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- PDB-6mye: Crystal structure of human Scribble PDZ1 domain in complex with i... -

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Basic information

Entry
Database: PDB / ID: 6mye
TitleCrystal structure of human Scribble PDZ1 domain in complex with internal PDZ binding motif of Src homology 3 domain-containing guanine nucleotide exchange factor (SGEF)
Components
  • Protein scribble homolog
  • Rho guanine nucleotide exchange factor 26, peptide
KeywordsCELL ADHESION / Guanyl nucleotide exchange factor / SGEF/Scribble/Dlg1 compelx / tight junction
Function / homology
Function and homology information


: / neurotransmitter receptor transport postsynaptic membrane to endosome / extrinsic component of postsynaptic density membrane / 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 ...: / neurotransmitter receptor transport postsynaptic membrane to endosome / extrinsic component of postsynaptic density membrane / 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 / ruffle assembly / protein localization to adherens junction / endothelial cell morphogenesis / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / regulation of small GTPase mediated signal transduction / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / NRAGE signals death through JNK / positive chemotaxis / receptor clustering / RHOJ GTPase cycle / RHOQ GTPase cycle / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / synaptic vesicle endocytosis / immunological synapse / negative regulation of mitotic cell cycle / signaling adaptor activity / ruffle / guanyl-nucleotide exchange factor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / G alpha (12/13) signalling events / cell migration / cell-cell junction / positive regulation of type II interferon production / presynapse / cell junction / lamellipodium / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / glutamatergic synapse / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
ARHGEF16/ARHGEF26, SH3 domain / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Leucine rich repeat / Leucine-rich repeat, typical subtype ...ARHGEF16/ARHGEF26, SH3 domain / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PH domain profile. / Pleckstrin homology domain. / PDZ domain / Leucine-rich repeat / Pleckstrin homology domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Protein scribble homolog / Rho guanine nucleotide exchange factor 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.1Oct 23, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 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
B: Rho guanine nucleotide exchange factor 26, peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1833
Polymers11,1372
Non-polymers461
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, 1 to 1 stoichiometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-5 kcal/mol
Surface area6100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.890, 67.890, 44.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1070-

HOH

21A-1073-

HOH

31B-702-

HOH

41B-717-

HOH

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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: Protein/peptide Rho guanine nucleotide exchange factor 26, peptide / SH3 domain-containing guanine exchange factor


Mass: 1239.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96DR7
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 60% (v/v) Tacsimate pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 13, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 1.1→48.01 Å / Num. obs: 42446 / % possible obs: 100 % / Redundancy: 15.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.7
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.8 / Num. measured obs: 77902 / Num. unique all: 6102 / CC1/2: 0.758 / Rpim(I) all: 0.409 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Blu-Icedata collection
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W4F

2w4f


Resolution: 1.1→48.005 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 2108 4.97 %RANDOM
Rwork0.1979 ---
obs0.1983 42382 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→48.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms774 0 3 127 904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051033
X-RAY DIFFRACTIONf_angle_d0.9011419
X-RAY DIFFRACTIONf_dihedral_angle_d3.532648
X-RAY DIFFRACTIONf_chiral_restr0.082153
X-RAY DIFFRACTIONf_plane_restr0.005199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.12560.33991340.28872656X-RAY DIFFRACTION100
1.1256-1.15370.30951410.27742624X-RAY DIFFRACTION100
1.1537-1.18490.24741370.25562644X-RAY DIFFRACTION100
1.1849-1.21980.24141540.25432617X-RAY DIFFRACTION100
1.2198-1.25920.24691390.24782658X-RAY DIFFRACTION100
1.2592-1.30420.23491500.232656X-RAY DIFFRACTION100
1.3042-1.35640.27321260.21442651X-RAY DIFFRACTION100
1.3564-1.41820.21961370.21832678X-RAY DIFFRACTION100
1.4182-1.49290.20081250.20662668X-RAY DIFFRACTION100
1.4929-1.58650.2191340.19932696X-RAY DIFFRACTION100
1.5865-1.7090.20141200.19772697X-RAY DIFFRACTION100
1.709-1.8810.20491460.19522706X-RAY DIFFRACTION100
1.881-2.15310.17851560.18192690X-RAY DIFFRACTION100
2.1531-2.71270.20281460.19112758X-RAY DIFFRACTION100
2.7127-48.05120.18141630.17542875X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 1.0421 Å / Origin y: 17.8856 Å / Origin z: -12.3071 Å
111213212223313233
T0.0603 Å2-0.007 Å20.0075 Å2-0.0577 Å20.0064 Å2--0.1571 Å2
L2.6973 °2-0.7841 °2-0.829 °2-1.4623 °20.3491 °2--1.1737 °2
S-0.0094 Å °-0.128 Å °-0.0036 Å °0.0608 Å °0.0079 Å °0.0701 Å °0.0113 Å °0.0114 Å °-0.0125 Å °
Refinement TLS groupSelection details: all

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