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- PDB-6mtu: Crystal structure of human Scribble PDZ1:pMCC complex -

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Basic information

Entry
Database: PDB / ID: 6mtu
TitleCrystal structure of human Scribble PDZ1:pMCC complex
Components
  • Colorectal mutant cancer protein
  • Protein scribble homolog
KeywordsCELL ADHESION / Cell Polarity / MCC / PDZ domain / phosphorylation
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 / polarized epithelial cell differentiation ...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 / negative regulation of epithelial cell migration / 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 / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / receptor clustering / RHOJ GTPase cycle / RHOQ GTPase cycle / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / immunological synapse / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / establishment of protein localization / negative regulation of canonical Wnt signaling pathway / cytoplasmic ribonucleoprotein granule / cell-cell adhesion / Wnt signaling pathway / negative regulation of epithelial cell proliferation / cell migration / cell-cell junction / positive regulation of type II interferon production / presynapse / signaling receptor activity / cell junction / lamellipodium / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / signal transduction / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Harmonin-binding protein USHBP1, PDZ-binding domain / Harmonin-binding protein USHBP1-like / Harmonin-binding protein USHBP1, PDZ-binding domain / 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. / Leucine-rich repeat ...Harmonin-binding protein USHBP1, PDZ-binding domain / Harmonin-binding protein USHBP1-like / Harmonin-binding protein USHBP1, PDZ-binding domain / 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. / Leucine-rich repeat / PDZ domain / 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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Colorectal mutant cancer protein / Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.141 Å
AuthorsCaria, S. / Stewart, B.Z. / Humbert, P.O. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: Febs J. / Year: 2019
Title: Structural analysis of phosphorylation-associated interactions of human MCC with Scribble PDZ domains.
Authors: Caria, S. / Stewart, B.Z. / Jin, R. / Smith, B.J. / Humbert, P.O. / Kvansakul, M.
History
DepositionOct 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
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

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Assembly

Deposited unit
A: Protein scribble homolog
B: Protein scribble homolog
C: Colorectal mutant cancer protein
D: Colorectal mutant cancer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,10421
Polymers26,8344
Non-polymers1,27117
Water79344
1
A: Protein scribble homolog
D: Colorectal mutant cancer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,25614
Polymers13,4172
Non-polymers83912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-1 kcal/mol
Surface area7680 Å2
MethodPISA
2
B: Protein scribble homolog
C: Colorectal mutant cancer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8487
Polymers13,4172
Non-polymers4315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-2 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.600, 53.600, 214.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11B-904-

PEG

21A-1003-

HOH

31A-1017-

HOH

41B-1012-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 12437.953 Da / Num. of mol.: 2 / Fragment: residues 700-816
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 (E. coli) / References: UniProt: Q14160
#2: Protein/peptide Colorectal mutant cancer protein / Protein MCC


Mass: 978.916 Da / Num. of mol.: 2 / Fragment: residues 822-829 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P23508

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Non-polymers , 5 types, 61 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: Phosphate/citrate, PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2018
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.141→42.884 Å / Num. obs: 8817 / % possible obs: 91.5 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.058 / Net I/σ(I): 12
Reflection shellResolution: 2.141→2.475 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 461 / CC1/2: 0.641 / Rpim(I) all: 0.616 / % possible all: 69.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VWC

5vwc


Resolution: 2.141→42.884 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 55.24 / Phase error: 26.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 902 10.24 %Random selection
Rwork0.197 ---
obs0.2066 8810 53.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.141→42.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 79 44 1734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031690
X-RAY DIFFRACTIONf_angle_d0.5162245
X-RAY DIFFRACTIONf_dihedral_angle_d23.0021005
X-RAY DIFFRACTIONf_chiral_restr0.046246
X-RAY DIFFRACTIONf_plane_restr0.002290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1868-2.32380.5829150.3131112X-RAY DIFFRACTION100
2.3238-2.50320.3424450.302355X-RAY DIFFRACTION100
2.5032-2.75510.3249820.2553825X-RAY DIFFRACTION32
2.7551-3.15370.27662260.21631968X-RAY DIFFRACTION75
3.1537-3.97280.22272590.18092301X-RAY DIFFRACTION90
3.9728-42.8840.27092650.19882346X-RAY DIFFRACTION90

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