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- PDB-3aco: Crystal structure of the EFC/F-BAR domain of human PACSIN2/Syndap... -

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Basic information

Entry
Database: PDB / ID: 3aco
TitleCrystal structure of the EFC/F-BAR domain of human PACSIN2/Syndapin II (2.7 A)
ComponentsProtein kinase C and casein kinase substrate in neurons protein 2
KeywordsENDOCYTOSIS / HELIX BUNDLE / COILED-COIL
Function / homology
Function and homology information


caveola assembly / cell projection morphogenesis / plasma membrane tubulation / protein localization to endosome / phosphatidic acid binding / negative regulation of endocytosis / caveolin-mediated endocytosis / regulation of endocytosis / centriolar satellite / cytoskeleton organization ...caveola assembly / cell projection morphogenesis / plasma membrane tubulation / protein localization to endosome / phosphatidic acid binding / negative regulation of endocytosis / caveolin-mediated endocytosis / regulation of endocytosis / centriolar satellite / cytoskeleton organization / cytoskeletal protein binding / caveola / modulation of chemical synaptic transmission / phospholipid binding / ruffle membrane / recycling endosome membrane / cell-cell junction / Clathrin-mediated endocytosis / actin cytoskeleton organization / early endosome / endosome / nuclear speck / cadherin binding / intracellular membrane-bounded organelle / focal adhesion / glutamatergic synapse / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PACSIN2, F-BAR domain / PACSIN1/PACSIN2, SH3 domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain ...PACSIN2, F-BAR domain / PACSIN1/PACSIN2, SH3 domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein kinase C and casein kinase substrate in neurons protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsShimada, A. / Shirouzu, M. / Hanawa-Suetsugu, K. / Terada, T. / Umehara, T. / Suetsugu, S. / Yamamoto, M. / Yokoyama, S.
CitationJournal: Febs Lett. / Year: 2010
Title: Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II
Authors: Shimada, A. / Takano, K. / Shirouzu, M. / Hanawa-Suetsugu, K. / Terada, T. / Toyooka, K. / Umehara, T. / Yamamoto, M. / Yokoyama, S. / Suetsugu, S.
History
DepositionJan 7, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C and casein kinase substrate in neurons protein 2
B: Protein kinase C and casein kinase substrate in neurons protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1414
Polymers82,0612
Non-polymers802
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-63 kcal/mol
Surface area31220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.607, 84.654, 357.335
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 Protein kinase C and casein kinase substrate in neurons protein 2 / PACSIN2


Mass: 41030.613 Da / Num. of mol.: 2 / Fragment: EFC/F-BAR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PACSIN2 / Plasmid: PX080424-07 / Production host: cell free system (Escherichia coli) / References: UniProt: Q9UNF0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 3350, 0.1M calcium chloride, 0.03M glycyl-glycyl-glycine, 0.05 M Tris-HCl, 0.075M NaCl, 0.001M DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2009 / Details: mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 27264 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 59.1 Å2 / Rsym value: 0.164 / Net I/σ(I): 14.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 2445 / Rsym value: 0.395 / % possible all: 90.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→39.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 56299.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1303 4.9 %RANDOM
Rwork0.226 ---
obs0.226 26723 96.2 %-
all-26723 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.9529 Å2 / ksol: 0.334815 e/Å3
Displacement parametersBiso mean: 65.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.31 Å20 Å20 Å2
2---2.36 Å20 Å2
3---7.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 2 273 4983
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it10.451.5
X-RAY DIFFRACTIONc_mcangle_it16.32
X-RAY DIFFRACTIONc_scbond_it13.962
X-RAY DIFFRACTIONc_scangle_it20.312.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 200 4.8 %
Rwork0.304 3964 -
obs--91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION5ion.paramion.top

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