+Open data
-Basic information
Entry | Database: PDB / ID: 1k8k | ||||||
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Title | Crystal Structure of Arp2/3 Complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / beta-propeller | ||||||
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 / positive regulation of double-strand break repair via homologous recombination / cilium assembly ...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 / positive regulation of double-strand break repair via homologous recombination / cilium assembly / 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 / 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 / MAD / Resolution: 2 Å | ||||||
Authors | Robinson, R.C. / Turbedsky, K. / Kaiser, D.A. / Higgs, H.N. / Marchand, J.-B. / Choe, S. / Pollard, T.D. | ||||||
Citation | Journal: Science / Year: 2001 Title: Crystal Structure of Arp2/3 Complex Authors: Robinson, R.C. / Turbedsky, K. / Kaiser, D.A. / Marchand, J.-B. / Higgs, H.N. / Choe, S. / Pollard, T.D. #1: Journal: Biochemistry / Year: 1999 Title: Influence of the Wiskott-Aldrich syndrome protein (WASp) C terminus and Arp2/3 complex on actin polymerization Authors: Higgs, H.N. / Blanchoin, L. / Pollard, T.D. #2: Journal: Curr.Opin.Struct.Biol. / Year: 1999 Title: Structure and function of the Arp2/3 complex Authors: Mullins, R.D. / Pollard, T.D. #3: Journal: Annu.Rev.Biophys.Biomol.Struct. / Year: 2000 Title: Biophysics of actin filament dynamics in nonmuscle cells Authors: Pollard, T.D. / Blanchoin, L. / Mullins, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k8k.cif.gz | 393.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k8k.ent.gz | 311.1 KB | Display | PDB format |
PDBx/mmJSON format | 1k8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/1k8k ftp://data.pdbj.org/pub/pdb/validation_reports/k8/1k8k | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-ACTIN-LIKE PROTEIN ... , 2 types, 2 molecules AB
#1: Protein | Mass: 47428.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: P61157 |
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#2: Protein | Mass: 44818.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: A7MB62 |
-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 / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q58CQ2 |
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#4: Protein | Mass: 34402.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q3MHR7 |
#5: Protein | Mass: 20572.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q3T035 |
#6: Protein | Mass: 19697.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q148J6 |
#7: Protein | Mass: 16295.317 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: part of the Arp2/3 Complex / Source: (natural) Bos taurus (cattle) / Organ: thymus / References: UniProt: Q3SYX9 |
-Non-polymers , 1 types, 1710 molecules
#8: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.03 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, KSCN, Hepes at pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2001 / Details: double crystal monochromator |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 196866 / Num. obs: 185141 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.064 / Net I/σ(I): 8.6 |
Reflection | *PLUS Highest resolution: 2.01 Å / Lowest resolution: 20 Å / Num. obs: 183319 / % possible obs: 92.8 % / Num. measured all: 852046 / Rmerge(I) obs: 0.064 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.01 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.249 | ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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