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- PDB-2z0n: Crystal structure of APPL1-BAR domain -

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Basic information

Entry
Database: PDB / ID: 2z0n
TitleCrystal structure of APPL1-BAR domain
ComponentsDCC-interacting protein 13-alpha
KeywordsSIGNALING PROTEIN / helix bundle / Cell cycle / Coiled coil / Endosome / Membrane / Nucleus / Phosphorylation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / maintenance of synapse structure / regulation of glucose import / protein kinase B binding / signaling / positive regulation of melanin biosynthetic process ...negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / maintenance of synapse structure / regulation of glucose import / protein kinase B binding / signaling / positive regulation of melanin biosynthetic process / regulation of toll-like receptor 4 signaling pathway / vesicle membrane / positive regulation of cytokine production involved in inflammatory response / early phagosome / Caspase activation via Dependence Receptors in the absence of ligand / regulation of innate immune response / cellular response to hepatocyte growth factor stimulus / intracellular vesicle / phosphatidylserine binding / beta-tubulin binding / regulation of G1/S transition of mitotic cell cycle / regulation of protein localization to plasma membrane / ruffle / phosphatidylinositol binding / transforming growth factor beta receptor signaling pathway / positive regulation of glucose import / protein import into nucleus / presynapse / insulin receptor signaling pathway / cytoplasmic vesicle / early endosome membrane / postsynapse / early endosome / endosome membrane / endosome / cell cycle / glutamatergic synapse / protein-containing complex binding / signal transduction / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
APPL1, BAR domain / : / : / : / BAR domain of APPL family / Arfaptin homology (AH) domain/BAR domain / BAR domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain ...APPL1, BAR domain / : / : / : / BAR domain of APPL family / Arfaptin homology (AH) domain/BAR domain / BAR domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DCC-interacting protein 13-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Sakamoto, A. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of APPL1-BAR domain
Authors: Murayama, K. / Kato-Murayama, M. / Sakamoto, A. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: 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: DCC-interacting protein 13-alpha


Theoretical massNumber of molelcules
Total (without water)32,7081
Polymers32,7081
Non-polymers00
Water1,72996
1
A: DCC-interacting protein 13-alpha

A: DCC-interacting protein 13-alpha


Theoretical massNumber of molelcules
Total (without water)65,4162
Polymers65,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7550 Å2
ΔGint-80 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.121, 128.329, 36.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DCC-interacting protein 13-alpha / APPL1 / Dip13-alpha / Adapter protein containing PH domain / PTB domain and leucine zipper motif 1


Mass: 32708.053 Da / Num. of mol.: 1 / Fragment: reisdues 1-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKG1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17.5% PEG3350, 0.2M Ammonium sulfate, 0.1M Hepes, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.979089, 0.979462, 0.964
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790891
20.9794621
30.9641
ReflectionResolution: 1.95→50 Å / Num. obs: 19533 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 16.8
Reflection shellResolution: 1.95→2.02 Å / Rsym value: 0.341 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→35.52 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1385109.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1920 9.9 %RANDOM
Rwork0.209 ---
obs0.209 19488 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.905 Å2 / ksol: 0.375848 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-9.4 Å20 Å20 Å2
2---6.23 Å20 Å2
3----3.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.95→35.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 0 96 2007
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.021.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it3.722
X-RAY DIFFRACTIONc_scangle_it5.282.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 306 9.7 %
Rwork0.222 2860 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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