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- PDB-6jue: The complex of PDZ and PBM -

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Basic information

Entry
Database: PDB / ID: 6jue
TitleThe complex of PDZ and PBM
Components
  • Partitioning defective 3 homolog
  • THR-ILE-ILE-THR-LEU
KeywordsPEPTIDE BINDING PROTEIN / PDZ-binding motif peptide / complex
Function / homology
Function and homology information


Tight junction interactions / Tight junction interactions / RHOV GTPase cycle / 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 ...Tight junction interactions / Tight junction interactions / RHOV GTPase cycle / 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 / centrosome cycle / wound healing, spreading of cells / centrosome localization / apical junction complex / establishment or maintenance of cell polarity / 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-containing complex assembly / protein phosphatase binding / cell adhesion / cell cycle / apical plasma membrane / cell division / neuronal cell body / protein-containing complex / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Partitioning defective protein 6, PB1 domain / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PDZ domain / Pdz3 Domain / PDZ domain ...Partitioning defective protein 6, PB1 domain / Par3/HAL, N-terminal / N-terminal of Par3 and HAL proteins / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Partitioning defective 6 homolog beta / Partitioning defective 3 homolog
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 Å
AuthorsLiu, Z.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31871394 China
National Natural Science Foundation of China31670730 China
National Natural Science Foundation of China31422015 China
Ministry of Science and Technology (China)2014CB910201 China
CitationJournal: Nat Commun / Year: 2020
Title: Par complex cluster formation mediated by phase separation.
Authors: Liu, Z. / Yang, Y. / Gu, A. / Xu, J. / Mao, Y. / Lu, H. / Hu, W. / Lei, Q.Y. / Li, Z. / Zhang, M. / Cai, Y. / Wen, W.
History
DepositionApr 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Refinement description / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / software / struct
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.name / _struct.title
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Partitioning defective 3 homolog
A: THR-ILE-ILE-THR-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1095
Polymers12,8202
Non-polymers2883
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-33 kcal/mol
Surface area6120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.454, 57.454, 52.313
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11L-324-

HOH

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Components

#1: Protein Partitioning defective 3 homolog


Mass: 11717.232 Da / Num. of mol.: 1 / Fragment: UNP residues 582-685
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z340
#2: Protein/peptide THR-ILE-ILE-THR-LEU


Mass: 1103.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9JK83*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 2.4M ammonium sulfate and 0.1M citrate (pH 4.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.549→49.757 Å / Num. obs: 14300 / % possible obs: 99.5 % / Redundancy: 9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.8
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3 / Num. unique obs: 2038 / CC1/2: 0.783 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2K1Z

2k1z


Resolution: 1.549→49.757 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.74
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 648 4.55 %Random selection
Rwork0.2109 ---
obs0.2115 14250 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.549→49.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms708 0 15 29 752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005730
X-RAY DIFFRACTIONf_angle_d0.729980
X-RAY DIFFRACTIONf_dihedral_angle_d15.31430
X-RAY DIFFRACTIONf_chiral_restr0.051120
X-RAY DIFFRACTIONf_plane_restr0.003123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5486-1.66820.30141330.25692625X-RAY DIFFRACTION97
1.6682-1.83610.27361160.22152742X-RAY DIFFRACTION100
1.8361-2.10180.25671260.21132741X-RAY DIFFRACTION100
2.1018-2.6480.22661310.21512735X-RAY DIFFRACTION100
2.648-49.78230.21420.20222759X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.0081-3.1022-0.42598.61-0.20433.11080.18620.01870.040.097-0.16840.06090.13310.20570.00650.1490.0026-0.00510.13820.00990.053425.97268.5247-6.5159
28.2949-5.86834.72765.8285-3.56315.9046-0.11240.03150.27470.22430.0586-0.52820.19540.45120.09040.17020.006-0.04960.1764-0.00140.300419.529-2.188-11.945
38.7928-3.93042.23595.5514-1.88423.5440.1083-0.21-0.34630.10840.07110.2840.1265-0.1863-0.17010.1343-0.00980.02680.1181-0.03580.116216.37763.032-9.4811
44.8095-1.59853.13814.4493-2.53847.82670.05150.1569-0.2046-0.1061-0.13820.0837-0.15290.08390.09480.1386-0.0127-0.01740.0838-0.03070.12923.68186.629-11.6
59.9958-6.2359-5.84237.32234.70396.1824-0.06220.0732-0.5489-0.1266-0.17480.0795-0.1497-0.03350.21570.175-0.01850.01170.2186-0.06070.175420.51992.4348-21.4477
62.34310.02121.94910.8741-0.05631.6182-0.0845-0.0396-0.29860.07990.2513-0.1110.40250.6215-0.12340.1680.05570.0210.17680.01980.162629.9722.6003-11.9655
73.4582-1.08-3.50762.7855-0.16444.20660.05710.17160.1344-0.5814-0.17690.27870.0645-0.11530.14370.21550.0255-0.05080.2369-0.01930.270716.5463-3.7926-15.1606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 5:18 )L5 - 18
2X-RAY DIFFRACTION2( CHAIN L AND RESID 24:33 )L24 - 33
3X-RAY DIFFRACTION3( CHAIN L AND RESID 34:58 )L34 - 58
4X-RAY DIFFRACTION4( CHAIN L AND RESID 59:79 )L59 - 79
5X-RAY DIFFRACTION5( CHAIN L AND RESID 80:91 )L80 - 91
6X-RAY DIFFRACTION6( CHAIN L AND RESID 92:108 )L92 - 108
7X-RAY DIFFRACTION7( CHAIN A AND RESID 86:90 )A86 - 90

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