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- PDB-4z8j: Crystal structure of the SNX27 PDZ domain bound to the C-terminal... -

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Basic information

Entry
Database: PDB / ID: 4z8j
TitleCrystal structure of the SNX27 PDZ domain bound to the C-terminal PTHR PDZ binding motif
Components
  • C-terminal PDZ binding motif from parathyroid hormone receptor (PTHR)
  • Sorting nexin-27
KeywordsPROTEIN TRANSPORT / PDZ domain / SNX27 / PTHR
Function / homology
Function and homology information


response to methamphetamine hydrochloride / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / parathyroid hormone receptor activity / WASH complex / endosome to plasma membrane protein transport / retromer complex / phosphatidylinositol-3-phosphate binding / G protein-coupled peptide receptor activity / endocytic recycling ...response to methamphetamine hydrochloride / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / parathyroid hormone receptor activity / WASH complex / endosome to plasma membrane protein transport / retromer complex / phosphatidylinositol-3-phosphate binding / G protein-coupled peptide receptor activity / endocytic recycling / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / endosomal transport / bone mineralization / regulation of postsynaptic membrane neurotransmitter receptor levels / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / peptide hormone binding / immunological synapse / chondrocyte differentiation / cell maturation / bone resorption / ionotropic glutamate receptor binding / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / skeletal system development / intracellular protein transport / Schaffer collateral - CA1 synapse / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / : / phospholipase C-activating G protein-coupled receptor signaling pathway / nervous system development / G alpha (s) signalling events / early endosome membrane / basolateral plasma membrane / cell population proliferation / in utero embryonic development / cell surface receptor signaling pathway / receptor complex / early endosome / endosome / G protein-coupled receptor signaling pathway / apical plasma membrane / negative regulation of cell population proliferation / glutamatergic synapse / positive regulation of cell population proliferation / signal transduction / protein homodimerization activity / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / GPCR, family 2, parathyroid hormone receptor / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / GPCR, family 2, parathyroid hormone receptor / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / 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) / PDZ domain / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Parathyroid hormone/parathyroid hormone-related peptide receptor / Sorting nexin-27
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsClairfeuille, T. / Pavlos, N. / Collins, B.M.
CitationJournal: To Be Published
Title: Role of SNX27-retromer in PTHR trafficking
Authors: Clairfeuille, T. / Teasdale, R.D. / Collins, B.M. / Pavlos, N.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-27
B: C-terminal PDZ binding motif from parathyroid hormone receptor (PTHR)


Theoretical massNumber of molelcules
Total (without water)11,6212
Polymers11,6212
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-3 kcal/mol
Surface area5830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.070, 48.625, 55.725
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 Sorting nexin-27 / / MAP-responsive gene protein / Methamphetamine-responsive transcript 1 protein / PDZ-protein Mrt1


Mass: 10569.952 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 39-133)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snx27, Mrt1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K4V4
#2: Protein/peptide C-terminal PDZ binding motif from parathyroid hormone receptor (PTHR)


Mass: 1051.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q03431*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis/Tris (pH 5.5) and 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 0.95→15.7 Å / Num. obs: 64036 / % possible obs: 99.8 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.7
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.7 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3111 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QDO

3qdo


Resolution: 0.95→14.851 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1444 3238 5.06 %
Rwork0.1436 --
obs0.1436 63961 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.95→14.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 0 185 965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008833
X-RAY DIFFRACTIONf_angle_d1.2781136
X-RAY DIFFRACTIONf_dihedral_angle_d11.446327
X-RAY DIFFRACTIONf_chiral_restr0.068132
X-RAY DIFFRACTIONf_plane_restr0.006152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.96420.25341370.24332581X-RAY DIFFRACTION100
0.9642-0.97920.24641200.23312647X-RAY DIFFRACTION100
0.9792-0.99530.19971480.20382610X-RAY DIFFRACTION100
0.9953-1.01250.18951660.19162592X-RAY DIFFRACTION100
1.0125-1.03090.16951440.16562629X-RAY DIFFRACTION100
1.0309-1.05070.15781570.1622586X-RAY DIFFRACTION100
1.0507-1.07210.20721300.16492618X-RAY DIFFRACTION100
1.0721-1.09540.16811420.15062619X-RAY DIFFRACTION100
1.0954-1.12090.14531510.12682621X-RAY DIFFRACTION100
1.1209-1.14890.14531340.12412613X-RAY DIFFRACTION100
1.1489-1.180.12481340.11622632X-RAY DIFFRACTION100
1.18-1.21470.13221490.12212632X-RAY DIFFRACTION100
1.2147-1.25390.14511490.12792623X-RAY DIFFRACTION100
1.2539-1.29870.12071480.1222616X-RAY DIFFRACTION100
1.2987-1.35060.14521290.12192658X-RAY DIFFRACTION100
1.3506-1.41210.12941300.12022645X-RAY DIFFRACTION100
1.4121-1.48640.14591500.1232654X-RAY DIFFRACTION100
1.4864-1.57950.13751560.12292643X-RAY DIFFRACTION100
1.5795-1.70130.13331400.12422662X-RAY DIFFRACTION100
1.7013-1.87220.13631080.13182730X-RAY DIFFRACTION100
1.8722-2.14240.14991560.13072661X-RAY DIFFRACTION100
2.1424-2.69650.12381260.14172753X-RAY DIFFRACTION100
2.6965-14.85260.14821340.17282698X-RAY DIFFRACTION94

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