+Open data
-Basic information
Entry | Database: PDB / ID: 1sa1 | ||||||
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Title | Tubulin-podophyllotoxin: stathmin-like domain complex | ||||||
Components |
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Keywords | CELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / COLCHICINE / GTPASE / MICROTUBULE PODOPHYLLOTOXIN / STATHMIN / TUBULIN | ||||||
Function / homology | Function and homology information positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development ...positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / nervous system development / growth cone / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | ||||||
Authors | Ravelli, R.B. / Gigant, B. / Curmi, P.A. / Jourdain, I. / Lachkar, S. / Sobel, A. / Knossow, M. | ||||||
Citation | Journal: Nature / Year: 2004 Title: Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain. Authors: Ravelli, R.B. / Gigant, B. / Curmi, P.A. / Jourdain, I. / Lachkar, S. / Sobel, A. / Knossow, M. | ||||||
History |
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Remark 999 | SEQUENCE THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN ...SEQUENCE THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN HETERODIMERS (CHAINS A-B AND C-D) AND ONE STATHMIN-LIKE DOMAIN OF RB3. AS THE SEQUENCE OF BOVINE BRAIN TUBULIN IS NOT AVAILABLE, THE PIG BRAIN TUBULIN SEQUENCE WAS USED AS A REFERENCE. ONE NOTICEABLE EXCEPTION IS RESIDUE ALPHA 265 WHICH IS COMMONLY ILE BUT ALA IN PIG ALPHA TUBULIN. ALPHA-TUBULIN AND BETA-TUBULIN HAVE BEEN ALIGNED AS IN NOGALES ET AL., NATURE VOL 391, PAGES 199-203. IN THIS ALIGNMENT, RESIDUES 45-46 AND 361-368 OF ALPHA-TUBULIN ARE MISSING IN BETA-TUBULIN. THE STATHMIN-LIKE DOMAIN OF RB3 (RB3-SLD) CORRESPONDS TO STAHMIN RESIDUES 5 TO 145 WITH THE ADDITION OF AN ALANINE AT THE N-TERMINUS, WHICH IS ACETYLATED. THE NUMBERING OF RB3-SLD IS ACCORDING TO THE STATHMIN SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sa1.cif.gz | 354.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sa1.ent.gz | 273.5 KB | Display | PDB format |
PDBx/mmJSON format | 1sa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sa1_validation.pdf.gz | 838 KB | Display | wwPDB validaton report |
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Full document | 1sa1_full_validation.pdf.gz | 991.4 KB | Display | |
Data in XML | 1sa1_validation.xml.gz | 57.3 KB | Display | |
Data in CIF | 1sa1_validation.cif.gz | 80 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/1sa1 ftp://data.pdbj.org/pub/pdb/validation_reports/sa/1sa1 | HTTPS FTP |
-Related structure data
Related structure data | 1sa0SC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 1
NCS ensembles :
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Details | THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN HETERODIMERS (CHAINS A-B AND C-D) AND ONE STATHMIN-LIKE DOMAIN OF RB3 (CHAIN E) |
-Components
-Protein , 3 types, 5 molecules ACBDE
#1: Protein | Mass: 50163.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P02550, UniProt: Q2HJ86*PLUS #2: Protein | Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P02554, UniProt: Q6B856*PLUS #3: Protein | | Mass: 16712.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: STMN4 / Plasmid: pET-8c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02554, UniProt: P63043*PLUS |
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-Non-polymers , 4 types, 8 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | |
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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: 3.88 Å3/Da / Density % sol: 68 % | |||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG, PIPES BUFFER, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Gigant, B., (2000) Cell, 102, 809. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 / Wavelength: 0.933 Å |
Detector | Type: ADSC / Detector: CCD / Date: Jun 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 4.2→30 Å / Num. obs: 24624 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.26 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18 |
Reflection shell | Resolution: 4.2→4.3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2 / % possible all: 90.2 |
Reflection | *PLUS Highest resolution: 4.2 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 4.2 Å / Lowest resolution: 4.3 Å / % possible obs: 90.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SA0 Resolution: 4.2→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 56.857 / SU ML: 0.695 / Cross valid method: THROUGHOUT / ESU R Free: 0.873 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL DUE TO THE LIMITED (4.2 ANGSTROMS) RESOLUTION. IN ADDITION, THE FOLLOWING WEAKLY DEFINED RESIDUES ARE MISSING IN THIS ENTRY: ...Details: CARE SHOULD BE EXERCISED IN INTERPRETING THE CURRENT MODEL DUE TO THE LIMITED (4.2 ANGSTROMS) RESOLUTION. IN ADDITION, THE FOLLOWING WEAKLY DEFINED RESIDUES ARE MISSING IN THIS ENTRY: RESIDUES 40 TO 44 AND THE C-TERMINUS STARTING FROM RESIDUE 440 ON ALPHA TUBULIN CHAIN A, RESIDUES 277 TO 281 AND THE C-TERMINUS STARTING FROM RESIDUE 438 ON BETA TUBULIN CHAIN B, RESIDUES 39 TO 46 AND THE C-TERMINUS STARTING FROM RESIDUE 440 ON ALPHA TUBULIN CHAIN C, THE C-TERMINUS STARTING FROM RESIDUES 438 ON BETA TUBULIN CHAIN D, AND RESIDUES 4, 5, 43, 44 AND 142 TO 145 OF RB3-SLD. CA 5% OF THE SIDE CHAINS ARE POORLY DEFINED AND ARE CURRENTLY MODELLED AS ALANINES.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 116.49 Å2
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Refinement step | Cycle: LAST / Resolution: 4.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 4.204→4.308 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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