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- PDB-3zee: Electron cyro-microscopy helical reconstruction of Par-3 N termin... -

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Basic information

Entry
Database: PDB / ID: 3zee
TitleElectron cyro-microscopy helical reconstruction of Par-3 N terminal domain
ComponentsPARTITIONING DEFECTIVE 3 HOMOLOG
KeywordsCELL CYCLE
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 / 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 / establishment of epithelial cell polarity / lateral loop / positive regulation of myelination / bicellular tight junction assembly / Schmidt-Lanterman incisure / myelination in peripheral nervous system / establishment or maintenance of epithelial cell apical/basal polarity / phosphatidylinositol-3-phosphate binding / protein targeting to membrane / wound healing, spreading of cells / apical junction complex / centrosome localization / establishment of cell polarity / negative regulation of peptidyl-threonine phosphorylation / positive regulation of receptor internalization / phosphatidylinositol-3,4,5-trisphosphate binding / bicellular tight junction / endomembrane system / axonal growth cone / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / adherens junction / microtubule cytoskeleton organization / spindle / cell-cell junction / protein localization / cell junction / 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
Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / : / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Partitioning defective 3 homolog
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsZhang, Y. / Wang, W. / Chen, J. / Zhang, K. / Gao, F. / Gong, W. / Zhang, M. / 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
DepositionDec 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model / Data collection
Category: atom_site / em_software / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _em_software.fitting_id / _em_software.image_processing_id
Revision 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-2237
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Assembly

Deposited unit
A: PARTITIONING DEFECTIVE 3 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)9,5531
Polymers9,5531
Non-polymers00
Water00
1
A: PARTITIONING DEFECTIVE 3 HOMOLOG
x 49


Theoretical massNumber of molelcules
Total (without water)468,09249
Polymers468,09249
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation48
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical 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 °)

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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: 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.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS / References: UniProt: Q9Z340

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: PAR-3 N-TERMINAL DUF3534 DOMAIN / Type: COMPLEX / Details: SUPPORTING FILM IS GIG HOLELY GRID.
Buffer solutionName: 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
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: 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 gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm
Specimen holderTemperature: 95 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 6460
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1NAMD2model fitting
2VMDmodel fitting
3IMAGIC3D reconstruction
CTF correctionDetails: INDIVIDUAL MICROGRAPHS
3D reconstructionMethod: 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 buildingProtocol: OTHER / Space: REAL / Target criteria: ENERGY FUNCTION IN NAMD2
Details: METHOD--CROSS CORRELATION REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 4I6P

4i6p


Accession code: 4I6P / Source name: PDB / Type: experimental model
RefinementHighest resolution: 6.1 Å
Refinement stepCycle: LAST / Highest resolution: 6.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 0 0 670

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