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- PDB-2q13: Crystal structure of BAR-PH domain of APPL1 -

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Basic information

Entry
Database: PDB / ID: 2q13
TitleCrystal structure of BAR-PH domain of APPL1
ComponentsDCC-interacting protein 13 alpha
KeywordsPROTEIN TRANSPORT / APPL1 / BAR domain / PH domain / BAR-PH domain
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 / regulation of glucose import / maintenance of synapse structure / 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 / regulation of glucose import / maintenance of synapse structure / 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 / cellular response to hepatocyte growth factor stimulus / intracellular vesicle / phosphatidylserine binding / beta-tubulin binding / regulation of innate immune response / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DCC-interacting protein 13-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsZhu, G. / Zhang, X.C.
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: Advisory / Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,1701
Polymers44,1701
Non-polymers00
Water2,828157
1
A: DCC-interacting protein 13 alpha

A: DCC-interacting protein 13 alpha


Theoretical massNumber of molelcules
Total (without water)88,3392
Polymers88,3392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area12900 Å2
ΔGint-91 kcal/mol
Surface area36450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.737, 105.675, 36.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological dimer is generated by asymmetric unit and opration: -x+1, -y, z

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Components

#1: Protein DCC-interacting protein 13 alpha / Dip13 alpha / Adapter protein containing PH domain


Mass: 44169.609 Da / Num. of mol.: 1 / Fragment: residues 5-385, BAR and PH domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APPL1, APPL, DIP13A, KIAA1428 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UKG1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 45.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 6% PEG6000, 0.6M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 23286 / Num. obs: 23286 / % possible obs: 89.9 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1989 / % possible all: 78

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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: 2.05→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.849 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1200 5.2 %RANDOM
Rwork0.205 ---
all0.208 22082 --
obs0.208 22082 89.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.594 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2--2.66 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 0 157 3100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222991
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9594028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33425.26154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41215566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5361517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022248
X-RAY DIFFRACTIONr_nbd_refined0.2060.21265
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22081
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.2126
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.223
X-RAY DIFFRACTIONr_mcbond_it2.77721885
X-RAY DIFFRACTIONr_mcangle_it4.04732934
X-RAY DIFFRACTIONr_scbond_it3.31321262
X-RAY DIFFRACTIONr_scangle_it4.84831094
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 67 -
Rwork0.206 1319 -
obs--73.8 %
Refinement TLS params.Method: refined / Origin x: 40.8878 Å / Origin y: -0.0215 Å / Origin z: 2.249 Å
111213212223313233
T-0.0135 Å2-0.0364 Å2-0.0201 Å2--0.0198 Å20.0067 Å2---0.0371 Å2
L0.6938 °20.5707 °20.0424 °2-0.475 °20.0372 °2--0.0036 °2
S-0.0115 Å °-0.0352 Å °0.1186 Å °-0.0395 Å °-0.012 Å °0.096 Å °-0.0197 Å °0.0098 Å °0.0235 Å °

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