1LI1 | pdb_00001li1

The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link

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	d1li1a1	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	Noncollagenous (NC1) domain of collagen IV	Noncollagenous (NC1) domain of collagen IV	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1li1b1	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	Noncollagenous (NC1) domain of collagen IV	Noncollagenous (NC1) domain of collagen IV	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1li1d1	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	Noncollagenous (NC1) domain of collagen IV	Noncollagenous (NC1) domain of collagen IV	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1li1e1	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	Noncollagenous (NC1) domain of collagen IV	Noncollagenous (NC1) domain of collagen IV	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1li1c1	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	Noncollagenous (NC1) domain of collagen IV	Noncollagenous (NC1) domain of collagen IV	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1li1f1	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	Noncollagenous (NC1) domain of collagen IV	Noncollagenous (NC1) domain of collagen IV	(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	SCOP2 Family	Noncollagenous (NC1) domain of collagen IV	8028918	4002828	SCOP2 (2022-06-29)
A	SCOP2 Family	Noncollagenous (NC1) domain of collagen IV	8028921	4002828	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C-type lectin-like	8041297	3001261	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C-type lectin-like	8041300	3001261	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	C-type lectin-like	8041297	3001261	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C-type lectin-like	8041300	3001261	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	C-type lectin-like	8041297	3001261	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	C-type lectin-like	8041300	3001261	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	C-type lectin-like	8041297	3001261	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	C-type lectin-like	8041300	3001261	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	RnaseA	e1li1A1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RnaseA	ECOD (v294.1)
A	Lyase_1	e1li1A2	A: a/b three-layered sandwiches	X: UBC-like	H: UBC-like	T: Concanavalin A-like lectins/glucanases	F: Lyase_1	ECOD (v294.1)
B	RnaseA	e1li1B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RnaseA	ECOD (v294.1)
B	Lyase_1	e1li1B2	A: a/b three-layered sandwiches	X: UBC-like	H: UBC-like	T: Concanavalin A-like lectins/glucanases	F: Lyase_1	ECOD (v294.1)
D	RnaseA	e1li1D1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RnaseA	ECOD (v294.1)
D	Lyase_1	e1li1D2	A: a/b three-layered sandwiches	X: UBC-like	H: UBC-like	T: Concanavalin A-like lectins/glucanases	F: Lyase_1	ECOD (v294.1)
E	RnaseA	e1li1E1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RnaseA	ECOD (v294.1)
E	Lyase_1	e1li1E2	A: a/b three-layered sandwiches	X: UBC-like	H: UBC-like	T: Concanavalin A-like lectins/glucanases	F: Lyase_1	ECOD (v294.1)
C	RnaseA	e1li1C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RnaseA	ECOD (v294.1)
C	Lyase_1	e1li1C2	A: a/b three-layered sandwiches	X: UBC-like	H: UBC-like	T: Concanavalin A-like lectins/glucanases	F: Lyase_1	ECOD (v294.1)
F	RnaseA	e1li1F1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RnaseA	ECOD (v294.1)
F	Lyase_1	e1li1F2	A: a/b three-layered sandwiches	X: UBC-like	H: UBC-like	T: Concanavalin A-like lectins/glucanases	F: Lyase_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.240.10	Mainly Beta	Beta Complex	Noncollagenous (NC1) domain of collagen IV	Collagen IV, non-collagenous	CATH (4.3.0)
B	2.170.240.10	Mainly Beta	Beta Complex	Noncollagenous (NC1) domain of collagen IV	Collagen IV, non-collagenous	CATH (4.3.0)
D	2.170.240.10	Mainly Beta	Beta Complex	Noncollagenous (NC1) domain of collagen IV	Collagen IV, non-collagenous	CATH (4.3.0)
E	2.170.240.10	Mainly Beta	Beta Complex	Noncollagenous (NC1) domain of collagen IV	Collagen IV, non-collagenous	CATH (4.3.0)
C	2.170.240.10	Mainly Beta	Beta Complex	Noncollagenous (NC1) domain of collagen IV	Collagen IV, non-collagenous	CATH (4.3.0)
F	2.170.240.10	Mainly Beta	Beta Complex	Noncollagenous (NC1) domain of collagen IV	Collagen IV, non-collagenous	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, D, E	PF01413	C-terminal tandem repeated domain in type 4 procollagen (C4)	C-terminal tandem repeated domain in type 4 procollagen	Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.	Domain
C, F	PF01413	C-terminal tandem repeated domain in type 4 procollagen (C4)	C-terminal tandem repeated domain in type 4 procollagen	Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, D, E	Collagen alpha 1(IV)	structural molecule activity extracellular matrix structural constituent extracellular matrix structural constituent conferring tensile strength platelet-derived growth factor binding protein binding binding growth factor binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development branching morphogenesis of an epithelial tube angiogenesis tube morphogenesis epithelial tube morphogenesis developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development branching morphogenesis of an epithelial tube angiogenesis tube morphogenesis epithelial tube morphogenesis blood vessel development epithelium development blood vessel morphogenesis tube development morphogenesis of an epithelium tissue development vasculature development circulatory system development branching involved in blood vessel morphogenesis anatomical structure morphogenesis tissue morphogenesis morphogenesis of a branching structure anatomical structure formation involved in morphogenesis morphogenesis of a branching epithelium renal system development renal tubule development renal tubule morphogenesis cellular response to acid chemical cellular response to stimulus cellular response to amino acid stimulus response to acid chemical cellular response to chemical stimulus response to stimulus response to chemical cellular process response to amino acid collagen-activated tyrosine kinase receptor signaling pathway regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction collagen-activated signaling pathway enzyme-linked receptor protein signaling pathway cellular component organization cell junction organization neuromuscular junction development synapse organization cellular component organization or biogenesis cellular developmental process cell differentiation epithelial cell differentiation sensory organ development retina vasculature development in camera-type eye eye development retina development in camera-type eye visual system development retina vasculature morphogenesis in camera-type eye camera-type eye development retinal blood vessel morphogenesis sensory system development collagen fibril organization extracellular matrix organization extracellular structure organization external encapsulating structure organization basement membrane organization	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region basement membrane extracellular matrix external encapsulating structure complex of network-forming collagens protein-containing complex network-forming collagen trimer collagen trimer solid phase of basement membrane chicken-wire-like collagen network collagenous component of basement membrane collagen type IV trimer complex of collagen trimers extracellular protein-containing complex supramolecular complex
C, F	Collagen alpha 2(IV)	structural molecule activity extracellular matrix structural constituent extracellular matrix structural constituent conferring tensile strength molecular adaptor activity	developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to endogenous stimulus response to growth factor cellular response to stimulus collagen-activated tyrosine kinase receptor signaling pathway regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication cellular process signal transduction collagen-activated signaling pathway enzyme-linked receptor protein signaling pathway formation of primary germ layer cellular developmental process embryonic morphogenesis tissue development embryo development gastrulation endoderm development cell differentiation endoderm formation endodermal cell differentiation response to activity cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization regulation of developmental process negative regulation of biological process regulation of vasculature development regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis negative regulation of vasculature development regulation of angiogenesis negative regulation of multicellular organismal process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process collagen fibril organization	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region extracellular exosome extracellular vesicle extracellular organelle vesicle extracellular membrane-bounded organelle complex of network-forming collagens basement membrane protein-containing complex extracellular matrix network-forming collagen trimer collagen trimer solid phase of basement membrane chicken-wire-like collagen network collagenous component of basement membrane external encapsulating structure collagen type IV trimer complex of collagen trimers extracellular protein-containing complex supramolecular complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, D, E	IPR008160	Collagen triple helix repeat	Repeat
A, B, D, E	IPR016187	C-type lectin fold	Homologous Superfamily
A, B, D, E	IPR001442	Collagen IV, non-collagenous	Domain
A, B, D, E	IPR036954	Collagen IV, non-collagenous domain superfamily	Homologous Superfamily
A, B, D, E	IPR050149	Collagen superfamily	Family
C, F	IPR008160	Collagen triple helix repeat	Repeat
C, F	IPR016187	C-type lectin fold	Homologous Superfamily
C, F	IPR001442	Collagen IV, non-collagenous	Domain
C, F	IPR036954	Collagen IV, non-collagenous domain superfamily	Homologous Superfamily
C, F	IPR050149	Collagen superfamily	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, D, E	Pharos: P02462	brain small vessel disease 1 with or without ocular anomalies porencephaly retinal arterial tortuosity autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome nephrotic syndrome schizencephaly muscular dystrophy-dystroglycanopathy, type A familial schizencephaly focal segmental glomerulosclerosis Brain small vessel disease with or without ocular anomalies intracerebral hemorrhage cerebrovascular disorder thoracic aortic aneurysm cutaneous lupus erythematosus lung cancer brain small vessel disease 1 with or without ocular anomalies porencephaly retinal arterial tortuosity autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome nephrotic syndrome schizencephaly muscular dystrophy-dystroglycanopathy, type A familial schizencephaly focal segmental glomerulosclerosis Brain small vessel disease with or without ocular anomalies intracerebral hemorrhage cerebrovascular disorder thoracic aortic aneurysm cutaneous lupus erythematosus lung cancer dermatomyositis malignant mesothelioma nephrosclerosis adrenal cortex carcinoma oligodendroglioma atypical teratoid rhabdoid tumor pancreatic ductal adenocarcinoma head and neck cancer periodontitis primitive neuroectodermal tumor cataract interstitial cystitis chronic obstructive pulmonary disease large cell medulloblastoma transitional cell carcinoma cystic fibrosis malignant ependymoma malignant pancreatic neoplasm Duchenne muscular dystrophy myocardial infarction esophageal adenocarcinoma arthrogryposis osteosarcoma gastric carcinoma pancreatic intraductal papillary-mucinous carcinoma heart disease peripheral arterial disease breast cancer hydrocephalus psoriasis leukodystrophy subependymal giant cell astrocytoma Crohn disease lung adenocarcinoma ulcerative colitis malignant glioma diabetic kidney disease medulloblastoma Emery-Dreifuss muscular dystrophy nasopharyngeal carcinoma astrocytic tumor ovarian cancer Becker muscular dystrophy glioblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pilocytic astrocytoma breast carcinoma hydrolethalus syndrome pterygium juvenile dermatomyositis congenital muscular dystrophy limb-girdle muscular dystrophy
C, F	Pharos: P08572	porencephaly nephrotic syndrome porencephaly 2 small cell lung carcinoma Liver Cirrhosis, Experimental intracerebral hemorrhage cerebrovascular disorder head and neck cancer psoriasis intellectual disability invasive ductal breast carcinoma limb-girdle muscular dystrophy ulcerative colitis malignant ependymoma arthrogryposis porencephaly nephrotic syndrome porencephaly 2 small cell lung carcinoma Liver Cirrhosis, Experimental intracerebral hemorrhage cerebrovascular disorder head and neck cancer psoriasis intellectual disability invasive ductal breast carcinoma limb-girdle muscular dystrophy ulcerative colitis malignant ependymoma arthrogryposis malignant pancreatic neoplasm breast cancer nasopharyngeal carcinoma chronic obstructive pulmonary disease osteosarcoma congenital muscular dystrophy pancreatic intraductal papillary-mucinous carcinoma dermatomyositis periodontitis ductal breast carcinoma in situ gastric carcinoma heart disease pterygium interstitial cystitis juvenile dermatomyositis malignant glioma atypical teratoid rhabdoid tumor medulloblastoma colorectal adenoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm peripheral arterial disease Emery-Dreifuss muscular dystrophy glioblastoma primitive neuroectodermal tumor hydrolethalus syndrome small cell carcinoma transitional cell carcinoma large cell medulloblastoma lung adenocarcinoma malignant mesothelioma Becker muscular dystrophy myocardial infarction oligodendroglioma colorectal cancer pancreatic ductal adenocarcinoma cystic fibrosis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Duchenne muscular dystrophy pilocytic astrocytoma

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.