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- PDB-4uu5: CRYSTAL STRUCTURE OF THE PDZ DOMAIN OF PALS1 IN COMPLEX WITH THE ... -

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Basic information

Entry
Database: PDB / ID: 4uu5
TitleCRYSTAL STRUCTURE OF THE PDZ DOMAIN OF PALS1 IN COMPLEX WITH THE CRB PEPTIDE
Components
  • MAGUK P55 SUBFAMILY MEMBER 5
  • PROTEIN CRUMBS HOMOLOG 1
KeywordsCELL ADHESION
Function / homology
Function and homology information


establishment of bipolar cell polarity involved in cell morphogenesis / post-embryonic retina morphogenesis in camera-type eye / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / subapical complex / myelin assembly / establishment or maintenance of polarity of embryonic epithelium / photoreceptor cell outer segment organization / morphogenesis of an epithelial sheet / Tight junction interactions ...establishment of bipolar cell polarity involved in cell morphogenesis / post-embryonic retina morphogenesis in camera-type eye / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / subapical complex / myelin assembly / establishment or maintenance of polarity of embryonic epithelium / photoreceptor cell outer segment organization / morphogenesis of an epithelial sheet / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / myelin sheath adaxonal region / regulation of transforming growth factor beta receptor signaling pathway / plasma membrane organization / retina layer formation / cellular response to light stimulus / lateral loop / eye photoreceptor cell development / detection of light stimulus involved in visual perception / glial cell differentiation / Schmidt-Lanterman incisure / establishment or maintenance of epithelial cell apical/basal polarity / peripheral nervous system myelin maintenance / photoreceptor cell maintenance / heterophilic cell-cell adhesion / apical junction complex / generation of neurons / central nervous system neuron development / establishment or maintenance of cell polarity / microvillus / blood vessel remodeling / glial cell projection / photoreceptor outer segment / bicellular tight junction / photoreceptor inner segment / endoplasmic reticulum-Golgi intermediate compartment membrane / protein localization to plasma membrane / adherens junction / cerebral cortex development / intracellular protein localization / cell-cell signaling / perikaryon / gene expression / apical plasma membrane / protein domain specific binding / axon / calcium ion binding / Golgi apparatus / protein-containing complex / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
L27-N / MPP5, SH3 domain / L27_N / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily ...L27-N / MPP5, SH3 domain / L27_N / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / Laminin G domain profile. / Laminin G domain / Laminin G domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / PDZ domain / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Concanavalin A-like lectin/glucanase domain superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
2,2,4,4,6,6,8-heptamethylnonane / Protein crumbs homolog 1 / Protein PALS1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsIvanova, M.E. / Purkiss, A.G. / McDonald, N.Q.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove.
Authors: Ivanova, M.E. / Fletcher, G.C. / O'Reilly, N. / Purkiss, A.G. / Thompson, B.J. / McDonald, N.Q.
History
DepositionJul 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 2.0Feb 28, 2018Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_conn_type / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAGUK P55 SUBFAMILY MEMBER 5
B: PROTEIN CRUMBS HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,28512
Polymers11,7522
Non-polymers53310
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.730, 74.730, 42.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-1341-

CL

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein MAGUK P55 SUBFAMILY MEMBER 5 / PALS1


Mass: 9650.056 Da / Num. of mol.: 1 / Fragment: PDZ DOMAIN, RESIDUES 251-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8N3R9
#2: Protein/peptide PROTEIN CRUMBS HOMOLOG 1


Mass: 2101.557 Da / Num. of mol.: 1 / Fragment: RESIDUES 1390-1406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P82279

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Non-polymers , 4 types, 130 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PUN / 2,2,4,4,6,6,8-heptamethylnonane


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES 251-335 N-TERMINAL RESIDUES GPLGS ARE VECTOR- DERIVED

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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: 2.64 Å3/Da / Density % sol: 53.37 %
Description: MODEL WAS GENERATED BY PHYRE SERVER BASED ON 1VA8
Crystal growpH: 7.5 / Details: 0.1M HEPES (PH 7.29), 2.68M NA CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.23→52.84 Å / Num. obs: 35567 / % possible obs: 99.7 % / Observed criterion σ(I): 1.9 / Redundancy: 6.2 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.7
Reflection shellResolution: 1.23→1.26 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1839)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VA8

1va8


Resolution: 1.23→52.842 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 16.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 1808 5.1 %
Rwork0.168 --
obs0.1688 35566 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.23→52.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 25 120 932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015955
X-RAY DIFFRACTIONf_angle_d1.9361320
X-RAY DIFFRACTIONf_dihedral_angle_d12.923387
X-RAY DIFFRACTIONf_chiral_restr0.124159
X-RAY DIFFRACTIONf_plane_restr0.007172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.26330.26041240.23582532X-RAY DIFFRACTION99
1.2633-1.30050.22361480.20332524X-RAY DIFFRACTION100
1.3005-1.34240.19771270.1822575X-RAY DIFFRACTION100
1.3424-1.39040.20071360.16462578X-RAY DIFFRACTION100
1.3904-1.44610.15751380.15552555X-RAY DIFFRACTION100
1.4461-1.51190.19031410.14962581X-RAY DIFFRACTION100
1.5119-1.59160.14951550.1352565X-RAY DIFFRACTION100
1.5916-1.69140.1491390.13872581X-RAY DIFFRACTION100
1.6914-1.8220.17331520.14482587X-RAY DIFFRACTION100
1.822-2.00530.17831280.1572617X-RAY DIFFRACTION100
2.0053-2.29550.15771550.15212601X-RAY DIFFRACTION100
2.2955-2.89210.16891260.18732672X-RAY DIFFRACTION99
2.8921-52.89090.20961390.17562790X-RAY DIFFRACTION99

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