+Open data
-Basic information
Entry | Database: PDB / ID: 4oum | ||||||
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Title | Crystal structure of human Caprin-2 C1q domain | ||||||
Components | Caprin-2 | ||||||
Keywords | SIGNALING PROTEIN / C1q domain / Wnt signaling | ||||||
Function / homology | Function and homology information dorsal/ventral axis specification / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / negative regulation of cell growth / positive regulation of canonical Wnt signaling pathway / cell differentiation / receptor complex / negative regulation of translation / signaling receptor binding / centrosome ...dorsal/ventral axis specification / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite morphogenesis / negative regulation of cell growth / positive regulation of canonical Wnt signaling pathway / cell differentiation / receptor complex / negative regulation of translation / signaling receptor binding / centrosome / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / nucleoplasm / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.491 Å | ||||||
Authors | Song, X. / Li, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural insights into the C1q domain of Caprin-2 in canonical Wnt signaling Authors: Miao, H. / Jia, Y. / Xie, S. / Wang, X. / Zhao, J. / Chu, Y. / Zhou, Z. / Shi, Z. / Song, X. / Li, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oum.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oum.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 4oum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oum_validation.pdf.gz | 473.1 KB | Display | wwPDB validaton report |
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Full document | 4oum_full_validation.pdf.gz | 475.4 KB | Display | |
Data in XML | 4oum_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 4oum_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/4oum ftp://data.pdbj.org/pub/pdb/validation_reports/ou/4oum | HTTPS FTP |
-Related structure data
Related structure data | 4oulC 4ousC 1o91S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15825.954 Da / Num. of mol.: 1 / Fragment: UNP residues 996-1127 / Mutation: D1078A, E1084A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C1QDC1, CAPRIN2, EEG1, KIAA1873, RNG140 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q6IMN6 | ||
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#2: Chemical | ChemComp-PG4 / | ||
#3: Chemical | ChemComp-FLC / | ||
#4: Chemical | #5: 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: 1.95 Å3/Da / Density % sol: 36.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.6 Details: 100mM sodium citrate pH5.6, 12% 2-propanol, 11% PEG4000, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50 Å / Num. all: 19557 / Num. obs: 19420 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 1.49→1.52 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 9.2 / Num. unique all: 984 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID: 1O91 Resolution: 1.491→22.372 Å / SU ML: 0.14 / σ(F): 2.04 / Phase error: 21.6 / Stereochemistry target values: ML
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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: 1.491→22.372 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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