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

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Basic information

Entry
Database: PDB / ID: 8bia
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 / apoptotic process involved in morphogenesis / cochlear nucleus development / astrocyte cell migration / 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 / apoptotic process involved in morphogenesis / cochlear nucleus development / astrocyte cell migration / Scrib-APC-beta-catenin complex / establishment of apical/basal cell polarity / : / polarized epithelial cell differentiation / epithelial structure maintenance / neurotransmitter receptor transport, endosome to postsynaptic membrane / myelin sheath abaxonal region / mammary gland duct morphogenesis / activation of GTPase activity / cell-cell contact zone / establishment or maintenance of epithelial cell apical/basal polarity / post-anal tail morphogenesis / protein localization to adherens junction / auditory receptor cell stereocilium organization / negative regulation of mitotic cell cycle / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / osteoblast development / RND2 GTPase cycle / RND3 GTPase cycle / regulation of postsynaptic neurotransmitter receptor internalization / positive chemotaxis / negative regulation of activated T cell proliferation / RHOJ GTPase cycle / bone mineralization / RHOQ GTPase cycle / receptor clustering / positive regulation of inositol phosphate biosynthetic process / positive regulation of receptor recycling / peptide hormone binding / CDC42 GTPase cycle / immunological synapse / chondrocyte differentiation / bone resorption / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / synaptic vesicle endocytosis / cell maturation / signaling adaptor activity / skeletal system development / adherens junction / neural tube closure / wound healing / Asymmetric localization of PCP proteins / cell-cell adhesion / positive regulation of type II interferon production / G protein-coupled receptor activity / intracellular calcium ion homeostasis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cell-cell junction / cell junction / cell migration / lamellipodium / adenylate cyclase-activating G protein-coupled receptor signaling pathway / presynapse / G alpha (s) signalling events / in utero embryonic development / basolateral plasma membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / cell surface receptor signaling pathway / signaling receptor complex / cell population proliferation / apical plasma membrane / postsynaptic density / cadherin binding / positive regulation of apoptotic process / 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 / Leucine-rich repeats, bacterial type / G-protein coupled receptors family 2 signature 1. / : / 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 / Leucine-rich repeats, bacterial type / G-protein coupled receptors family 2 signature 1. / : / 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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Leucine-rich repeat / PDZ superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Parathyroid hormone/parathyroid hormone-related peptide receptor / Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2026Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,4403
Polymers13,3452
Non-polymers951
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-10 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.161, 53.161, 217.010
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: 12293.823 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: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q03431
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.48 Å3/Da / Density % sol: 64.72 % / Description: triangular diamond prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M phosphate/citrate pH 5.2, 43% 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: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.4→51.66 Å / Num. obs: 6472 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 56.57 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 623 / CC1/2: 0.891 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MTV

6mtv


Resolution: 2.4→51.63 Å / SU ML: 0.1752 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.0619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2713 334 5.17 %
Rwork0.2519 6122 -
obs0.2529 6456 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→51.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 5 35 870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022843
X-RAY DIFFRACTIONf_angle_d0.4681137
X-RAY DIFFRACTIONf_chiral_restr0.0457127
X-RAY DIFFRACTIONf_plane_restr0.0028151
X-RAY DIFFRACTIONf_dihedral_angle_d15.3955314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-3.020.35271660.29222962X-RAY DIFFRACTION98.21
3.02-51.630.25071680.24273160X-RAY DIFFRACTION99.08
Refinement TLS params.Method: refined / Origin x: 15.0246235025 Å / Origin y: 27.1692229986 Å / Origin z: -12.4512720899 Å
111213212223313233
T0.230110054175 Å2-0.0639716849453 Å2-0.0488469731104 Å2-0.650524895469 Å20.0415935387309 Å2--0.31821877712 Å2
L2.76337219683 °2-0.32163057626 °2-0.533962449309 °2-3.16192194133 °20.354010096047 °2--4.43886529039 °2
S0.151571297231 Å °-0.493345706885 Å °0.0803329460972 Å °0.360721483764 Å °-0.127093554452 Å °-0.380804390687 Å °-0.315521536613 Å °0.371193604613 Å °-0.0815395042216 Å °
Refinement TLS groupSelection details: all

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