+Open data
-Basic information
Entry | Database: PDB / ID: 5fmu | ||||||
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Title | MmIFT54 CH-domain | ||||||
Components | TRAF3-INTERACTING PROTEIN 1 | ||||||
Keywords | PROTEIN TRANSPORT / CALPONIN HOMOLOGY DOMAIN / IFT / TUBULIN-BINDING DOMAIN / TRAF3IP1 / MIP-T3 | ||||||
Function / homology | Function and homology information negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning / regulation of DNA binding / intraciliary transport particle B / Intraflagellar transport / neural tube patterning / negative regulation of defense response to virus / embryonic camera-type eye development / intraciliary transport / ciliary transition zone / negative regulation of tyrosine phosphorylation of STAT protein ...negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning / regulation of DNA binding / intraciliary transport particle B / Intraflagellar transport / neural tube patterning / negative regulation of defense response to virus / embryonic camera-type eye development / intraciliary transport / ciliary transition zone / negative regulation of tyrosine phosphorylation of STAT protein / ciliary tip / morphogenesis of a polarized epithelium / negative regulation of interferon-beta production / post-anal tail morphogenesis / embryonic heart tube development / ciliary base / negative regulation of type I interferon production / embryonic digit morphogenesis / axoneme / cilium assembly / negative regulation of protein-containing complex assembly / regulation of microtubule cytoskeleton organization / tubulin binding / ciliary basal body / negative regulation of protein phosphorylation / kidney development / cilium / microtubule cytoskeleton / microtubule binding / signaling receptor binding / centrosome / negative regulation of transcription by RNA polymerase II / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.593 Å | ||||||
Authors | Weber, K. / Lorentzen, E. | ||||||
Citation | Journal: Embo J. / Year: 2016 Title: Intraflagellar Transport Proteins 172, 80, 57, 54, 38, and 20 Form a Stable Tubulin-Binding Ift-B2 Complex. Authors: Taschner, M. / Weber, K. / Mourao, A. / Vetter, M. / Awasthi, M. / Stiegler, M. / Bhogaraju, S. / Lorentzen, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fmu.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fmu.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 5fmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fmu_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
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Full document | 5fmu_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 5fmu_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 5fmu_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/5fmu ftp://data.pdbj.org/pub/pdb/validation_reports/fm/5fmu | HTTPS FTP |
-Related structure data
Related structure data | 5fmrC 5fmsC 5fmtSC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15125.798 Da / Num. of mol.: 4 / Fragment: TUBULIN-BINDING DOMAIN, RESIDUES 1-133 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q149C2 #2: Chemical | ChemComp-MES / | #3: 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: 2.03 Å3/Da / Density % sol: 39.5 % / Description: NONE |
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Crystal grow | Details: 50MM MES PH 5.8, 200MM AMMONIUM ACETATE, 4% MPD, 32%PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.593→36.47 Å / Num. obs: 60996 / % possible obs: 93.9 % / Observed criterion σ(I): 1.6 / Redundancy: 2.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.45 |
Reflection shell | Resolution: 1.59→1.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.59 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FMT Resolution: 1.593→36.471 Å / SU ML: 0.18 / σ(F): 1.96 / Phase error: 23.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.593→36.471 Å
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Refine LS restraints |
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LS refinement shell |
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