+Open data
-Basic information
Entry | Database: PDB / ID: 3ryc | ||||||
---|---|---|---|---|---|---|---|
Title | Tubulin: RB3 stathmin-like domain complex | ||||||
Components |
| ||||||
Keywords | CELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / GTPASE / MICROTUBULE / STATHMIN S-TUBULIN / SUBTILISIN / TUBULIN | ||||||
Function / homology | Function and homology information axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / microtubule depolymerization / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / response to mechanical stimulus / condensed chromosome / homeostasis of number of cells within a tissue / cellular response to calcium ion / tubulin binding / adult locomotory behavior / intracellular protein transport / neuron migration / synapse organization / visual learning / neuromuscular junction / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / mitotic cell cycle / gene expression / growth cone / neuron apoptotic process / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / protein-containing complex binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nawrotek, A. / Knossow, M. / Gigant, B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: The Determinants That Govern Microtubule Assembly from the Atomic Structure of GTP-Tubulin. Authors: Nawrotek, A. / Knossow, M. / Gigant, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ryc.cif.gz | 776.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ryc.ent.gz | 636.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ryc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ryc_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ryc_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 3ryc_validation.xml.gz | 75.5 KB | Display | |
Data in CIF | 3ryc_validation.cif.gz | 104.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/3ryc ftp://data.pdbj.org/pub/pdb/validation_reports/ry/3ryc | HTTPS FTP |
-Related structure data
Related structure data | 3ryfC 3ryhC 3ryiC 3hkbS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 3 types, 5 molecules ACBDE
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: brain / Source: (natural) Ovis aries (sheep) / Organ: BRAIN / References: UniProt: D0VWZ0 #2: Protein | Mass: 50043.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: brain / Source: (natural) Ovis aries (sheep) / Organ: BRAIN / References: UniProt: D0VWY9 #3: Protein | | Mass: 16745.975 Da / Num. of mol.: 1 / Fragment: Residues 48-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Plasmid: PET-8C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63043 |
---|
-Non-polymers , 5 types, 745 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-GDP / | #8: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | AUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN SEQUENCE WAS ...AUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.51 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG, LISO4, PIPES BUFFER, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45 Å / Num. obs: 118648 / % possible obs: 94.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.91 Å2 / Rsym value: 0.084 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.65 / % possible all: 77 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HKB Resolution: 2.1→43.14 Å / Cor.coef. Fo:Fc: 0.9586 / Cor.coef. Fo:Fc free: 0.9447 / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.31 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.275 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→43.14 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|