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- PDB-4wsi: Crystal Structure of PALS1/Crb complex -

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Basic information

Entry
Database: PDB / ID: 4wsi
TitleCrystal Structure of PALS1/Crb complex
Components
  • MAGUK p55 subfamily member 5
  • Protein crumbs
KeywordsPEPTIDE BINDING PROTEIN / Supramodule
Function / homology
Function and homology information


liquid clearance, open tracheal system / maintenance of apical/basal cell polarity / dorsal closure, amnioserosa morphology change / cell morphogenesis involved in Malpighian tubule morphogenesis / rhabdomere morphogenesis / nuclear chromosome segregation / assembly of apicomedial cortex actomyosin / tube morphogenesis / compound eye photoreceptor development / amnioserosa maintenance ...liquid clearance, open tracheal system / maintenance of apical/basal cell polarity / dorsal closure, amnioserosa morphology change / cell morphogenesis involved in Malpighian tubule morphogenesis / rhabdomere morphogenesis / nuclear chromosome segregation / assembly of apicomedial cortex actomyosin / tube morphogenesis / compound eye photoreceptor development / amnioserosa maintenance / Malpighian tubule morphogenesis / establishment or maintenance of polarity of follicular epithelium / regulation of imaginal disc growth / subapical complex / protein localization to myelin sheath abaxonal region / zonula adherens maintenance / zonula adherens assembly / wing disc dorsal/ventral pattern formation / SARS-CoV-1 targets PDZ proteins in cell-cell junction / positive regulation of hippo signaling / establishment or maintenance of polarity of embryonic epithelium / open tracheal system development / myelin assembly / dorsal closure / compound eye morphogenesis / establishment or maintenance of apical/basal cell polarity / rhabdomere development / rhabdomere / trachea development / morphogenesis of an epithelial sheet / apical constriction / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / photoreceptor connecting cilium / lateral loop / myelin sheath adaxonal region / regulation of transforming growth factor beta receptor signaling pathway / negative regulation of organ growth / Schmidt-Lanterman incisure / apicolateral plasma membrane / apical protein localization / membrane organization / photoreceptor cell maintenance / peripheral nervous system myelin maintenance / establishment or maintenance of epithelial cell apical/basal polarity / Notch binding / adherens junction organization / centrosome localization / apical junction complex / establishment or maintenance of cell polarity / spectrin binding / generation of neurons / negative regulation of Notch signaling pathway / regulation of intracellular protein transport / central nervous system neuron development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / bicellular tight junction / salivary gland morphogenesis / endoplasmic reticulum-Golgi intermediate compartment membrane / protein localization to plasma membrane / protein kinase C binding / adherens junction / cerebral cortex development / spindle / regulation of protein localization / nervous system development / gene expression / perikaryon / protein stabilization / apical plasma membrane / protein domain specific binding / cell division / axon / calcium ion binding / positive regulation of cell population proliferation / Golgi apparatus / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
L27-N / MPP5, SH3 domain / L27_N / L27 domain, C-terminal / L27 domain / Laminin G 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 / Laminin G 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 / Calcium-binding EGF domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / SH3 Domains / 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. / Growth factor receptor cysteine-rich domain superfamily / PDZ domain / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Concanavalin A-like lectin/glucanase domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein crumbs / Protein PALS1
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsWei, Z. / Li, Y. / Zhang, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of Crumbs tail in complex with the PALS1 PDZ-SH3-GK tandem reveals a highly specific assembly mechanism for the apical Crumbs complex.
Authors: Li, Y. / Wei, Z. / Yan, Y. / Wan, Q. / Du, Q. / Zhang, M.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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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: MAGUK p55 subfamily member 5
X: Protein crumbs
Y: Protein crumbs


Theoretical massNumber of molelcules
Total (without water)99,4384
Polymers99,4384
Non-polymers00
Water36020
1
A: MAGUK p55 subfamily member 5
X: Protein crumbs


Theoretical massNumber of molelcules
Total (without water)49,7192
Polymers49,7192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-13 kcal/mol
Surface area20430 Å2
MethodPISA
2
B: MAGUK p55 subfamily member 5
Y: Protein crumbs


Theoretical massNumber of molelcules
Total (without water)49,7192
Polymers49,7192
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-14 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.928, 111.928, 223.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MAGUK p55 subfamily member 5


Mass: 44806.543 Da / Num. of mol.: 2 / Fragment: UNP residues 236-410, 460-675
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPP5 / Plasmid: pET32m / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N3R9
#2: Protein/peptide Protein crumbs / 95F


Mass: 4912.500 Da / Num. of mol.: 2 / Fragment: UNP residues 2111-2146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: crb, CG6383 / Plasmid: pET32m / Production host: Escherichia coli (E. coli) / References: UniProt: P10040
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 5% PEG3350, 5-10% Tacsimate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 30528 / % possible obs: 99.6 % / Redundancy: 11.8 % / Biso Wilson estimate: 90.77 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.466 / Net I/av σ(I): 33.892 / Net I/σ(I): 12.1 / Num. measured all: 359841
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.95-312.70.76114881.097100
3-3.0612.50.62415051.122100
3.06-3.1112.60.53215001.155100
3.11-3.1812.60.42715131.205100
3.18-3.2512.50.3214921.276100
3.25-3.3212.50.24915091.338100
3.32-3.4112.50.20114891.441100
3.41-3.512.50.17115231.466100
3.5-3.612.40.1415311.578100
3.6-3.7212.40.12514911.605100
3.72-3.8512.20.10815281.663100
3.85-412.10.09815001.662100
4-4.1911.70.08615291.828100
4.19-4.4111.20.08215231.7399.9
4.41-4.6810.80.07515341.644100
4.68-5.0410.60.07115431.616100
5.04-5.5510.70.06915581.55199.9
5.55-6.35110.06215631.64699.9
6.35-8110.05416051.46499.9
8-509.40.04816041.34693.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data processing
PHENIXphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.95→41.523 Å / FOM work R set: 0.799 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1521 5 %
Rwork0.2069 28898 -
obs0.2084 30419 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.94 Å2 / Biso mean: 90.7 Å2 / Biso min: 38.69 Å2
Refinement stepCycle: final / Resolution: 2.95→41.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6013 0 0 20 6033
Biso mean---67.11 -
Num. residues----767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036141
X-RAY DIFFRACTIONf_angle_d0.6848333
X-RAY DIFFRACTIONf_chiral_restr0.048930
X-RAY DIFFRACTIONf_plane_restr0.0031107
X-RAY DIFFRACTIONf_dihedral_angle_d12.9862318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.0450.30361330.27722517265097
3.045-3.15380.28071360.259325772713100
3.1538-3.28010.28321370.256126052742100
3.2801-3.42930.30541360.235926062742100
3.4293-3.610.25861380.219326242762100
3.61-3.8360.28341370.219625932730100
3.836-4.13190.22881390.201626242763100
4.1319-4.54730.20691380.17882631276999
4.5473-5.20420.20181400.174526562796100
5.2042-6.55260.25061430.216427232866100
6.5526-41.52740.20921440.20342742288696
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)
13.483-1.47962.78781.018-0.71883.51980.2753-0.0116-0.1675-0.1183-0.003-0.00010.19510.3207-0.25120.5175-0.0509-0.09960.6032-0.17840.5242-6.1564.634129.515
23.8314-1.31732.6062.2333-0.58494.36440.1268-0.06060.4994-0.23850.0355-0.5361-0.24830.106-0.20630.4678-0.0810.11970.4565-0.11810.6081-30.086319.119837.4008
32.4993-1.85432.60082.9736-2.21333.2429-0.23750.0073-0.005-0.20480.28880.149-0.2211-0.048-0.04560.90770.0124-0.07260.39270.01180.5469-43.145527.5702-2.773
43.1501-1.30850.39284.1228-1.00052.14150.54650.57350.4105-0.5915-0.0773-0.41480.02050.4831-0.45041.14220.152-0.10630.7469-0.32040.8906-23.38418.5989-11.805
57.69634.76242.17048.0136-3.01954.37080.2077-0.83760.86930.3738-0.5758-0.1632-0.7102-0.10070.36310.73150.0041-0.00920.5429-0.16160.9002-22.250518.700247.5858
62.0052-4.3309-4.36892.55681.28492.76230.0483-0.12790.6329-0.0094-0.10890.3498-0.27330.27340.05120.6340.04320.01250.676-0.24850.7474-7.797114.104934.9389
70.16270.9897-0.19386.0055-1.17690.23040.21230.46370.4768-0.4165-0.15080.0681-0.46080.1378-0.06321.9530.0418-0.22561.09050.0161.2625-28.270913.5987-22.5643
83.0875-6.1306-1.60782.00544.23332.6653-0.02320.3248-0.2624-0.92-0.0949-1.05290.50650.29670.12811.09280.2455-0.00870.68610.00981.0283-35.815227.681-10.5377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 244 through 468 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 469 through 675 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 252 through 468 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 469 through 675 )B0
5X-RAY DIFFRACTION5chain 'X' and (resid 2129 through 2136 )X0
6X-RAY DIFFRACTION6chain 'X' and (resid 2137 through 2146 )X0
7X-RAY DIFFRACTION7chain 'Y' and (resid 2129 through 2136 )Y0
8X-RAY DIFFRACTION8chain 'Y' and (resid 2137 through 2146 )Y0

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