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- PDB-2aq5: Crystal Structure of Murine Coronin-1 -

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Basic information

Entry
Database: PDB / ID: 2aq5
TitleCrystal Structure of Murine Coronin-1
ComponentsCoronin-1A
KeywordsSTRUCTURAL PROTEIN / WD40 repeat / 7-Bladed beta-propeller
Function / homology
Function and homology information


negative regulation of vesicle fusion / uropod organization / negative regulation of actin nucleation / thymocyte migration / phagolysosome assembly / natural killer cell degranulation / early endosome to recycling endosome transport / epithelial cell migration / T cell migration / regulation of actin polymerization or depolymerization ...negative regulation of vesicle fusion / uropod organization / negative regulation of actin nucleation / thymocyte migration / phagolysosome assembly / natural killer cell degranulation / early endosome to recycling endosome transport / epithelial cell migration / T cell migration / regulation of actin polymerization or depolymerization / stereocilium tip / vesicle fusion / nerve growth factor signaling pathway / regulation of actin filament polymerization / regulation of release of sequestered calcium ion into cytosol / leukocyte chemotaxis / cortical actin cytoskeleton / positive chemotaxis / cell-substrate adhesion / cell leading edge / myosin heavy chain binding / T cell homeostasis / phagocytic cup / immunological synapse / actin monomer binding / positive regulation of T cell migration / cellular response to interleukin-4 / phosphatidylinositol 3-kinase binding / T cell proliferation / positive regulation of T cell proliferation / homeostasis of number of cells within a tissue / cytoskeletal protein binding / T cell activation / response to cytokine / establishment of localization in cell / actin filament / actin filament organization / phagocytic vesicle membrane / calcium ion transport / cell-cell junction / actin filament binding / cell migration / actin cytoskeleton / positive regulation of T cell activation / lamellipodium / regulation of cell shape / neuron apoptotic process / negative regulation of neuron apoptotic process / early endosome / axon / glutamatergic synapse / synapse / protein homodimerization activity / protein-containing complex / identical protein binding / plasma membrane
Similarity search - Function
Trimerisation motif / Trimerisation motif / DUF1900 / Type of WD40 repeat / Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / DUF1899 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller ...Trimerisation motif / Trimerisation motif / DUF1900 / Type of WD40 repeat / Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / DUF1899 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsAppleton, B.A. / Wu, P. / Wiesmann, C.
CitationJournal: Structure / Year: 2006
Title: The crystal structure of murine coronin-1: a regulator of actin cytoskeletal dynamics in lymphocytes.
Authors: Appleton, B.A. / Wu, P. / Wiesmann, C.
History
DepositionAug 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coronin-1A


Theoretical massNumber of molelcules
Total (without water)44,5011
Polymers44,5011
Non-polymers00
Water8,341463
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.996, 80.443, 88.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coronin-1A / Coronin-like protein p57 / Coronin-like protein A / CLIPINA / Tryptophan aspartate-containing coat ...Coronin-like protein p57 / Coronin-like protein A / CLIPINA / Tryptophan aspartate-containing coat protein / TACO


Mass: 44500.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Coro1a, Coro1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O89053
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 292 K / pH: 8
Details: 30% PEG-MME 2000, 150 mM potassium chloride, 5 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 292K, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795, 0.9797, 0.9570
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 17, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.9571
ReflectionResolution: 1.75→50 Å / Num. obs: 38545 / % possible obs: 99.5 % / Redundancy: 12.1 % / Rsym value: 0.081 / Net I/σ(I): 33.9
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 11.8 / Rsym value: 0.245 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.602 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1927 5 %RANDOM
Rwork0.158 ---
obs0.16 36618 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.32 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 0 463 3524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223139
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9734269
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.17623.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51615506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.481522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022382
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21309
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22118
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2389
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8561.52012
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40623196
X-RAY DIFFRACTIONr_scbond_it2.34831272
X-RAY DIFFRACTIONr_scangle_it3.6844.51073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 138 -
Rwork0.173 2600 -
obs--98.24 %
Refinement TLS params.Method: refined / Origin x: 16.0221 Å / Origin y: 54.315 Å / Origin z: 21.0648 Å
111213212223313233
T-0.071 Å20.0078 Å2-0.0044 Å2--0.082 Å20.0049 Å2---0.0709 Å2
L0.5419 °20.1566 °20.0308 °2-0.4909 °20.068 °2--0.602 °2
S0.0013 Å °0.0535 Å °0.0226 Å °-0.0646 Å °-0.0076 Å °0.0355 Å °-0.0218 Å °-0.0512 Å °0.0064 Å °

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