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Yorodumi- PDB-5ctd: Crystal structure of the type IX collagen NC2 hetero-trimerizatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ctd | ||||||
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Title | Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest fragment a2a1a1 of type I collagen | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / collagen / hetero-trimerization / chain stagger / chain register / triple helix | ||||||
Function / homology | Function and homology information collagen type IX trimer / cellular response to fluoride / collagen type I trimer / tooth mineralization / protein heterotrimerization / cellular response to vitamin E / collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process ...collagen type IX trimer / cellular response to fluoride / collagen type I trimer / tooth mineralization / protein heterotrimerization / cellular response to vitamin E / collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / extracellular matrix assembly / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / platelet-derived growth factor binding / bone trabecula formation / extracellular matrix structural constituent conferring tensile strength / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / intramembranous ossification / Extracellular matrix organization / embryonic skeletal system development / Collagen biosynthesis and modifying enzymes / cartilage development involved in endochondral bone morphogenesis / collagen metabolic process / skin morphogenesis / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / Platelet Adhesion to exposed collagen / endochondral ossification / NCAM1 interactions / cellular response to fibroblast growth factor stimulus / collagen fibril organization / negative regulation of cell-substrate adhesion / response to steroid hormone / face morphogenesis / odontogenesis / Scavenging by Class A Receptors / extracellular matrix structural constituent / skin development / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / GP1b-IX-V activation signalling / blood vessel development / bone mineralization / SMAD binding / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / Rho protein signal transduction / Collagen degradation / protein localization to nucleus / Non-integrin membrane-ECM interactions / ECM proteoglycans / response to hyperoxia / Integrin cell surface interactions / positive regulation of epithelial to mesenchymal transition / response to mechanical stimulus / cellular response to retinoic acid / GPVI-mediated activation cascade / cellular response to epidermal growth factor stimulus / response to cAMP / cellular response to transforming growth factor beta stimulus / visual perception / extracellular matrix organization / ossification / transforming growth factor beta receptor signaling pathway / secretory granule / skeletal system development / Cell surface interactions at the vascular wall / cellular response to glucose stimulus / sensory perception of sound / animal organ morphogenesis / cellular response to amino acid stimulus / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / response to insulin / response to hydrogen peroxide / regulation of blood pressure / osteoblast differentiation / cellular response to mechanical stimulus / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of canonical Wnt signaling pathway / protein transport / response to estradiol / protein-macromolecule adaptor activity / cellular response to tumor necrosis factor / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / protease binding / positive regulation of cell migration / response to xenobiotic stimulus / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5991 Å | ||||||
Authors | Boudko, S.P. / Bachinger, H.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2016 Title: Structural insight for chain selection and stagger control in collagen. Authors: Boudko, S.P. / Bachinger, H.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ctd.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ctd.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ctd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/5ctd ftp://data.pdbj.org/pub/pdb/validation_reports/ct/5ctd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7161.650 Da / Num. of mol.: 1 / Fragment: UNP Residues 572-583, UNP Residues 754-789 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COL1A1, COL9A1 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P02452, UniProt: P20849 |
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#2: Protein | Mass: 6895.721 Da / Num. of mol.: 1 / Fragment: UNP Residues 484-495, UNP Residues 517-552 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COL1A2, COL9A2 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P08123, UniProt: Q14055 |
#3: Protein | Mass: 6999.000 Da / Num. of mol.: 1 / Fragment: UNP Residues 572-583, UNP Residues 517-553 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COL1A1, COL9A3 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P02452, UniProt: Q14050 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 50 mM sodium acetate, 17% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97872, 0.97918, 0.96487 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Mar 23, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Redundancy: 3.8 % / Number: 92373 / Rmerge(I) obs: 0.084 / Χ2: 1.56 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 24414 / % possible obs: 96.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.599→50 Å / Num. obs: 24414 / % possible obs: 96.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.2502146055 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.049 / Rrim(I) all: 0.097 / Χ2: 1.562 / Net I/av σ(I): 17.13 / Net I/σ(I): 15.6 / Num. measured all: 92373 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: MAD | ||||||||||||||||||||||||||||
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Phasing set |
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Phasing MAD | D res high: 1.6 Å / D res low: 1000 Å / FOM : 0.4 / Reflection: 24386 | ||||||||||||||||||||||||||||
Phasing MAD set |
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Phasing MAD set site |
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Phasing MAD shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5991→41.532 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.2 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5991→41.532 Å
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Refine LS restraints |
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LS refinement shell |
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