+Open data
-Basic information
Entry | Database: PDB / ID: 1tyq | ||||||
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Title | Crystal structure of Arp2/3 complex with bound ATP and calcium | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / cilium assembly / positive regulation of double-strand break repair via homologous recombination ...EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / cilium assembly / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / actin filament polymerization / cell projection / structural constituent of cytoskeleton / actin filament binding / cell migration / site of double-strand break / actin binding / cell cortex / neuron projection / synapse / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Nolen, B.J. / Littlefield, R.S. / Pollard, T.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004 Title: Crystal structures of actin-related protein 2/3 complex with bound ATP or ADP Authors: Nolen, B.J. / Littlefield, R.S. / Pollard, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tyq.cif.gz | 353.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tyq.ent.gz | 277.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tyq_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1tyq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1tyq_validation.xml.gz | 63.8 KB | Display | |
Data in CIF | 1tyq_validation.cif.gz | 87.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/1tyq ftp://data.pdbj.org/pub/pdb/validation_reports/ty/1tyq | HTTPS FTP |
-Related structure data
Related structure data | 1u2vC 1k8kS C: citing same article (ref.) S: Starting model for refinement |
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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
-Actin-related ... , 2 types, 2 molecules AB
#1: Protein | Mass: 47428.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61157 |
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#2: Protein | Mass: 44818.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A7MB62*PLUS |
-Arp2/3 complex ... , 5 types, 5 molecules CDEFG
#3: Protein | Mass: 41016.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q58CQ2*PLUS |
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#4: Protein | Mass: 34402.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3MHR7*PLUS |
#5: Protein | Mass: 20572.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T035*PLUS |
#6: Protein | Mass: 19697.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q148J6*PLUS |
#7: Protein | Mass: 16295.317 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: thymus / References: UniProt: Q3SYX9*PLUS |
-Non-polymers , 3 types, 185 molecules
#8: Chemical | #9: Chemical | #10: 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: 3.21 Å3/Da / Density % sol: 61.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, potassium thiocyanate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 Å |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. all: 73162 / Num. obs: 72816 / % possible obs: 79.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.093 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.55→2.64 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.358 / % possible all: 68.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K8K Resolution: 2.55→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.55→30 Å
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Refine LS restraints |
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