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- PDB-6eey: Crystal structure of human Scribble PDZ4 R1110G Mutant -

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Basic information

Entry
Database: PDB / ID: 6eey
TitleCrystal structure of human Scribble PDZ4 R1110G Mutant
ComponentsProtein scribble homolog
KeywordsSTRUCTURAL PROTEIN / PDZ domain / Cell Polarity
Function / homology
Function and homology information


extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation ...extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to adherens junction / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / activation of GTPase activity / establishment or maintenance of epithelial cell apical/basal polarity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / synaptic vesicle endocytosis / immunological synapse / negative regulation of mitotic cell cycle / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / presynapse / cell junction / lamellipodium / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.145 Å
AuthorsJanezic, E.M. / Hsu, P. / Hague, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007750 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100893 United States
CitationJournal: Sci Rep / Year: 2019
Title: Scribble co-operatively binds multiple alpha1D-adrenergic receptor C-terminal PDZ ligands.
Authors: Janezic, E.M. / Harris, D.A. / Dinh, D. / Lee, K.S. / Stewart, A. / Hinds, T.R. / Hsu, P.L. / Zheng, N. / Hague, C.
History
DepositionAug 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
A: Protein scribble homolog


Theoretical massNumber of molelcules
Total (without water)9,9791
Polymers9,9791
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.286, 40.235, 32.260
Angle α, β, γ (deg.)90.000, 97.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein scribble homolog / hScrib / Protein LAP4


Mass: 9979.455 Da / Num. of mol.: 1 / Fragment: PDZ 4 domain residues 1098-1189 / Mutation: R1110G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14160
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.77 Å3/Da / Density % sol: 30.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 3350, 0.25 M Ammonium Nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00004 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.14→40.23 Å / Num. obs: 20632 / % possible obs: 82.3 % / Redundancy: 4.4 % / Biso Wilson estimate: 6.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.033 / Rrim(I) all: 0.075 / Net I/σ(I): 12.8 / Num. measured all: 90869 / Scaling rejects: 145
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsNet I/σ(I) obs% possible allRmerge(I) obsCC1/2Rpim(I) allRrim(I) all
1.14-1.17134343.31.9
5.12-40.234.4124628018.992.70.0540.9950.0280.061

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHASER1.13phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WYT

4wyt


Resolution: 1.145→31.958 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 18.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1818 2000 9.7 %
Rwork0.1571 18614 -
obs0.1595 20614 82.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 37.7 Å2 / Biso mean: 9.0999 Å2 / Biso min: 2.65 Å2
Refinement stepCycle: final / Resolution: 1.145→31.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms692 0 0 131 823
Biso mean---16.2 -
Num. residues----94
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1446-1.17330.051930.153628312
1.1733-1.2050.2156240.143523225615
1.205-1.24050.2049900.160382791751
1.2405-1.28050.17611500.1661397154787
1.2805-1.32630.18831700.159615871757100
1.3263-1.37940.20631720.156616021774100
1.3794-1.44210.17981760.162116341810100
1.4421-1.51820.17231740.155316191793100
1.5182-1.61330.19711720.166316021774100
1.6133-1.73780.19191720.157415931765100
1.7378-1.91270.18951730.161416181791100
1.9127-2.18940.17231740.148516211795100
2.1894-2.75820.17761750.156116251800100
2.7582-31.97010.17411750.15571629180498

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