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- PDB-2q12: Crystal Structure of BAR domain of APPL1 -

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Basic information

Entry
Database: PDB / ID: 2q12
TitleCrystal Structure of BAR domain of APPL1
ComponentsDCC-interacting protein 13 alpha
KeywordsPROTEIN TRANSPORT / APPL1 / BAR domain
Function / homology
Function and homology information


positive regulation of macropinocytosis / regulation of toll-like receptor 4 signaling pathway / negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of fibroblast migration / adiponectin-activated signaling pathway / regulation of glucose import / macropinosome / protein kinase B binding / signaling / positive regulation of melanin biosynthetic process ...positive regulation of macropinocytosis / regulation of toll-like receptor 4 signaling pathway / negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of fibroblast migration / adiponectin-activated signaling pathway / regulation of glucose import / macropinosome / protein kinase B binding / signaling / positive regulation of melanin biosynthetic process / regulation of G1/S transition of mitotic cell cycle / positive regulation of cytokine production involved in inflammatory response / Caspase activation via Dependence Receptors in the absence of ligand / early phagosome / intracellular vesicle / beta-tubulin binding / phosphatidylserine binding / regulation of innate immune response / cellular response to hepatocyte growth factor stimulus / regulation of protein localization to plasma membrane / phosphatidylinositol binding / vesicle membrane / ruffle / transforming growth factor beta receptor signaling pathway / positive regulation of glucose import / protein import into nucleus / insulin receptor signaling pathway / early endosome membrane / cytoplasmic vesicle / early endosome / endosome membrane / endosome / cell cycle / protein-containing complex binding / signal transduction / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
APPL1, BAR domain / BAR domain of APPL family / Arfaptin homology (AH) 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 ...APPL1, BAR domain / BAR domain of APPL family / Arfaptin homology (AH) 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 / SAD / Resolution: 1.79 Å
AuthorsZhang, X.C. / Zhu, G.
CitationJournal: Embo J. / Year: 2007
Title: Structure of the APPL1 BAR-PH domain and characterization of its interaction with Rab5.
Authors: Zhu, G. / Chen, J. / Liu, J. / Brunzelle, J.S. / Huang, B. / Wakeham, N. / Terzyan, S. / Li, X. / Rao, Z. / Li, G. / Zhang, X.C.
History
DepositionMay 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / 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)31,1571
Polymers31,1571
Non-polymers00
Water2,648147
1
A: DCC-interacting protein 13 alpha

A: DCC-interacting protein 13 alpha


Theoretical massNumber of molelcules
Total (without water)62,3142
Polymers62,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area8640 Å2
ΔGint-87 kcal/mol
Surface area25590 Å2
MethodPISA, PQS
Unit cell
γ
α
β
Length a, b, c (Å)52.985, 129.199, 36.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological dimer is generated from molecules in asymmetric unit and operation -x+1, -y, z

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Components

#1: Protein DCC-interacting protein 13 alpha / Dip13 alpha


Mass: 31157.240 Da / Num. of mol.: 1 / Fragment: residues 5-265, BAR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APPL1, APPL, DIP13A, KIAA1428 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9UKG1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M magnesium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2006
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 23548 / Num. obs: 23518 / % possible obs: 95.7 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.19 / Num. unique all: 1897 / % possible all: 78.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.355 / SU ML: 0.106 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1200 5.1 %RANDOM
Rwork0.212 ---
all0.214 23473 --
obs0.214 22273 95.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.596 Å2
Baniso -1Baniso -2Baniso -3
1-3.99 Å20 Å20 Å2
2---2.54 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 0 147 2113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222025
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9622734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5865254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52425.577104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69515398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2611510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021512
X-RAY DIFFRACTIONr_nbd_refined0.2160.2914
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21440
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.2125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.218
X-RAY DIFFRACTIONr_mcbond_it3.37421277
X-RAY DIFFRACTIONr_mcangle_it4.26931993
X-RAY DIFFRACTIONr_scbond_it4.3282841
X-RAY DIFFRACTIONr_scangle_it6.1553734
LS refinement shellResolution: 1.792→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 67 -
Rwork0.266 1249 -
obs--72.79 %

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