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- PDB-3ub5: Profilin:actin with a wide open nucleotide cleft -

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Basic information

Entry
Database: PDB / ID: 3ub5
TitleProfilin:actin with a wide open nucleotide cleft
Components
  • Actin, cytoplasmic 1
  • Profilin-1
KeywordsSTRUCTURAL PROTEIN / ATPase / nucleotide exchange
Function / homology
Function and homology information


PCP/CE pathway / Adherens junctions interactions / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / Gap junction degradation / Formation of annular gap junctions / MAP2K and MAPK activation / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs ...PCP/CE pathway / Adherens junctions interactions / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / Gap junction degradation / Formation of annular gap junctions / MAP2K and MAPK activation / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / structural constituent of postsynaptic actin cytoskeleton / VEGFA-VEGFR2 Pathway / positive regulation of actin filament bundle assembly / dense body / regulation of actin filament polymerization / Clathrin-mediated endocytosis / NuA4 histone acetyltransferase complex / axonogenesis / cell motility / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / actin binding / actin cytoskeleton organization / cytoskeleton / hydrolase activity / axon / focal adhesion / synapse / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Profilin1/2/3, vertebrate / : / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / ATPase, substrate binding domain, subdomain 4 ...Profilin1/2/3, vertebrate / : / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Beta-Lactamase / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Profilin-1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPorta, J.C. / Borgstahl, G.E.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural basis for profilin-mediated actin nucleotide exchange.
Authors: Porta, J.C. / Borgstahl, G.E.
History
DepositionOct 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, cytoplasmic 1
P: Profilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3357
Polymers56,6202
Non-polymers7155
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-30 kcal/mol
Surface area21490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.000, 72.000, 186.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AP

#1: Protein Actin, cytoplasmic 1 / / Beta-actin / Actin / cytoplasmic 1 / N-terminally processed


Mass: 41651.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P60712
#2: Protein Profilin-1 / / Profilin I


Mass: 14968.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02584

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Non-polymers , 5 types, 88 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 1.3M potassium phosphate pH 7.3, 0.5M ATP, 0.2M CaCl2, 1mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 11, 2010
RadiationMonochromator: Osmic VariMax Confocal Max-Flux Optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→93.4 Å / Num. all: 20743 / Num. obs: 26998 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.2 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.6.0119refinement
EVAL15data reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.24 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.057 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28977 1302 5.1 %RANDOM
Rwork0.21545 ---
obs0.21928 24323 94.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.826 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2---3.46 Å2-0 Å2
3---3.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 40 83 4055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.9745489
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9775507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78423.976166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.41115694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1791523
X-RAY DIFFRACTIONr_chiral_restr0.1250.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213014
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 59 -
Rwork0.315 1224 -
obs--68.46 %

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