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- PDB-5vwc: Crystal structure of human Scribble PDZ1 domain -

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Basic information

Entry
Database: PDB / ID: 5vwc
TitleCrystal structure of human Scribble PDZ1 domain
ComponentsProtein scribble homolog
KeywordsSTRUCTURAL PROTEIN / PDZ / LAP / Scribble / 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 / protein localization to adherens junction / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / 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 / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / 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 / lamellipodium / cell junction / 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 Repeat / Leucine-rich repeats, bacterial type / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat ...Leucine Rich Repeat / Leucine-rich repeats, bacterial type / PDZ domain / Pdz3 Domain / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.911 Å
AuthorsLim, K.Y.B. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1007918 Australia
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural basis for the differential interaction of Scribble PDZ domains with the guanine nucleotide exchange factor beta-PIX.
Authors: Lim, K.Y.B. / Godde, N.J. / Humbert, P.O. / Kvansakul, M.
History
DepositionMay 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7264
Polymers10,5401
Non-polymers1863
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint5 kcal/mol
Surface area5800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.490, 41.693, 51.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 10539.828 Da / Num. of mol.: 1 / Fragment: UNP Residues 725-815
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 K-12 (bacteria) / Strain (production host): DE3 / References: UniProt: Q14160
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.81 Å3/Da / Density % sol: 32.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% (w/v) polyethylene glycol 3350, 0.2M magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.91→41.69 Å / Num. obs: 6245 / % possible obs: 99.3 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.2
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2229 / CC1/2: 0.856 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W4F

2w4f


Resolution: 1.911→32.422 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.33
RfactorNum. reflection% reflection
Rfree0.2268 296 4.74 %
Rwork0.1954 --
obs0.197 6245 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.911→32.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms703 0 12 48 763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008726
X-RAY DIFFRACTIONf_angle_d0.923974
X-RAY DIFFRACTIONf_dihedral_angle_d17.593433
X-RAY DIFFRACTIONf_chiral_restr0.059110
X-RAY DIFFRACTIONf_plane_restr0.006130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9106-2.40710.2411320.20032922X-RAY DIFFRACTION99
2.4071-32.4270.22251640.19333027X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.12240.168-0.1570.3148-0.31940.34140.2410.06610.0979-0.00150.26590.37330.0776-0.19480.12610.1653-0.0044-0.10120.1363-0.15630.1919-12.2659-12.93783.3037
20.04720.07440.11230.1650.04940.1683-0.0827-0.0929-0.0718-0.0052-0.07610.03680.0151-0.0789-0.00380.1314-0.00270.01980.1367-0.02780.1236-2.5949-4.464411.6333
30.1585-0.02590.19950.4018-0.16720.28320.0811-0.2794-0.08920.25350.17360.3350.0003-0.00090.18290.1089-0.02340.01470.1597-0.00390.1241-10.8479-10.043714.7774
40.23440.0509-0.25390.0432-0.0530.273-0.0611-0.1732-0.0685-0.2467-0.08570.1897-0.1009-0.0087-0.1230.1677-0.0181-0.04150.09650.01230.1052-6.8037-10.49626.8797
50.01530.0056-0.00260.0088-0.02440.0132-0.011-0.02970.0322-0.0923-0.0041-0.0649-0.03550.1202-00.18430.02430.01290.12820.04040.2751-3.9898-0.80731.1151
60.08530.098-0.03150.1649-0.02850.00650.05370.03040.1617-0.1398-0.28840.382-0.058-0.1051-0.0040.16190.0372-0.0360.1533-0.04660.1489-9.4037-1.33775.9837
70.0123-0.00810.01480.0085-0.00010.00250.07070.022-0.0229-0.0189-0.0794-0.05230.01280.002400.16-0.00030.00240.13960.03330.16481.2907-20.83237.8518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 724 through 732 )
2X-RAY DIFFRACTION2chain 'A' and (resid 733 through 757 )
3X-RAY DIFFRACTION3chain 'A' and (resid 758 through 772 )
4X-RAY DIFFRACTION4chain 'A' and (resid 773 through 783 )
5X-RAY DIFFRACTION5chain 'A' and (resid 784 through 792 )
6X-RAY DIFFRACTION6chain 'A' and (resid 793 through 812 )
7X-RAY DIFFRACTION7chain 'A' and (resid 813 through 819 )

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