin-111 trimer laminin trimer laminin network cell periphery cellular anatomical structure external encapsulating structure non-collagenous component of basement membrane supramolecular complex extracellular exosome membrane-bounded organelle basement membrane protein-containing complex extracellular matrix solid phase of basement membrane laminin-111 trimer laminin trimer laminin network cell periphery cellular anatomical structure external encapsulating structure non-collagenous component of basement membrane supramolecular complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle laminin-511 trimer intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen endoplasmic reticulum cytoplasm laminin-521 trimer protein complex involved in cell-matrix adhesion protein complex involved in cell adhesion
B	Laminin subunit beta-1	glycosphingolipid binding binding sphingolipid binding lipid binding glycolipid binding carbohydrate derivative binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding structural molecule activity extracellular matrix structural constituent enzyme binding	regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation cellular process developmental process regulation of developmental process cellular developmental process positive regulation of biological process regulation of cell differentiation muscle cell differentiation positive regulation of muscle cell differentiation muscle structure development regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation cellular process developmental process regulation of developmental process cellular developmental process positive regulation of biological process regulation of cell differentiation muscle cell differentiation positive regulation of muscle cell differentiation muscle structure development positive regulation of developmental process regulation of muscle cell differentiation positive regulation of cell differentiation cell differentiation anatomical structure development positive regulation of cellular process multicellular organismal process formation of primary germ layer embryonic morphogenesis tissue development embryo development gastrulation anatomical structure morphogenesis multicellular organism development endoderm development anatomical structure formation involved in morphogenesis endoderm formation endodermal cell differentiation substrate adhesion-dependent cell spreading cell-substrate adhesion cell population proliferation positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion cellular response to stimulus response to stimulus signaling signal transduction cell communication multi-multicellular organism process reproductive process female pregnancy embryo implantation multi-organism reproductive process positive regulation of cell adhesion positive regulation of cell communication regulation of integrin-mediated signaling pathway positive regulation of signal transduction regulation of signal transduction positive regulation of response to stimulus positive regulation of integrin-mediated signaling pathway regulation of signaling integrin-mediated signaling pathway cell surface receptor signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling odontogenesis animal organ development animal organ morphogenesis positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility forebrain development glial cell migration telencephalon glial cell migration cerebral cortex development neurogenesis cell-cell adhesion telencephalon cell migration forebrain cell migration gliogenesis system development cerebral cortex cell migration head development neuronal-glial interaction involved in cerebral cortex radial glia guided migration brain development nervous system development cerebral cortex radially oriented cell migration pallium development central nervous system development cerebral cortex radial glia-guided migration telencephalon development regulation of embryonic development regulation of multicellular organismal development regulation of multicellular organismal process regulation of cellular component organization extracellular matrix organization cellular component organization cellular component organization or biogenesis regulation of basement membrane organization regulation of extracellular matrix organization extracellular structure organization external encapsulating structure organization basement membrane organization plasma membrane bounded cell projection organization cell projection organization cell development neuron projection development generation of neurons neuron differentiation neuron development negative regulation of cellular process negative regulation of biological process negative regulation of cell adhesion	basement membrane protein-containing complex extracellular matrix solid phase of basement membrane laminin-111 trimer laminin trimer laminin network cell periphery cellular anatomical structure external encapsulating structure non-collagenous component of basement membrane supramolecular complex extracellular exosome membrane-bounded organelle basement membrane protein-containing complex extracellular matrix solid phase of basement membrane laminin-111 trimer laminin trimer laminin network cell periphery cellular anatomical structure external encapsulating structure non-collagenous component of basement membrane supramolecular complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle laminin-511 trimer laminin-211 trimer intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen endoplasmic reticulum cytoplasm perinuclear region of cytoplasm protein complex involved in cell-matrix adhesion protein complex involved in cell adhesion laminin-411 trimer nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008211	Laminin, N-terminal	Domain
A	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A	IPR002049	Laminin-type EGF domain	Domain
A	IPR010307	Laminin domain II	Domain
A	IPR000742	EGF-like domain	Domain
A	IPR001791	Laminin G domain	Domain
A	IPR056863	Laminin/attractin/netrin-like, EGF domain	Domain
A	IPR009254	Laminin alpha, domain I	Domain
A	IPR050440	Laminin/Netrin Extracellular Matrix	Family
A	IPR000034	Laminin IV	Domain
C [auth G]	IPR008211	Laminin, N-terminal	Domain
C [auth G]	IPR002049	Laminin-type EGF domain	Domain
C [auth G]	IPR000742	EGF-like domain	Domain
C [auth G]	IPR056863	Laminin/attractin/netrin-like, EGF domain	Domain
C [auth G]	IPR050440	Laminin/Netrin Extracellular Matrix	Family
C [auth G]	IPR000034	Laminin IV	Domain
B	IPR008211	Laminin, N-terminal	Domain
B	IPR013015	Laminin IV type B	Domain
B	IPR002049	Laminin-type EGF domain	Domain
B	IPR056558	LAMB1/2/3/4, helical domain	Domain
B	IPR000742	EGF-like domain	Domain
B	IPR056863	Laminin/attractin/netrin-like, EGF domain	Domain
B	IPR050440	Laminin/Netrin Extracellular Matrix	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth G]	Pharos: P11047	Marfan syndrome aortic disease colorectal cancer prostate cancer malignant glioma nasopharyngeal carcinoma ovarian cancer plasma cell myeloma acne Prostatic Neoplasms atypical teratoid rhabdoid tumor colorectal adenoma Duchenne muscular dystrophy Fuchs' endothelial dystrophy invasive ductal breast carcinoma Marfan syndrome aortic disease colorectal cancer prostate cancer malignant glioma nasopharyngeal carcinoma ovarian cancer plasma cell myeloma acne Prostatic Neoplasms atypical teratoid rhabdoid tumor colorectal adenoma Duchenne muscular dystrophy Fuchs' endothelial dystrophy invasive ductal breast carcinoma lung cancer malignant mesothelioma medulloblastoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma primitive neuroectodermal tumor subependymal giant cell astrocytoma breast carcinoma ductal breast carcinoma in situ gastric carcinoma juvenile dermatomyositis malignant ependymoma malignant pancreatic neoplasm myopathy osteosarcoma pilocytic astrocytoma astrocytic tumor ulcerative colitis breast fibroadenoma dermatomyositis Emery-Dreifuss muscular dystrophy glioblastoma large cell medulloblastoma
B	Pharos: P07942	ulcerative colitis lissencephaly spectrum disorders cobblestone lissencephaly without muscular or ocular involvement coloboma endometriosis pulmonary fibrosis hydrocephalus intellectual disability Malformations of Cortical Development acute myeloid leukemia malignant pancreatic neoplasm nasopharyngeal carcinoma Crohn disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia diabetes mellitus ulcerative colitis lissencephaly spectrum disorders cobblestone lissencephaly without muscular or ocular involvement coloboma endometriosis pulmonary fibrosis hydrocephalus intellectual disability Malformations of Cortical Development acute myeloid leukemia malignant pancreatic neoplasm nasopharyngeal carcinoma Crohn disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia diabetes mellitus psoriasis Sjogren syndrome glioblastoma idiopathic interstitial pneumonia juvenile dermatomyositis lung adenocarcinoma malignant glioma medulloblastoma breast cancer oligodendroglioma pancreatic ductal adenocarcinoma cystic fibrosis pilocytic astrocytoma Duchenne muscular dystrophy pterygium inflammatory bowel disease large cell medulloblastoma lung carcinoma malignant mesothelioma autism myopathy cerebrovascular disorder ovarian cancer pancreatic intraductal papillary-mucinous neoplasm dermatomyositis pituitary cancer Emery-Dreifuss muscular dystrophy gastric carcinoma