[English] 日本語
Yorodumi
- PDB-4i6p: Crystal structure of Par3-NTD domain -

+
Open data


ID or keywords:

Loading...

-
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 / establishment of epithelial cell polarity / positive regulation of myelination ...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 / establishment of epithelial cell polarity / positive regulation of myelination / lateral loop / bicellular tight junction assembly / Schmidt-Lanterman incisure / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of peptidyl-threonine phosphorylation / myelination in peripheral nervous system / phosphatidylinositol-3-phosphate binding / protein targeting to membrane / wound healing, spreading of cells / centrosome localization / apical junction complex / establishment of cell polarity / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / bicellular tight junction / axonal growth cone / phosphatidylinositol-4,5-bisphosphate binding / endomembrane system / phosphatidylinositol binding / adherens junction / microtubule cytoskeleton organization / spindle / cell junction / protein localization / cell-cell junction / cell cortex / protein phosphatase binding / cell adhesion / 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) ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more