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Yorodumi- PDB-5nax: Crystal structures of homooligomers of the non-collagenous domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nax | ||||||||||||
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Title | Crystal structures of homooligomers of the non-collagenous domains of collagen type IV. alpha121NC1 | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Non-collagenous domain of collagen type IV / A principal structural component of basement membranes | ||||||||||||
Function / homology | Function and homology information collagen type IV trimer / retinal blood vessel morphogenesis / Anchoring fibril formation / renal tubule morphogenesis / Crosslinking of collagen fibrils / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / basement membrane organization / Extracellular matrix organization ...collagen type IV trimer / retinal blood vessel morphogenesis / Anchoring fibril formation / renal tubule morphogenesis / Crosslinking of collagen fibrils / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / basement membrane organization / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Laminin interactions / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / NCAM1 interactions / blood vessel morphogenesis / Scavenging by Class A Receptors / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / branching involved in blood vessel morphogenesis / neuromuscular junction development / endodermal cell differentiation / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / epithelial cell differentiation / extracellular matrix organization / negative regulation of angiogenesis / response to activity / cellular response to amino acid stimulus / brain development / angiogenesis / collagen-containing extracellular matrix / molecular adaptor activity / endoplasmic reticulum lumen / DNA-templated transcription / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.82 Å | ||||||||||||
Authors | Casino, P. / Marina, A. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: IUCrJ / Year: 2018 Title: Structures of collagen IV globular domains: insight into associated pathologies, folding and network assembly. Authors: Casino, P. / Gozalbo-Rovira, R. / Rodriguez-Diaz, J. / Banerjee, S. / Boutaud, A. / Rubio, V. / Hudson, B.G. / Saus, J. / Cervera, J. / Marina, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nax.cif.gz | 269.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nax.ent.gz | 217.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/5nax ftp://data.pdbj.org/pub/pdb/validation_reports/na/5nax | HTTPS FTP |
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-Related structure data
Related structure data | 5nayC 5nazC 5nb0C 5nb1C 5nb2C 1t60S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 25356.871 Da / Num. of mol.: 4 / Fragment: UNP residues 1443-1667 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02462 #2: Protein | Mass: 25114.551 Da / Num. of mol.: 2 / Fragment: UNP residues 1485-1712 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08572 #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.93 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 10% PEG8000, Magnesium acetate 0.2 M |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.25 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 5, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.25 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.82→48.75 Å / Num. all: 48121 / Num. obs: 48121 / % possible obs: 98.9 % / Redundancy: 5.4 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Rsym value: 0.092 / Net I/av σ(I): 7.1 / Net I/σ(I): 12.7 / Num. measured all: 258124 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T60 Resolution: 2.82→48.45 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.152 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 147.79 Å2 / Biso mean: 65.262 Å2 / Biso min: 27.85 Å2
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Refinement step | Cycle: final / Resolution: 2.82→48.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.82→2.893 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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