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- PDB-4i6p: Crystal structure of Par3-NTD domain -

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Basic information

Entry
Database: PDB / ID: 4i6p
TitleCrystal structure of Par3-NTD domain
ComponentsPartitioning defective 3 homolog
KeywordsSIGNALING PROTEIN / PB1 like motif / DUF3534 / Cell polarity protein
Function / homology
Function and homology information


Tight junction interactions / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / internode region of axon / regulation of cellular localization / PAR polarity complex / apical constriction / establishment of centrosome localization / positive regulation of myelination / lateral loop ...Tight junction interactions / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / internode region of axon / regulation of cellular localization / PAR polarity complex / apical constriction / establishment of centrosome localization / positive regulation of myelination / lateral loop / establishment of epithelial cell polarity / Schmidt-Lanterman incisure / myelination in peripheral nervous system / bicellular tight junction assembly / phosphatidylinositol-3-phosphate binding / establishment or maintenance of epithelial cell apical/basal polarity / protein targeting to membrane / wound healing, spreading of cells / centrosome localization / apical junction complex / establishment of cell polarity / negative regulation of peptidyl-threonine phosphorylation / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / bicellular tight junction / endomembrane system / axonal growth cone / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / adherens junction / protein localization / spindle / microtubule cytoskeleton organization / cell-cell junction / apical part of cell / cell junction / cell cortex / protein phosphatase binding / cell adhesion / cell cycle / apical plasma membrane / cell division / neuronal cell body / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Partitioning defective 3 homolog
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, W. / Gao, F. / Gong, W. / Sun, F. / Feng, W.
CitationJournal: Structure / Year: 2013
Title: Structural insights into the intrinsic self-assembly of Par-3 N-terminal domain.
Authors: Yan Zhang / Wenjuan Wang / Jia Chen / Kai Zhang / Feng Gao / Bingquan Gao / Shuai Zhang / Mingdong Dong / Flemming Besenbacher / Weimin Gong / Mingjie Zhang / Fei Sun / Wei Feng /
Abstract: Par-3, the central organizer of the Par-3/Par-6/atypical protein kinase C complex, is a multimodular scaffold protein that is essential for cell polarity establishment and maintenance. The N-terminal ...Par-3, the central organizer of the Par-3/Par-6/atypical protein kinase C complex, is a multimodular scaffold protein that is essential for cell polarity establishment and maintenance. The N-terminal domain (NTD) of Par-3 is capable of self-association to form filament-like structures, although the underlying mechanism is poorly understood. Here, we determined the crystal structure of Par-3 NTD and solved the filament structure by cryoelectron microscopy. We found that an intrinsic "front-to-back" interaction mode is important for Par-3 NTD self-association and that both the lateral and longitudinal packing within the filament are mediated by electrostatic interactions. Disruptions of the lateral or longitudinal packing significantly impaired Par-3 NTD self-association and thereby impacted the Par-3-mediated epithelial polarization. We finally demonstrated that a Par-3 NTD-like domain from histidine ammonia-lyase also harbors a similar self-association capacity. This work unequivocally provides the structural basis for Par-3 NTD self-association and characterizes one type of protein domain that can self-assemble via electrostatic interactions.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Partitioning defective 3 homolog
B: Partitioning defective 3 homolog


Theoretical massNumber of molelcules
Total (without water)19,7582
Polymers19,7582
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Partitioning defective 3 homolog


Theoretical massNumber of molelcules
Total (without water)9,8791
Polymers9,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Partitioning defective 3 homolog


Theoretical massNumber of molelcules
Total (without water)9,8791
Polymers9,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.780, 108.780, 46.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-119-

HOH

DetailsThis protein forms helical filament in solution. Cryo-electron microscopic reconstruction revealed that the dimer in the crystallographic asymmetric unit is the same as the building block of the helical filament.

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Components

#1: Protein Partitioning defective 3 homolog / PAR-3 / PARD-3 / Atypical PKC isotype-specific-interacting protein / ASIP / Atypical PKC-specific- ...PAR-3 / PARD-3 / Atypical PKC isotype-specific-interacting protein / ASIP / Atypical PKC-specific-binding protein / ASBP


Mass: 9879.212 Da / Num. of mol.: 2 / Fragment: N-terminal domain of Par3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pard3, Par3 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus / References: UniProt: Q9Z340
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.5 Å3/Da / Density % sol: 64.84 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 M ammonium sulfate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 1, 2010
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 6597 / Num. obs: 6406 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 7.6 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 17
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 5.3 / Num. unique all: 617 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NS5

2ns5


Resolution: 2.9→39.94 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.86 / SU B: 19.255 / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.008 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29361 301 4.7 %RANDOM
Rwork0.23005 ---
obs0.23296 6058 96.33 %-
all-6289 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.809 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 0 34 1357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191345
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.9481816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7695164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9323.33369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.81215235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5711514
X-RAY DIFFRACTIONr_chiral_restr0.120.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021022
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 21 -
Rwork0.307 343 -
obs-343 89.88 %

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