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- PDB-5vwi: Crystal structure of human Scribble PDZ1:Beta-PIX complex -

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Basic information

Entry
Database: PDB / ID: 5vwi
TitleCrystal structure of human Scribble PDZ1:Beta-PIX complex
Components
  • Protein scribble homolog
  • beta-PIX
KeywordsSTRUCTURAL PROTEIN / polarity
Function / homology
Function and homology information


neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / extrinsic component of postsynaptic density membrane / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / synaptic vesicle targeting ...neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / extrinsic component of postsynaptic density membrane / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / synaptic vesicle targeting / 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 / 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 / cell junction / lamellipodium / presynapse / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / protein kinase binding / 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 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: 1.75 Å
AuthorsLim, K.Y.B. / 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: 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 22, 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
B: Protein scribble homolog
C: beta-PIX
D: beta-PIX


Theoretical massNumber of molelcules
Total (without water)22,0554
Polymers22,0554
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein scribble homolog
C: beta-PIX


Theoretical massNumber of molelcules
Total (without water)11,0282
Polymers11,0282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-3 kcal/mol
Surface area5600 Å2
MethodPISA
3
B: Protein scribble homolog
D: beta-PIX


Theoretical massNumber of molelcules
Total (without water)11,0282
Polymers11,0282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-3 kcal/mol
Surface area5580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.869, 44.163, 60.465
Angle α, β, γ (deg.)90.00, 93.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 10082.529 Da / Num. of mol.: 2 / Fragment: residues 1002-1092
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: Protein/peptide beta-PIX


Mass: 944.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): DE3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: 16.6% (w/v) polyethylene glycol 3350 and 0.1M citrate-bis-tris propane pH8.9

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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: 1.75→44.16 Å / Num. obs: 20310 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.759 / Mean I/σ(I) obs: 1 / CC1/2: 0.307 / % possible all: 99.9

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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: 4WYT

4wyt


Resolution: 1.75→31.16 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07
RfactorNum. reflection% reflection
Rfree0.2356 2029 10 %
Rwork0.194 --
obs0.1983 20292 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 0 167 1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111468
X-RAY DIFFRACTIONf_angle_d1.1951984
X-RAY DIFFRACTIONf_dihedral_angle_d17.105895
X-RAY DIFFRACTIONf_chiral_restr0.065230
X-RAY DIFFRACTIONf_plane_restr0.008264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.38191460.33981289X-RAY DIFFRACTION100
1.7938-1.84230.32091260.30741301X-RAY DIFFRACTION100
1.8423-1.89650.33291430.27861303X-RAY DIFFRACTION100
1.8965-1.95770.29611440.25471291X-RAY DIFFRACTION100
1.9577-2.02770.31311610.2271277X-RAY DIFFRACTION100
2.0277-2.10880.27911320.2121318X-RAY DIFFRACTION100
2.1088-2.20480.28351440.2151291X-RAY DIFFRACTION100
2.2048-2.3210.25371490.19331298X-RAY DIFFRACTION100
2.321-2.46640.25721450.18481292X-RAY DIFFRACTION100
2.4664-2.65670.2481520.19251300X-RAY DIFFRACTION100
2.6567-2.92390.24171400.18841329X-RAY DIFFRACTION100
2.9239-3.34650.24581460.18561292X-RAY DIFFRACTION100
3.3465-4.21460.18961470.16511322X-RAY DIFFRACTION100
4.2146-31.16470.18021540.17151360X-RAY DIFFRACTION100
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)
11.43180.7505-1.04333.4335-0.4563.05610.1098-0.16630.06790.3386-0.11190.13550.059-0.06730.01010.25680.0025-0.00610.2409-0.00570.26112.72388.191328.2315
25.9015-4.9764-3.24034.32442.71132.27970.20660.0772-0.0517-0.1811-0.0919-0.3124-0.4017-0.1389-0.0110.381-0.0657-0.08980.17050.02930.227813.70393.088828.1768
36.11534.78283.33824.69632.15442.41380.24670.6239-0.7431-0.44310.18410.13310.84280.1504-0.24930.3504-0.0117-0.0450.2052-0.04640.287513.65790.40815.1044
42.81920.7938-0.01673.66940.63784.38010.1142-0.1420.14270.4387-0.06450.2322-0.117-0.26070.00570.2627-0.0130.00880.1732-0.0060.219910.191912.076726.4349
53.54720.894.05349.2094-3.57867.5082-0.0406-0.20270.43890.20490.0549-0.2641-0.44430.0896-0.26680.20710.03530.07160.2736-0.00620.174920.127619.279310.0207
62.59880.80772.90635.22021.84149.2551-0.01610.1709-0.11770.18960.2971-0.53090.21960.7094-0.18710.1944-0.00870.00570.3056-0.04850.353929.80387.61688.5707
72.9719-3.27961.72036.05380.84454.0860.32780.6685-0.1273-1.03560.17630.5728-0.76930.69740.09620.4078-0.136-0.07370.41760.10040.434923.103512.6396-8.3754
85.03090.3215-1.99624.02022.36052.33990.00040.0298-0.38170.20830.1315-0.15630.50.1624-0.15210.22090.0154-0.01210.151-0.01770.267222.26716.036810.4795
93.87413.9285-4.1034.1544-4.1934.4732-0.27140.10180.0529-0.48370.3524-0.23170.267-0.0724-0.10990.2258-0.0075-0.02810.20130.00690.267320.637814.09154.3781
101.85631.50690.20975.97544.08853.9604-0.00721.04360.3775-0.57460.2383-0.3807-1.2680.9317-0.00650.4536-0.08560.05450.50240.0930.351429.162219.9894-2.0274
114.9374-0.74370.64672.4858-0.7142.0287-0.08140.34540.1265-0.056-0.0677-0.2838-0.11110.3330.14390.2067-0.03110.03320.24180.01760.238428.877914.85933.6817
121.5499-0.63731.91685.3834-7.45642.0001-0.1075-0.3411-0.0763-0.17980.82070.23890.5334-0.6545-0.19330.36240.09530.02080.2801-0.04060.24058.4078-1.19733.0626
137.59373.58011.59295.62594.31293.5557-0.83420.8392-0.1666-0.5291.10560.2253-0.04680.7159-0.40340.3494-0.07160.01260.39270.01480.307525.46453.1934-4.1538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 102 )
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 17 )
6X-RAY DIFFRACTION6chain 'B' and (resid 18 through 29 )
7X-RAY DIFFRACTION7chain 'B' and (resid 30 through 46 )
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 60 )
9X-RAY DIFFRACTION9chain 'B' and (resid 61 through 71 )
10X-RAY DIFFRACTION10chain 'B' and (resid 72 through 80 )
11X-RAY DIFFRACTION11chain 'B' and (resid 81 through 102 )
12X-RAY DIFFRACTION12chain 'C' and (resid 10 through 17 )
13X-RAY DIFFRACTION13chain 'D' and (resid 10 through 17 )

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