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Yorodumi- PDB-3hqv: Low resolution, molecular envelope structure of type I collagen i... -
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-Basic information
Entry | Database: PDB / ID: 3hqv | |||||||||
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Title | Low resolution, molecular envelope structure of type I collagen in situ determined by fiber diffraction. Single type I collagen molecule, rigid body refinement | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / CONTRACTILE PROTEIN / NATIVE / IN SITU / Molecular envelope / TRIPLE-helical / SUPERMOLECULAR / supramolecular / PACKING STRUCTURE / STRUCTURAL PROTEIN-CONTRACTILE PROTEIN COMPLEX / Collagen / Extracellular matrix / Glycoprotein / Hydroxylation / Pyrrolidone carboxylic acid / Secreted | |||||||||
Function / homology | Function and homology information cellular response to aldehyde / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Crosslinking of collagen fibrils / Non-integrin membrane-ECM interactions / Platelet Aggregation (Plug Formation) / MET activates PTK2 signaling / Collagen chain trimerization / response to norepinephrine / GP1b-IX-V activation signalling ...cellular response to aldehyde / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Crosslinking of collagen fibrils / Non-integrin membrane-ECM interactions / Platelet Aggregation (Plug Formation) / MET activates PTK2 signaling / Collagen chain trimerization / response to norepinephrine / GP1b-IX-V activation signalling / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / Integrin cell surface interactions / ECM proteoglycans / Platelet Adhesion to exposed collagen / response to fluoride / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / GPVI-mediated activation cascade / Cell surface interactions at the vascular wall / cellular response to fluoride / collagen type I trimer / cellular response to vitamin E / tooth mineralization / protein heterotrimerization / collagen biosynthetic process / extracellular matrix assembly / platelet-derived growth factor binding / bone trabecula formation / extracellular matrix structural constituent conferring tensile strength / intramembranous ossification / embryonic skeletal system development / cartilage development involved in endochondral bone morphogenesis / skin morphogenesis / collagen metabolic process / collagen-activated tyrosine kinase receptor signaling pathway / endochondral ossification / collagen trimer / cellular response to thyroid hormone stimulus / cellular response to fibroblast growth factor stimulus / skeletal system morphogenesis / collagen fibril organization / negative regulation of cell-substrate adhesion / response to steroid hormone / face morphogenesis / extracellular matrix structural constituent / skin development / bone mineralization / blood vessel development / SMAD binding / Rho protein signal transduction / protein localization to nucleus / response to hyperoxia / response to mechanical stimulus / cellular response to retinoic acid / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / response to cAMP / cellular response to epidermal growth factor stimulus / visual perception / extracellular matrix / extracellular matrix organization / ossification / transforming growth factor beta receptor signaling pathway / response to nutrient / response to nutrient levels / secretory granule / skeletal system development / cellular response to amino acid stimulus / cellular response to glucose stimulus / sensory perception of sound / response to insulin / response to hydrogen peroxide / response to organic cyclic compound / response to peptide hormone / regulation of blood pressure / cellular response to mechanical stimulus / osteoblast differentiation / positive regulation of canonical Wnt signaling pathway / protein transport / cellular response to tumor necrosis factor / response to estradiol / protein-macromolecule adaptor activity / protease binding / collagen-containing extracellular matrix / positive regulation of cell migration / response to xenobiotic stimulus / positive regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | FIBER DIFFRACTION / SYNCHROTRON / MIR / Resolution: 5.16 Å | |||||||||
Authors | Orgel, J.P. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: Microfibrillar Structure of Type I Collagen in Situ Authors: Orgel, J.P. / Irving, T.C. / Miller, A. / Wess, T.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hqv.cif.gz | 120 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hqv.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hqv_validation.pdf.gz | 291.9 KB | Display | wwPDB validaton report |
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Full document | 3hqv_full_validation.pdf.gz | 291.8 KB | Display | |
Data in XML | 3hqv_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 3hqv_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/3hqv ftp://data.pdbj.org/pub/pdb/validation_reports/hq/3hqv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | BIOMOLECULE: THIS ENTRY CONTAINS ONE COLLAGEN TYPE I MOLECULE. FOR RELATION TO THE FIBRILLAR PACKING OF COLLAGEN MOLECULES/MICRO-FIBRIL, REFER TO CITATION. IN SUMMARY: EACH COLLAGEN MOLECULE IS STAGGERED BY AN INTEGER MULTIPLE OF THE C-CELL AXIS. THE STRUCTURE CAN BE EXTENDED IN THE AXIAL (~C-CELL AXIS) DIRECTION BY APPLYING THE FOLLOWING TRANSLATION: NX,0Y,NZ TO THE MOLECULE, WHERE N IS AN INTEGER. A VISUALIZATION OF FIVE SUCCESSIVE 'D'-REPEATS OF THE BIOMOLECULE / MICRO-FIBRIL CAN BE OBTAINED FROM THESE COORDINATES BY APPLYING THE FOLLOWING TRANSLATIONS TO NINE COORDINATE SETS: A) 0, 0, 0; B) -1, 0,-1; C) -2, 0,-2; D) -3, 0,-3; E) -4, 0,-4; B1) 1, 0, 1; C1) 2, 0, 2; D1) 3, 0, 3; E1) 4, 0, 4. |
-Components
#1: Protein | Mass: 96747.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Tissue: tail tendon / References: UniProt: P02454 #2: Protein | | Mass: 93481.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Tissue: tail tendon / References: UniProt: P02466 |
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-Experimental details
-Experiment
Experiment | Method: FIBER DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Description: THE RESOLUTION LIMITS FOR THE DATA COLLECTION ARE 38.5 TO 11.1A LATERAL AND 112.6 TO 5.16A AXIAL, INTENSITY-INTEGRATION SOFTWARE : FIT2D/IN-HOUSE, DATA SCALING SOFTWARE : IN-HOUSE |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 1.03 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 5.16→112.6 Å / Num. all: 436 / Num. obs: 424 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 5.16→112.6 Å / % possible all: 97 |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||
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Refinement | Method to determine structure: MIR / Resolution: 5.16→112.62 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber Details: 305 EQUATORIAL AND 109 MERIDIONAL REFLECTIONS WERE USED FOR REFINEMENT WITH CNS. INITIAL REFINEMENT OF WHOLE MOLECULAR PATHS WAS PERFORMED IN THE STEPWISE FASHION DESCRIBED IN THE CITED ...Details: 305 EQUATORIAL AND 109 MERIDIONAL REFLECTIONS WERE USED FOR REFINEMENT WITH CNS. INITIAL REFINEMENT OF WHOLE MOLECULAR PATHS WAS PERFORMED IN THE STEPWISE FASHION DESCRIBED IN THE CITED PUBLICATION. MODEL STRUCTURE FACTORS WHERE INITIALLY GENERATED FROM THE WHOLE RESIDUE SCATTERING FACTORS OF HULMES ET AL 1977 WHICH WERE SUBSTITUTED FOR THE CALPHA POSITIONS AND THE SQUARE FC'S WERE CALCULATED FOR COMPARISON BETWEEN A SIMULATED DIFFRACTION PATTERN AND THE OBSERVED PATTERNS. STRUCTURE FACTORS FROM THE FINAL MODEL WERE GENERATED IN THE NORMAL MANNER FOR REFINEMENT OF THE TELOPEPTIDE CONFORMATIONS USING CNS (SEE ABOVE). TWO ROUNDS OF Q-FACTOR REFINEMENT FOLLOWED BY ONE ROUND OF CONSTRAINED THEN UNCONSTRAINED ANNEALING FOR THE WHOLE STRUCTURE. THE R- FACTOR WHEN MEASURED VIA SIMULATED/OBSERVED DIFFRACTION PATTERN COMPARISON WAS FOUND TO BE 16.7% AND 6.6% BY MEASURE OF THE INTERGRATED STRUCTURE FACTORS. REFLECTIONS MISSING FROM THE MERIDONAL(OOL) SERIES WERE EITHER TOO WEAK TO MEASURE AND/OR VAIRED SIGNIFICANTLY BETWEEN COLLECTED PATTERNS (SEVEN IN TOTAL). THE FIRST FIVE REFLECTIONS WHERE EXCLUDED DUE TO THEIR LOW RESOLUTION (677.9 TO ~120 ANGSTROMS). EXLUDED REFLECTIONS ARE NOT INCLUDED IN THE 414 TOTAL. THE COORDINATES CONTAIN CA ATOMS ONLY.
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Refinement step | Cycle: LAST / Resolution: 5.16→112.62 Å
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