[English] 日本語
Yorodumi- PDB-4ae2: Crystal structure of Human fibrillar procollagen type III C- prop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ae2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Human fibrillar procollagen type III C- propeptide trimer | ||||||
Components | COLLAGEN ALPHA-1(III) CHAIN | ||||||
Keywords | STRUCTURAL PROTEIN / FIBRILLAR COLLAGEN / EXTRACELLULAR MATRIX / FIBROSIS | ||||||
Function / homology | Function and homology information collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / basement membrane organization ...collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / basement membrane organization / Extracellular matrix organization / layer formation in cerebral cortex / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / peptide cross-linking / tissue homeostasis / Signaling by PDGF / negative regulation of immune response / NCAM1 interactions / digestive tract development / response to angiotensin / collagen fibril organization / Scavenging by Class A Receptors / skin development / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / extracellular matrix structural constituent / Syndecan interactions / positive regulation of Rho protein signal transduction / SMAD binding / Collagen degradation / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / supramolecular fiber organization / extracellular matrix organization / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / response to cytokine / integrin-mediated signaling pathway / cellular response to amino acid stimulus / neuron migration / lung development / wound healing / response to radiation / multicellular organism growth / cerebral cortex development / platelet activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / heart development / fibroblast proliferation / collagen-containing extracellular matrix / protease binding / in utero embryonic development / endoplasmic reticulum lumen / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Bourhis, J.M. / Mariano, N. / Zhao, Y. / Harlos, K. / Jones, E.Y. / Moali, C. / Aghajari, N. / Hulmes, D.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Structural Basis of Fibrillar Collagen Trimerization and Related Genetic Disorders. Authors: Bourhis, J.M. / Mariano, N. / Zhao, Y. / Harlos, K. / Exposito, J.Y. / Jones, E.Y. / Moali, C. / Aghajari, N. / Hulmes, D.J. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Production and Crystallization of the C-Propeptide Trimer from Human Procollagen III. Authors: Bourhis, J.M. / Mariano, N. / Zhao, Y. / Walter, T.S. / El Omari, K. / Delolme, F. / Moali, C. / Hulmes, D.J. / Aghajari, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ae2.cif.gz | 276.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ae2.ent.gz | 230.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ae2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ae2_validation.pdf.gz | 460 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ae2_full_validation.pdf.gz | 463.4 KB | Display | |
Data in XML | 4ae2_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 4ae2_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/4ae2 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/4ae2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28815.340 Da / Num. of mol.: 3 Fragment: CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P02461 #2: Chemical | #3: Chemical | ChemComp-NO3 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39.9 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 20% PEG 3350, 0.1 M BIS TRIS PROPANE PH 6.5, POTASSIUM NITRATE 0.2 M |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→61.2 Å / Num. obs: 78019 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.7→61 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / % possible all: 96.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→61.27 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.44 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.855 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→61.27 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|