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- PDB-8bj0: Crystal structure of Scribble PDZ1 with PTHR -

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Basic information

Entry
Database: PDB / ID: 8bj0
TitleCrystal structure of Scribble PDZ1 with PTHR
Components
  • Parathyroid hormone/parathyroid hormone-related peptide receptor
  • Protein scribble homolog
KeywordsPROTEIN BINDING / Scribble / PTHR / PDZ domain / cell polarity
Function / homology
Function and homology information


extrinsic component of postsynaptic density membrane / establishment of T cell polarity / parathyroid hormone receptor activity / cochlear nucleus development / apoptotic process involved in morphogenesis / astrocyte cell migration / myelin sheath abaxonal region / Scrib-APC-beta-catenin complex / establishment of apical/basal cell polarity / polarized epithelial cell differentiation ...extrinsic component of postsynaptic density membrane / establishment of T cell polarity / parathyroid hormone receptor activity / cochlear nucleus development / apoptotic process involved in morphogenesis / astrocyte cell migration / myelin sheath abaxonal region / Scrib-APC-beta-catenin complex / establishment of apical/basal cell polarity / polarized epithelial cell differentiation / synaptic vesicle targeting / epithelial structure maintenance / neurotransmitter receptor transport, endosome to postsynaptic membrane / mammary gland duct morphogenesis / cell-cell contact zone / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / protein localization to adherens junction / Class B/2 (Secretin family receptors) / auditory receptor cell stereocilium organization / G protein-coupled peptide receptor activity / negative regulation of mitotic cell cycle / osteoblast development / RND2 GTPase cycle / RND3 GTPase cycle / positive chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of inositol phosphate biosynthetic process / receptor clustering / negative regulation of activated T cell proliferation / RHOJ GTPase cycle / bone mineralization / RHOQ GTPase cycle / positive regulation of receptor recycling / peptide hormone binding / CDC42 GTPase cycle / immunological synapse / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / synaptic vesicle endocytosis / chondrocyte differentiation / bone resorption / cell maturation / signaling adaptor activity / skeletal system development / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of type II interferon production / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / cell-cell junction / cell junction / cell migration / presynapse / lamellipodium / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / basolateral plasma membrane / in utero embryonic development / cell surface receptor signaling pathway / cell population proliferation / receptor complex / postsynaptic density / apical plasma membrane / positive regulation of apoptotic process / cadherin binding / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / protein kinase binding / nucleolus / glutamatergic synapse / protein homodimerization activity / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GPCR, family 2, parathyroid hormone receptor / : / : / Leucine-rich repeat region / G-protein coupled receptors family 2 signature 1. / : / Leucine-rich repeats, bacterial type / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors ...GPCR, family 2, parathyroid hormone receptor / : / : / Leucine-rich repeat region / G-protein coupled receptors family 2 signature 1. / : / Leucine-rich repeats, bacterial type / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / 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
Parathyroid hormone/parathyroid hormone-related peptide receptor / Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsStewart, B.Z. / 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: To Be Published
Title: Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide
Authors: Stewart, B.Z. / Caria, S. / Humbert, P.O. / Kvansakul, M.
History
DepositionNov 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein scribble homolog
B: Parathyroid hormone/parathyroid hormone-related peptide receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1693
Polymers11,1342
Non-polymers351
Water1448
1
A: Protein scribble homolog
B: Parathyroid hormone/parathyroid hormone-related peptide receptor
hetero molecules

A: Protein scribble homolog
B: Parathyroid hormone/parathyroid hormone-related peptide receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3386
Polymers22,2674
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y,-z+3/41
Buried area3820 Å2
ΔGint-51 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.454, 82.454, 59.659
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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


Mass: 10082.529 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) / Strain (production host): Codon+ / References: UniProt: Q14160
#2: Protein/peptide Parathyroid hormone/parathyroid hormone-related peptide receptor / PTH/PTHrP type I receptor / PTH/PTHr receptor / Parathyroid hormone 1 receptor / PTH1 receptor


Mass: 1051.126 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTH1R, PTHR, PTHR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon+ / References: UniProt: Q03431
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 41.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium cacodylate pH 5.8, 53% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.6→41.27 Å / Num. obs: 3144 / % possible obs: 94.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 68.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.7
Reflection shellResolution: 2.6→2.694 Å / Num. unique obs: 313 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VWI

5vwi


Resolution: 2.6→31.37 Å / SU ML: 0.2527 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1402
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2852 180 5.74 %
Rwork0.2768 2955 -
obs0.2775 3135 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.45 Å2
Refinement stepCycle: LAST / Resolution: 2.6→31.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 1 8 739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023738
X-RAY DIFFRACTIONf_angle_d0.5181998
X-RAY DIFFRACTIONf_chiral_restr0.0443117
X-RAY DIFFRACTIONf_plane_restr0.0047133
X-RAY DIFFRACTIONf_dihedral_angle_d12.4276275
LS refinement shellResolution: 2.6→31.37 Å
RfactorNum. reflection% reflection
Rfree0.2852 180 -
Rwork0.2768 2955 -
obs--92.92 %
Refinement TLS params.Method: refined / Origin x: 14.7152516996 Å / Origin y: -1.73178536196 Å / Origin z: 10.9191120726 Å
111213212223313233
T0.623167792179 Å2-0.23642342894 Å2-0.17194997817 Å2-0.910768864893 Å20.0286313670069 Å2--0.436613869362 Å2
L9.72375091498 °2-0.586740998034 °24.83986852308 °2-8.22193087223 °2-1.02906057804 °2--7.95055735606 °2
S-0.9533183873 Å °0.889338833528 Å °0.772900136938 Å °-0.248889829504 Å °0.623895110151 Å °-0.381646649461 Å °-1.22952098051 Å °0.55221451446 Å °0.152143113421 Å °
Refinement TLS groupSelection details: all

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