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- PDB-2akf: Crystal structure of the coiled-coil domain of coronin 1 -

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Basic information

Entry
Database: PDB / ID: 2akf
TitleCrystal structure of the coiled-coil domain of coronin 1
ComponentsCoronin-1A
KeywordsPROTEIN BINDING / coiled coil / coronin 1
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 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...Trimerisation motif / Trimerisation motif / DUF1900 / Type of WD40 repeat / Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / DUF1899 / 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
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKammerer, R.A. / Kostrewa, D. / Progias, P. / Honnappa, S. / Avila, D. / Lustig, A. / Winkler, F.K. / Pieters, J. / Steinmetz, M.O.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: A conserved trimerization motif controls the topology of short coiled coils
Authors: Kammerer, R.A. / Kostrewa, D. / Progias, P. / Honnappa, S. / Avila, D. / Lustig, A. / Winkler, F.K. / Pieters, J. / Steinmetz, M.O.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coronin-1A
B: Coronin-1A
C: Coronin-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6607
Polymers11,3983
Non-polymers2624
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-69 kcal/mol
Surface area6870 Å2
MethodPISA
2
B: Coronin-1A
hetero molecules

A: Coronin-1A
hetero molecules

C: Coronin-1A


Theoretical massNumber of molelcules
Total (without water)11,6607
Polymers11,3983
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1610 Å2
ΔGint-121 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.587, 23.569, 46.402
Angle α, β, γ (deg.)92.51, 96.85, 119.63
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is the trimer in the asymmetric unit.

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Components

#1: Protein/peptide 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: 3799.293 Da / Num. of mol.: 3 / Fragment: Coiled-coil domain / Source method: obtained synthetically
Details: Synthetic peptide with natural sequence of the C-terminal coiled-coil domain of mouse coronin 1.
References: UniProt: O89053
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.9 Å3/Da / Density % sol: 36.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, zinc sulfate, PEG MME 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9004 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 13, 2001 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9004 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. all: 24694 / Num. obs: 24694 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.74 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.056 / Net I/σ(I): 13.1
Reflection shellResolution: 1.2→1.25 Å / Redundancy: 2.92 % / Mean I/σ(I) obs: 7.1 / Num. unique all: 2593 / Rsym value: 0.131 / % possible all: 81.6

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.113 / SU ML: 0.024 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.048 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1237 5 %RANDOM
Rwork0.16 ---
all0.162 23457 --
obs0.162 23457 92.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.191 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.08 Å2-0.31 Å2
2---0.09 Å2-0.45 Å2
3----0.4 Å2
Refine analyze
FreeObs
Luzzati sigma a0.048 Å0.049 Å
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms798 0 7 98 903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022795
X-RAY DIFFRACTIONr_bond_other_d0.0010.02780
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9951065
X-RAY DIFFRACTIONr_angle_other_deg0.81131806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.592593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.3682548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6815174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5851512
X-RAY DIFFRACTIONr_chiral_restr0.090.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02141
X-RAY DIFFRACTIONr_nbd_refined0.2530.2185
X-RAY DIFFRACTIONr_nbd_other0.170.2807
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.2541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.253
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2110.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3770.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.032656
X-RAY DIFFRACTIONr_mcbond_other1.262198
X-RAY DIFFRACTIONr_mcangle_it2.9253777
X-RAY DIFFRACTIONr_scbond_it5.274.5373
X-RAY DIFFRACTIONr_scangle_it6.1956288
X-RAY DIFFRACTIONr_rigid_bond_restr2.30931857
X-RAY DIFFRACTIONr_sphericity_free8.043105
X-RAY DIFFRACTIONr_sphericity_bonded4.66831578
LS refinement shellResolution: 1.203→1.235 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.207 86
Rwork0.188 1568
Refinement TLS params.Method: refined / Origin x: -4.847 Å / Origin y: 0.0756 Å / Origin z: 3.2185 Å
111213212223313233
T-0.0421 Å2-0.0091 Å2-0.0014 Å2--0.0191 Å2-0.0063 Å2---0.0389 Å2
L0.0909 °20.4749 °21.4515 °2-2.481 °27.5828 °2--23.1754 °2
S-0.0786 Å °0.0184 Å °0.0042 Å °0.0023 Å °-0.0007 Å °0.0471 Å °0.1517 Å °-0.1266 Å °0.0793 Å °

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