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- PDB-1d7m: COILED-COIL DIMERIZATION DOMAIN FROM CORTEXILLIN I -

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Basic information

Entry
Database: PDB / ID: 1d7m
TitleCOILED-COIL DIMERIZATION DOMAIN FROM CORTEXILLIN I
ComponentsCORTEXILLIN I
KeywordsCONTRACTILE PROTEIN / COILED-COIL / COILED-COIL TRIGGER SITE / ALPHA HELIX / DIMERIZATION
Function / homology
Function and homology information


lateral part of motile cell / sorocarp stalk morphogenesis / negative regulation of protein localization to cell cortex / protein localization to cleavage furrow / actomyosin contractile ring contraction / adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway / regulation of myosin II filament assembly / chemotaxis to cAMP / positive regulation of cytoskeleton organization / protein localization => GO:0008104 ...lateral part of motile cell / sorocarp stalk morphogenesis / negative regulation of protein localization to cell cortex / protein localization to cleavage furrow / actomyosin contractile ring contraction / adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway / regulation of myosin II filament assembly / chemotaxis to cAMP / positive regulation of cytoskeleton organization / protein localization => GO:0008104 / cell trailing edge / actin filament network formation / basal cortex / aggregation involved in sorocarp development / actomyosin contractile ring / mitotic spindle midzone / sexual reproduction / actin crosslink formation / detection of mechanical stimulus / cleavage furrow formation / bleb assembly / alpha-catenin binding / epithelial cell morphogenesis / protein kinase regulator activity / cortical actin cytoskeleton organization / regulation of GTPase activity / cell leading edge / actin filament bundle / cleavage furrow / actin filament bundle assembly / mitotic cytokinesis / response to mechanical stimulus / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / actin filament / response to bacterium / cell morphogenesis / establishment of protein localization / protein localization / actin filament binding / actin cytoskeleton / cell cortex / regulation of gene expression / vesicle / positive regulation of protein phosphorylation / positive regulation of gene expression / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cortexillin, coiled coil / Cortexillin I, coiled coil / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. ...Cortexillin, coiled coil / Cortexillin I, coiled coil / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cortexillin-1 / Cortexillin-1
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsBurkhard, P. / Kammerer, R.A. / Steinmetz, M.O. / Bourenkov, G.P. / Aebi, U.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: The coiled-coil trigger site of the rod domain of cortexillin I unveils a distinct network of interhelical and intrahelical salt bridges.
Authors: Burkhard, P. / Kammerer, R.A. / Steinmetz, M.O. / Bourenkov, G.P. / Aebi, U.
#1: Journal: J.Struct.Biol. / Year: 1998
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of the 190 A Long Coiled-Coil Dimerization Domain of the Actin-Bundling Protein Cortexillin I from Dictyostelium discoideum
Authors: Burkhard, P. / Steinmetz, M.O. / Schulthess, T. / Landwehr, R. / Aebi, U. / Kammerer, R.A.
History
DepositionOct 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CORTEXILLIN I
B: CORTEXILLIN I


Theoretical massNumber of molelcules
Total (without water)23,2472
Polymers23,2472
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-53 kcal/mol
Surface area14090 Å2
MethodPISA
2
A: CORTEXILLIN I
B: CORTEXILLIN I

A: CORTEXILLIN I
B: CORTEXILLIN I


Theoretical massNumber of molelcules
Total (without water)46,4934
Polymers46,4934
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area12670 Å2
ΔGint-116 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.420, 128.650, 91.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-91-

HOH

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Components

#1: Protein CORTEXILLIN I


Mass: 11623.278 Da / Num. of mol.: 2 / Fragment: COILED-COIL DIMERIZATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: O15813, UniProt: Q54HG2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.43 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5 M AMMONIUM SULFATE 100 MM TRIS (PH 6.5) 2.5 % PEG 400 1.0 % DIOXANE, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
pH: 7.4 / Details: Burkhard, P., (1998) J.Struct.Biol., 122, 293.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMsodium phosphate1drop
215 mg/mlprotein1drop
3150 mM1dropNaCl
41.5 Mammonium sulfate1reservoir
50.1 MTris1reservoir
62.5 %PEG4001reservoir
71 %dioxane1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG BW7B10.951
SYNCHROTRONMPG/DESY, HAMBURG BW620.977
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATENov 14, 1998
MARRESEARCH2IMAGE PLATEJun 1, 1988
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9511
20.9771
ReflectionResolution: 2.7→30 Å / Num. all: 31909 / Num. obs: 11302 / % possible obs: 95.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 5.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.462 / % possible all: 88.2
Reflection
*PLUS
% possible obs: 94.6 % / Num. measured all: 49645 / Rmerge(I) obs: 0.078

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→37.3 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1675937.19 / Data cutoff high rms absF: 1675937.19 / Data cutoff low absF: 0 / Isotropic thermal model: CONSTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.249 469 5 %RANDOM
Rwork0.205 ---
obs0.205 9316 79.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.69 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso mean: 56.9 Å2
Baniso -1Baniso -2Baniso -3
1-25.56 Å20 Å20 Å2
2---23.35 Å20 Å2
3----2.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 0 93 1715
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.411.5
X-RAY DIFFRACTIONc_mcangle_it9.122
X-RAY DIFFRACTIONc_scbond_it12.22
X-RAY DIFFRACTIONc_scangle_it15.82.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 53 5.1 %
Rwork0.268 990 -
obs--54.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 3 / % reflection Rfree: 5 % / Rfactor obs: 0.218 / Rfactor Rfree: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 56.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.17
X-RAY DIFFRACTIONc_angle_deg1.77
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.381 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.268

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