3HQV | pdb_00003hqv

Low resolution, molecular envelope structure of type I collagen in situ determined by fiber diffraction. Single type I collagen molecule, rigid body refinement

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3hqvb_	Low resolution protein structures	Collagen fibre	Collagen fibre	Collagen fibre	Collagen I alpha	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d3hqvc_	Low resolution protein structures	Collagen fibre	Collagen fibre	Collagen fibre	Collagen I alpha	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d3hqva_	Low resolution protein structures	Collagen fibre	Collagen fibre	Collagen fibre	Collagen I alpha	(Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF01391	Collagen triple helix repeat (20 copies) (Collagen)	Collagen triple helix repeat (20 copies)	-	Repeat
A, C	PF01391	Collagen triple helix repeat (20 copies) (Collagen)	Collagen triple helix repeat (20 copies)	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Collagen alpha-2(I) chain	protein binding binding enzyme binding protease binding protein-macromolecule adaptor activity molecular adaptor activity structural molecule activity extracellular matrix structural constituent extracellular matrix structural constituent conferring tensile strength SMAD binding platelet-derived growth factor binding growth factor binding cation binding ion binding protein binding binding enzyme binding protease binding protein-macromolecule adaptor activity molecular adaptor activity structural molecule activity extracellular matrix structural constituent extracellular matrix structural constituent conferring tensile strength SMAD binding platelet-derived growth factor binding growth factor binding cation binding ion binding metal ion binding small molecule binding identical protein binding	response to norepinephrine response to stimulus response to catecholamine response to chemical response to monoamine response to oxygen-containing compound response to nitrogen compound cellular response to stimulus cellular response to chemical stimulus cellular response to aldehyde cellular process cellular response to oxygen-containing compound multicellular organismal process system process response to norepinephrine response to stimulus response to catecholamine response to chemical response to monoamine response to oxygen-containing compound response to nitrogen compound cellular response to stimulus cellular response to chemical stimulus cellular response to aldehyde cellular process cellular response to oxygen-containing compound multicellular organismal process system process circulatory system process regulation of blood pressure biological regulation regulation of biological quality blood circulation developmental process ossification bone mineralization animal organ development anatomical structure development biomineral tissue development tissue development multicellular organism development skeletal system development system development protein-containing complex organization protein trimerization protein heterotrimerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis protein heterooligomerization response to lipid response to retinoic acid cellular response to retinoic acid cellular response to lipid collagen fibril organization extracellular matrix organization extracellular structure organization external encapsulating structure organization cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid collagen metabolic process metabolic process response to thyroid hormone response to endogenous stimulus cellular response to endogenous stimulus response to hormone cellular response to thyroid hormone stimulus cellular response to hormone stimulus vasculature development blood vessel development circulatory system development anatomical structure morphogenesis skin development skin morphogenesis animal organ morphogenesis extracellular matrix assembly regulation of biological process small GTPase-mediated signal transduction regulation of cellular process signaling Rho protein signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway cell surface receptor signaling pathway cellular response to transforming growth factor beta stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway enzyme-linked receptor protein signaling pathway	protein-containing complex collagen trimer solid phase of interstitial matrix extracellular matrix fibrillar collagen trimer cell periphery cellular anatomical structure external encapsulating structure complex of collagen trimers fibrillar collagen collagen type I trimer supramolecular complex collagenous component of interstitial matrix interstitial matrix protein-containing complex collagen trimer solid phase of interstitial matrix extracellular matrix fibrillar collagen trimer cell periphery cellular anatomical structure external encapsulating structure complex of collagen trimers fibrillar collagen collagen type I trimer supramolecular complex collagenous component of interstitial matrix interstitial matrix extracellular region extracellular space
A, C	Collagen alpha-1(I) chain	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 cation binding ion binding metal ion binding small molecule binding identical protein binding enzyme binding protease binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development system development endochondral ossification replacement ossification animal organ development endochondral bone morphogenesis anatomical structure morphogenesis response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development system development endochondral ossification replacement ossification animal organ development endochondral bone morphogenesis anatomical structure morphogenesis ossification skeletal system morphogenesis animal organ morphogenesis bone morphogenesis bone development cellular response to stimulus response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid cellular response to lipid cellular process response to fibroblast growth factor cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus response to growth factor cellular response to fibroblast growth factor stimulus cellular component organization collagen fibril organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization direct ossification intramembranous ossification cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid response to hormone response to steroid hormone embryo development ending in birth or egg hatching chordate embryonic development embryonic skeletal system development embryo development system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus response to organophosphorus response to nitrogen compound response to purine-containing compound response to cAMP vasculature development blood vessel development circulatory system development response to nutrient levels skin development skin morphogenesis tooth mineralization odontogenesis biomineral tissue development tissue development response to hydrogen peroxide response to oxidative stress response to stress response to reactive oxygen species cellular developmental process cell differentiation osteoblast differentiation response to peptide hormone response to transforming growth factor beta cellular response to transforming growth factor beta stimulus head development face morphogenesis head morphogenesis face development body morphogenesis cellular response to fluoride response to fluoride regulation of epithelial to mesenchymal transition regulation of cellular process regulation of developmental process positive regulation of biological process positive regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal process positive regulation of cellular process regulation of biological process biological regulation epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation homeostatic process cellular response to glucose stimulus intracellular glucose homeostasis response to hexose cellular response to carbohydrate stimulus cellular homeostasis response to monosaccharide response to carbohydrate chemical homeostasis response to glucose glucose homeostasis carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus collagen-activated tyrosine kinase receptor signaling pathway cell surface receptor signaling pathway signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction collagen-activated signaling pathway enzyme-linked receptor protein signaling pathway localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization bone trabecula formation bone trabecula morphogenesis anatomical structure formation involved in morphogenesis trabecula formation trabecula morphogenesis biosynthetic process collagen biosynthetic process metabolic process collagen metabolic process cellular response to vitamin E response to nutrient response to vitamin response to vitamin E cellular response to nutrient levels cellular response to vitamin cellular response to nutrient response to peptide cellular response to tumor necrosis factor response to cytokine cellular response to cytokine stimulus response to tumor necrosis factor response to mechanical stimulus response to abiotic stimulus response to external stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion response to insulin regulation of cell-substrate adhesion regulation of cell adhesion negative regulation of biological process cell-substrate adhesion negative regulation of cell adhesion cell adhesion negative regulation of cellular process negative regulation of cell-substrate adhesion positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process sensory perception of light stimulus visual perception connective tissue development cartilage development involved in endochondral bone morphogenesis cartilage development positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway regulation of signal transduction positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of signaling regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling cellular response to epidermal growth factor stimulus response to epidermal growth factor protein localization to organelle protein localization to nucleus response to estradiol response to oxygen levels response to hyperoxia response to increased oxygen levels	protein-containing complex collagen trimer solid phase of interstitial matrix extracellular matrix fibrillar collagen trimer cell periphery cellular anatomical structure external encapsulating structure complex of collagen trimers fibrillar collagen collagen type I trimer supramolecular complex collagenous component of interstitial matrix interstitial matrix protein-containing complex collagen trimer solid phase of interstitial matrix extracellular matrix fibrillar collagen trimer cell periphery cellular anatomical structure external encapsulating structure complex of collagen trimers fibrillar collagen collagen type I trimer supramolecular complex collagenous component of interstitial matrix interstitial matrix membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR008160	Collagen triple helix repeat	Repeat
B	IPR000885	Fibrillar collagen, C-terminal	Domain
B	IPR050149	Collagen superfamily	Family
A, C	IPR008160	Collagen triple helix repeat	Repeat
A, C	IPR000885	Fibrillar collagen, C-terminal	Domain
A, C	IPR001007	VWFC domain	Domain
A, C	IPR050149	Collagen superfamily	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	HYP	Parent Component: PRO RESID: AA0030 PSI-MOD : 4-hydroxy-L-proline MOD:00039
B	LYZ	Parent Component: LYS RESID: AA0030 , AA0028 PSI-MOD : 4-hydroxy-L-proline MOD:00039 , 5-hydroxy-L-lysine MOD:00037
A, C	HYP	Parent Component: PRO RESID: AA0030 , AA0028 , AA0030 PSI-MOD : 4-hydroxy-L-proline MOD:00039 , 5-hydroxy-L-lysine MOD:00037 , 4-hydroxy-L-proline MOD:00039
A, C	LYZ	Parent Component: LYS RESID: AA0030 , AA0028 , AA0030 , AA0028 PSI-MOD : 4-hydroxy-L-proline MOD:00039 , 5-hydroxy-L-lysine MOD:00037 , 4-hydroxy-L-proline MOD:00039 , 5-hydroxy-L-lysine MOD:00037

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.