[English] 日本語
![](img/lk-miru.gif)
- PDB-3zee: Electron cyro-microscopy helical reconstruction of Par-3 N termin... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3zee | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Electron cyro-microscopy helical reconstruction of Par-3 N terminal domain | |||||||||
![]() | PARTITIONING DEFECTIVE 3 HOMOLOG | |||||||||
![]() | CELL CYCLE | |||||||||
Function / homology | ![]() 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 / lateral loop / 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 / lateral loop / positive regulation of myelination / establishment of epithelial cell polarity / Schmidt-Lanterman incisure / bicellular tight junction assembly / myelination in peripheral nervous system / phosphatidylinositol-3-phosphate binding / establishment or maintenance of epithelial cell apical/basal polarity / protein targeting to membrane / wound healing, spreading of cells / apical junction complex / centrosome localization / 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 / microtubule cytoskeleton organization / spindle / cell junction / cell-cell junction / protein localization / apical part of cell / 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
![]() | Zhang, Y. / Wang, W. / Chen, J. / Zhang, K. / Gao, F. / Gong, W. / Zhang, M. / Sun, F. / Feng, W. | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 28.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 17.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2237MC ![]() 4i6pC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 | ![]()
| x 49
2 |
|
3 | ![]()
|
Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 49 / Rise per n subunits: 3.532 Å / Rotation per n subunits: -43.835 °) |
-
Components
#1: Protein | Mass: 9552.906 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DUF3534 DOMAIN, RESIDUES 2-82 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-
Sample preparation
Component | Name: PAR-3 N-TERMINAL DUF3534 DOMAIN / Type: COMPLEX / Details: SUPPORTING FILM IS GIG HOLELY GRID. |
---|---|
Buffer solution | Name: 50 MM TRIS, 100 MM NACL, 1 MM DTT AND 1 MM EDTA / pH: 8 / Details: 50 MM TRIS, 100 MM NACL, 1 MM DTT AND 1 MM EDTA |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS / Date: Dec 1, 2010 Details: THE MICROSCOPE MODEL IS FEI TITAN KRIOS. 6460 RAW IMAGES WERE COLLECTED AUTOMATICALLY USING THE PACKAGE LEGINON. GOOD MICROGRAPHS WERE SELECTED ONE BY ONE |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm |
Specimen holder | Temperature: 95 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 6460 |
Radiation wavelength | Relative weight: 1 |
-
Processing
EM software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: INDIVIDUAL MICROGRAPHS | ||||||||||||||||
3D reconstruction | Method: THE INITIAL MODEL WAS OBTAINED USING IHRSR. THEN THE FINAL RECONSTRUCTION WERE OBTAINED BY PROJECTION MATCHING IN EMAN. Resolution: 6.1 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 84000 / Actual pixel size: 0.933 Å Details: THE INITIAL MODEL WAS OBTAINED USING IHRSR. THEN THE FINAL RECONSTRUCTION WERE OBTAINED BY PROJECTION MATCHING IN EMAN. THE RESOLUTION CRITERIA USED WAS GOLDEN CRITERIA FSC 0.5. SUBMISSION ...Details: THE INITIAL MODEL WAS OBTAINED USING IHRSR. THEN THE FINAL RECONSTRUCTION WERE OBTAINED BY PROJECTION MATCHING IN EMAN. THE RESOLUTION CRITERIA USED WAS GOLDEN CRITERIA FSC 0.5. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2237. (DEPOSITION ID: 11249). Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: HELICAL | ||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: ENERGY FUNCTION IN NAMD2 Details: METHOD--CROSS CORRELATION REFINEMENT PROTOCOL--X-RAY | ||||||||||||||||
Atomic model building | PDB-ID: 4I6P Accession code: 4I6P / Source name: PDB / Type: experimental model | ||||||||||||||||
Refinement | Highest resolution: 6.1 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6.1 Å
|