+Open data
-Basic information
Entry | Database: PDB / ID: 6xz3 | |||||||||
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Title | Crystal structure of TLNRD1 4-helix bundle | |||||||||
Components | Talin rod domain-containing protein 1 | |||||||||
Keywords | CELL ADHESION / Actin binding protein / Protein complex / 4-helix bundle / Cytoskeleton | |||||||||
Function / homology | Talin rod domain-containing protein 1 / stress fiber / actin binding / identical protein binding / Talin rod domain-containing protein 1 Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | |||||||||
Authors | Cowell, A. / Singh, A.K. / Brown, D.G. / Goult, B.T. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: J.Cell Biol. / Year: 2021 Title: Talin rod domain-containing protein 1 (TLNRD1) is a novel actin-bundling protein which promotes filopodia formation. Authors: Cowell, A.R. / Jacquemet, G. / Singh, A.K. / Varela, L. / Nylund, A.S. / Ammon, Y.C. / Brown, D.G. / Akhmanova, A. / Ivaska, J. / Goult, B.T. #1: Journal: Biorxiv / Year: 2020 Title: Talin Rod Domain Containing Protein 1 (TLNRD1) is a novel actin- bundling protein which promotes filopodia formation. Authors: Cowell, A. / Jacquemet, G. / Singh, A.K. / Ammon, Y.-K. / Brown, D.G. / Akhmanova, A. / Ivaska, J. / Goult, B.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xz3.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xz3.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/6xz3 ftp://data.pdbj.org/pub/pdb/validation_reports/xz/6xz3 | HTTPS FTP |
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-Related structure data
Related structure data | 6xz4C 2x0cS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14461.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TLNRD1 4-helix bundle residues 143-273 / Source: (gene. exp.) Homo sapiens (human) / Gene: TLNRD1, MESDC1 / Plasmid: pET151 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H1K6 |
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#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.73 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.3 M ammonium citrate dibasic, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97855 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97855 Å / Relative weight: 1 |
Reflection | Resolution: 2.188→57.36 Å / Num. obs: 10508 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.037 / Rrim(I) all: 0.135 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.188→2.31 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.034 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1491 / CC1/2: 0.938 / Rpim(I) all: 0.288 / Rrim(I) all: 1.074 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2X0C Resolution: 2.19→57.36 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.34 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.177 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.72 Å2 / Biso mean: 61.321 Å2 / Biso min: 35.77 Å2
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Refinement step | Cycle: final / Resolution: 2.19→57.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.245 Å / Rfactor Rfree error: 0
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