[English] 日本語
Yorodumi- PDB-1ux4: Crystal structures of a Formin Homology-2 domain reveal a tethere... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ux4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structures of a Formin Homology-2 domain reveal a tethered-dimer architecture | ||||||
Components | BNI1 PROTEIN | ||||||
Keywords | STRUCTURAL PROTEIN / FH2 ACTIN CYTOSKELETON / COILED COIL | ||||||
Function / homology | Function and homology information polarisome / formin-nucleated actin cable assembly / budding cell apical bud growth / vesicle targeting / mitotic actomyosin contractile ring assembly / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / actin nucleation / incipient cellular bud site / cellular bud tip ...polarisome / formin-nucleated actin cable assembly / budding cell apical bud growth / vesicle targeting / mitotic actomyosin contractile ring assembly / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / actin nucleation / incipient cellular bud site / cellular bud tip / profilin binding / cellular bud neck / mating projection tip / barbed-end actin filament capping / establishment of cell polarity / cell division site / establishment of mitotic spindle orientation / actin filament bundle assembly / actin filament / regulation of actin cytoskeleton organization / small GTPase binding / regulation of protein localization / actin binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Xu, Y. / Moseley, J.B. / Sagot, I. / Poy, F. / Pellman, D. / Goode, B.L. / Eck, M.J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2004 Title: Crystal Structures of a Formin Homology-2 Domain Reveal a Tethered Dimer Architecture Authors: Xu, Y. / Moseley, J.B. / Sagot, I. / Poy, F. / Pellman, D. / Goode, B.L. / Eck, M.J. #1: Journal: Nat.Cell Biol. / Year: 2002 Title: Yeast Formins Regulate Cell Polarity by Controlling the Assembly of Actin Cables Authors: Sagot, I. / Klee, S.K. / Pellman, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ux4.cif.gz | 163.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ux4.ent.gz | 127.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ux4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ux4_validation.pdf.gz | 428.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ux4_full_validation.pdf.gz | 475.9 KB | Display | |
Data in XML | 1ux4_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 1ux4_validation.cif.gz | 46.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/1ux4 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/1ux4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9999, -0.0011, -0.016), Vector: |
-Components
#1: Protein | Mass: 47207.695 Da / Num. of mol.: 2 / Fragment: FH2 DOMAIN, RESIDUES 1352-1765 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P41832 Compound details | ENGINEERED MUTATION IN CHAIN A AND B, ARG 1411 GLU ENGINEERED MUTATION IN CHAIN A AND B, LYS 1412 ...ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.99 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP AGAINST 0.8M SODIUM POTASSIUM PHOSPHATE, 30% GLYCEROL, HEPES PH7.5, pH 7.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.978 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. obs: 22747 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.5 |
Reflection | *PLUS Highest resolution: 3.3 Å / % possible obs: 82 % / Num. measured all: 50090 / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 61 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: OCCUPANCY WAS ASSIGNED TO 0 FOR ATOMS WITH NO OBSERVED ELECTRON DENSITY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.288 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.37 |