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- PDB-6ms1: Crystal structure of the human Scribble PDZ1 domain bound to the ... -

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Basic information

Entry
Database: PDB / ID: 6ms1
TitleCrystal structure of the human Scribble PDZ1 domain bound to the PDZ-binding motif of APC
Components
  • APC C-terminus peptide
  • Protein scribble homolog
KeywordsSTRUCTURAL PROTEIN / Scribble / APC / 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 / Resolution: 1.35 Å
AuthorsHow, J.Y. / Kvansakul, M. / Caria, S. / Humbert, P.O.
CitationJournal: FEBS Lett. / Year: 2019
Title: Crystal structure of the human Scribble PDZ1 domain bound to the PDZ-binding motif of APC.
Authors: How, J.Y. / Caria, S. / Humbert, P.O. / Kvansakul, M.
History
DepositionOct 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 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: Protein scribble homolog
C: APC C-terminus peptide
D: APC C-terminus peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8649
Polymers21,5544
Non-polymers3105
Water3,873215
1
A: Protein scribble homolog
D: APC C-terminus peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0256
Polymers10,7772
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint7 kcal/mol
Surface area6100 Å2
MethodPISA
2
B: Protein scribble homolog
C: APC C-terminus peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8393
Polymers10,7772
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-4 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.338, 51.102, 57.051
Angle α, β, γ (deg.)90.00, 92.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 9952.138 Da / Num. of mol.: 2 / Fragment: PDZ1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Plasmid: pGex-PDZ1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q14160
#2: Protein/peptide APC C-terminus peptide


Mass: 824.920 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Potassium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.35→39.503 Å / Num. obs: 38341 / % possible obs: 97.5 % / Redundancy: 4.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Χ2: 0.76 / Net I/σ(I): 7
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1786 / CC1/2: 0.856 / Rpim(I) all: 0.284 / Rrim(I) all: 0.606 / Χ2: 0.44 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
PHENIXphasing
xia2data reduction
Blu-Icedata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VWK

5vwk


Resolution: 1.35→39.503 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 28.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 1871 4.88 %
Rwork0.1776 --
obs0.1788 38309 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→39.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 20 215 1736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051546
X-RAY DIFFRACTIONf_angle_d0.6732076
X-RAY DIFFRACTIONf_dihedral_angle_d25.037567
X-RAY DIFFRACTIONf_chiral_restr0.067234
X-RAY DIFFRACTIONf_plane_restr0.005277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.38650.4231190.3442655X-RAY DIFFRACTION91
1.3865-1.42730.32331240.32062739X-RAY DIFFRACTION95
1.4273-1.47340.32581650.27612732X-RAY DIFFRACTION97
1.4734-1.5260.26991610.23452731X-RAY DIFFRACTION97
1.526-1.58710.26671550.21162782X-RAY DIFFRACTION97
1.5871-1.65940.29071610.20332781X-RAY DIFFRACTION97
1.6594-1.74690.2681610.19282788X-RAY DIFFRACTION97
1.7469-1.85630.22641480.17972809X-RAY DIFFRACTION98
1.8563-1.99960.19791440.16152823X-RAY DIFFRACTION98
1.9996-2.20080.20531330.15382865X-RAY DIFFRACTION99
2.2008-2.51930.18931060.1562894X-RAY DIFFRACTION99
2.5193-3.17380.17731380.17182894X-RAY DIFFRACTION99
3.1738-39.51960.16271560.1632945X-RAY DIFFRACTION100

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