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- PDB-6myf: Crystal structure of free human Scribble PDZ1 domain -

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Basic information

Entry
Database: PDB / ID: 6myf
TitleCrystal structure of free human Scribble PDZ1 domain
ComponentsProtein scribble homolog
KeywordsPEPTIDE BINDING PROTEIN / Cell adhesion / tight junction / PDZ binding motif binding
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 / Resolution: 1.6 Å
AuthorsSun, Y.J. / Hou, T. / Gakhar, L. / Fuentes, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association15GRNT25740021 United States
CitationJournal: J.Cell Biol. / Year: 2019
Title: SGEF forms a complex with Scribble and Dlg1 and regulates epithelial junctions and contractility.
Authors: Awadia, S. / Huq, F. / Arnold, T.R. / Goicoechea, S.M. / Sun, Y.J. / Hou, T. / Kreider-Letterman, G. / Massimi, P. / Banks, L. / Fuentes, E.J. / Miller, A.L. / Garcia-Mata, R.
History
DepositionNov 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 21, 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_author.identifier_ORCID
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
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

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Assembly

Deposited unit
A: Protein scribble homolog


Theoretical massNumber of molelcules
Total (without water)9,8971
Polymers9,8971
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, In-line SEC-MALS-SAXS data indicates that this molecule is in monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.108, 42.824, 91.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 9897.129 Da / Num. of mol.: 1
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.: 99 / 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: 1.93 Å3/Da / Density % sol: 36.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Citric acid pH 3.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.976251 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 11, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.6→45.62 Å / Num. obs: 10237 / % possible obs: 97.8 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 18.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1290 / CC1/2: 0.751 / Rpim(I) all: 0.339 / Rrim(I) all: 0.683 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Blu-Icedata collection
REFMACrefinement
ARP/wARPmodel building
Cootmodel building
Aimlessdata scaling
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W4F

2w4f


Resolution: 1.6→45.617 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2103 542 5.31 %
Rwork0.171 --
obs0.1731 10209 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→45.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms679 0 0 99 778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008707
X-RAY DIFFRACTIONf_angle_d0.994957
X-RAY DIFFRACTIONf_dihedral_angle_d10.833417
X-RAY DIFFRACTIONf_chiral_restr0.064106
X-RAY DIFFRACTIONf_plane_restr0.006130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.7610.29551200.22912175X-RAY DIFFRACTION90
1.761-2.01590.23271240.17522463X-RAY DIFFRACTION100
2.0159-2.53970.17171620.17172441X-RAY DIFFRACTION100
2.5397-45.63550.21471360.15812588X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 1.0939 Å / Origin y: 7.217 Å / Origin z: -10.7494 Å
111213212223313233
T0.0906 Å2-0.0098 Å2-0.0121 Å2-0.0873 Å2-0.0164 Å2--0.0845 Å2
L0.9204 °2-0.4484 °2-0.0425 °2-0.6967 °20.0564 °2--1.0512 °2
S-0.0271 Å °0.065 Å °0 Å °0.0237 Å °-0.0073 Å °-0.0265 Å °-0.0901 Å °0.0956 Å °0.0212 Å °
Refinement TLS groupSelection details: all

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