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- PDB-1vf6: 2.1 Angstrom crystal structure of the PALS-1-L27N and PATJ L27 he... -

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Basic information

Entry
Database: PDB / ID: 1vf6
Title2.1 Angstrom crystal structure of the PALS-1-L27N and PATJ L27 heterodimer complex
Components
  • MAGUK p55 subfamily member 5
  • PALS1-associated tight junction protein
KeywordsPROTEIN BINDING/PROTEIN TRANSPORT / L27 domain / heterodimer / four-helical bundle / coiled-coil / hydrophobic packing interactions / PROTEIN BINDING-PROTEIN TRANSPORT COMPLEX
Function / homology
Function and homology information


protein localization to myelin sheath abaxonal region / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / tight junction assembly / Tight junction interactions / microtubule organizing center organization / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of apical/basal cell polarity / guanylate kinase activity ...protein localization to myelin sheath abaxonal region / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / tight junction assembly / Tight junction interactions / microtubule organizing center organization / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of apical/basal cell polarity / guanylate kinase activity / plasma membrane organization / myelin sheath adaxonal region / lateral loop / regulation of transforming growth factor beta receptor signaling pathway / Schmidt-Lanterman incisure / establishment or maintenance of epithelial cell apical/basal polarity / peripheral nervous system myelin maintenance / apical junction complex / generation of neurons / central nervous system neuron development / centriolar satellite / bicellular tight junction / regulation of microtubule cytoskeleton organization / protein localization to plasma membrane / adherens junction / protein localization / cerebral cortex development / apical part of cell / cell junction / gene expression / perikaryon / intracellular signal transduction / apical plasma membrane / axon / protein domain specific binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular exosome / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
L27 domain / L27-N / MPP5, SH3 domain / L27_N / L27-2 / L27_2 / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain ...L27 domain / L27-N / MPP5, SH3 domain / L27_N / L27-2 / L27_2 / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Helix Hairpins / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
InaD-like protein / Protein PALS1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsLi, Y. / Lavie, A. / Margolis, B. / Karnak, D.
CitationJournal: Embo J. / Year: 2004
Title: Structural basis for L27 domain-mediated assembly of signaling and cell polarity complexes.
Authors: Li, Y. / Karnak, D. / Demeler, B. / Margolis, B. / Lavie, A.
History
DepositionApr 9, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2016Group: Other
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PALS1-associated tight junction protein
B: PALS1-associated tight junction protein
C: MAGUK p55 subfamily member 5
D: MAGUK p55 subfamily member 5


Theoretical massNumber of molelcules
Total (without water)35,5644
Polymers35,5644
Non-polymers00
Water1,69394
1
A: PALS1-associated tight junction protein
C: MAGUK p55 subfamily member 5


Theoretical massNumber of molelcules
Total (without water)17,7822
Polymers17,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-17 kcal/mol
Surface area7120 Å2
MethodPISA
2
B: PALS1-associated tight junction protein
D: MAGUK p55 subfamily member 5


Theoretical massNumber of molelcules
Total (without water)17,7822
Polymers17,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-21 kcal/mol
Surface area7000 Å2
MethodPISA
3
A: PALS1-associated tight junction protein
B: PALS1-associated tight junction protein
C: MAGUK p55 subfamily member 5
D: MAGUK p55 subfamily member 5

A: PALS1-associated tight junction protein
B: PALS1-associated tight junction protein
C: MAGUK p55 subfamily member 5
D: MAGUK p55 subfamily member 5


Theoretical massNumber of molelcules
Total (without water)71,1298
Polymers71,1298
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area14270 Å2
ΔGint-130 kcal/mol
Surface area22420 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-58 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.060, 111.060, 193.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein PALS1-associated tight junction protein / PALS-1


Mass: 9537.022 Da / Num. of mol.: 2 / Fragment: L27N domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pACYCDuet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NI35
#2: Protein MAGUK p55 subfamily member 5 / PATJ / Protein associated with Lin-7 1


Mass: 8245.114 Da / Num. of mol.: 2 / Fragment: L27 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pACYCDuet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JLB2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, glycerol, CHAPS, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0722 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 17, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 25593 / Num. obs: 25593 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.1→2.2 Å / % possible all: 99.1

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Processing

Software
NameClassification
HKL-2000data collection
XDSdata reduction
SOLVEphasing
CNSrefinement
HKL-2000data reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 1236 RANDOM
Rwork0.242 --
obs0.242 24357 -
all-24357 -
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 0 94 1867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg0.9184
LS refinement shellResolution: 2.1→2.13 Å / Rfactor Rfree: 0.338 / Rfactor Rwork: 0.335

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