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- PDB-2b4e: Crystal Structure of Murine Coronin-1: monoclinic form -

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Basic information

Entry
Database: PDB / ID: 2b4e
TitleCrystal Structure of Murine Coronin-1: monoclinic form
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 / actin cytoskeleton / cell migration / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionSep 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,3611
Polymers44,3611
Non-polymers00
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.358, 80.284, 52.889
Angle α, β, γ (deg.)90.00, 111.92, 90.00
Int Tables number4
Space group name H-MP1211

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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: 44360.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: coro1, coro1a / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O89053
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200 mM ammonium acetate, 100 mM Bis-Tris PH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 16388 / % possible obs: 92.6 % / Redundancy: 3.6 % / Rsym value: 0.087 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.391 / % possible all: 87.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AQ5

2aq5


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.527 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22867 835 5.1 %RANDOM
Rwork0.15532 ---
obs0.15905 15553 92.21 %-
all-15556 --
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: 28.862 Å2
Baniso -1Baniso -2Baniso -3
1-3.23 Å20 Å21.12 Å2
2---1.88 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 0 278 3262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223059
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9664163
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04823.516128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9315500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.011521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022325
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21302
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22005
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6791.51970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11123120
X-RAY DIFFRACTIONr_scbond_it1.71631234
X-RAY DIFFRACTIONr_scangle_it2.7174.51043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 52 -
Rwork0.184 1062 -
obs--86.09 %
Refinement TLS params.Method: refined / Origin x: -4.5412 Å / Origin y: 0.6339 Å / Origin z: 9.3549 Å
111213212223313233
T-0.1295 Å20.0343 Å2-0.0066 Å2--0.0901 Å20.0104 Å2---0.11 Å2
L1.2058 °20.1953 °2-0.2033 °2-2.1656 °2-0.4152 °2--1.2737 °2
S-0.0314 Å °-0.0611 Å °0.0016 Å °0.055 Å °0.0842 Å °0.1467 Å °-0.0771 Å °-0.0486 Å °-0.0528 Å °

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