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Yorodumi- PDB-2llp: Solution structure of a THP type 1 alpha 1 collagen fragment (772-786) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2llp | ||||||
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Title | Solution structure of a THP type 1 alpha 1 collagen fragment (772-786) | ||||||
Components | Collagen alpha-1(I) chain | ||||||
Keywords | STRUCTURAL PROTEIN / CONTRACTILE PROTEIN / triple helical peptide / Structural Genomics / Structural Proteomics in Europe 2 / SPINE-2 | ||||||
Function / homology | Function and homology information cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / bone trabecula formation / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength ...cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / bone trabecula formation / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / intramembranous ossification / Extracellular matrix organization / embryonic skeletal system development / Collagen biosynthesis and modifying enzymes / cartilage development involved in endochondral bone morphogenesis / skin morphogenesis / collagen-activated tyrosine kinase receptor signaling pathway / Platelet Adhesion to exposed collagen / endochondral ossification / cellular response to fibroblast growth factor stimulus / collagen fibril organization / negative regulation of cell-substrate adhesion / face morphogenesis / response to steroid hormone / Scavenging by Class A Receptors / skin development / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / GP1b-IX-V activation signalling / blood vessel development / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / Collagen degradation / protein localization to nucleus / Non-integrin membrane-ECM interactions / ECM proteoglycans / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / Integrin cell surface interactions / response to mechanical stimulus / cellular response to retinoic acid / response to cAMP / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / visual perception / extracellular matrix organization / ossification / secretory granule / skeletal system development / cellular response to glucose stimulus / cellular response to amino acid stimulus / Cell surface interactions at the vascular wall / sensory perception of sound / response to insulin / response to hydrogen peroxide / osteoblast differentiation / cellular response to mechanical stimulus / positive regulation of canonical Wnt signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein transport / response to estradiol / cellular response to tumor necrosis factor / collagen-containing extracellular matrix / protease binding / positive regulation of cell migration / response to xenobiotic stimulus / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, minimisation | ||||||
Model details | fewest violations, model 1 | ||||||
Authors | Bertini, I. / Fragai, M. / Luchinat, C. / Melikian, M. / Toccafondi, M. / Lauer, J.L. / Fields, G.B. / Structural Proteomics in Europe 2 (SPINE-2) | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: Structural basis for matrix metalloproteinase 1-catalyzed collagenolysis. Authors: Bertini, I. / Fragai, M. / Luchinat, C. / Melikian, M. / Toccafondi, M. / Lauer, J.L. / Fields, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2llp.cif.gz | 408.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2llp.ent.gz | 353.4 KB | Display | PDB format |
PDBx/mmJSON format | 2llp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/2llp ftp://data.pdbj.org/pub/pdb/validation_reports/ll/2llp | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 1657.892 Da / Num. of mol.: 3 / Fragment: UNP residues 949-965 / Source method: obtained synthetically / Details: synthesis from Fmoc solid-phase chemistry / Source: (synth.) Homo sapiens (human) / References: UniProt: P02452 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.4-0.8 mM [U-98% 13C; U-98% 15N] THP type I collagen, 150 mM sodium chloride, 10 mM calcium chloride, 0.1 mM zinc chloride, 20 mM [U-2H] tris buffer, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.15 / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, minimisation / Software ordinal: 1 Details: Annealing and structure calculation from constraints, minimisation by using AMBER force field and keeping the constraints | ||||||||||||||||
NMR constraints | NOE constraints total: 307 / NOE intraresidue total count: 125 / NOE long range total count: 103 / NOE medium range total count: 1 / NOE sequential total count: 78 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 17 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 17 | ||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 900 / Conformers submitted total number: 30 |