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- PDB-5emb: Crystal structure of the SNX27 PDZ domain bound to the C-terminal... -

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Basic information

Entry
Database: PDB / ID: 5emb
TitleCrystal structure of the SNX27 PDZ domain bound to the C-terminal phosphorylated PTHR PDZ binding motif
Components
  • GLU-GLU-TRP-SEP-THR-VAL-MET
  • Sorting nexin-27
KeywordsPROTEIN TRANSPORT / Endosome / PDZ domain / sorting nexin
Function / homology
Function and homology information


postsynaptic early endosome / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / response to methamphetamine hydrochloride / neurotransmitter receptor transport to plasma membrane / parathyroid hormone receptor activity / WASH complex / postsynaptic recycling endosome / retromer complex / endosome to plasma membrane protein transport ...postsynaptic early endosome / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / response to methamphetamine hydrochloride / neurotransmitter receptor transport to plasma membrane / parathyroid hormone receptor activity / WASH complex / postsynaptic recycling endosome / retromer complex / endosome to plasma membrane protein transport / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / osteoblast development / endosomal transport / positive regulation of inositol phosphate biosynthetic process / endosome to lysosome transport / bone mineralization / peptide hormone binding / immunological synapse / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / chondrocyte differentiation / regulation of postsynaptic membrane neurotransmitter receptor levels / bone resorption / cell maturation / ionotropic glutamate receptor binding / phosphatidylinositol binding / skeletal system development / intracellular protein transport / cellular response to nerve growth factor stimulus / 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 / calcium-dependent protein binding / nervous system development / early endosome membrane / basolateral plasma membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / in utero embryonic development / early endosome / cell population proliferation / receptor complex / cell surface receptor signaling pathway / postsynapse / endosome / G protein-coupled receptor signaling pathway / apical plasma membrane / negative regulation of cell population proliferation / positive regulation of cell population proliferation / nucleolus / glutamatergic synapse / signal transduction / protein homodimerization activity / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / GPCR, family 2, parathyroid hormone receptor / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain ...SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / GPCR, family 2, parathyroid hormone receptor / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / 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. / : / 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. / PDZ domain / 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: 0.85 Å
AuthorsCollins, B.M. / Clairfeuille, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: A molecular code for endosomal recycling of phosphorylated cargos by the SNX27-retromer complex.
Authors: Clairfeuille, T. / Mas, C. / Chan, A.S. / Yang, Z. / Tello-Lafoz, M. / Chandra, M. / Widagdo, J. / Kerr, M.C. / Paul, B. / Merida, I. / Teasdale, R.D. / Pavlos, N.J. / Anggono, V. / Collins, B.M.
History
DepositionNov 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Sep 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_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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-27
B: GLU-GLU-TRP-SEP-THR-VAL-MET


Theoretical massNumber of molelcules
Total (without water)11,6592
Polymers11,6592
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-8 kcal/mol
Surface area5760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.570, 48.330, 56.177
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 GLU-GLU-TRP-SEP-THR-VAL-MET


Mass: 1089.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q03431*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 10% PEG1000, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.7085 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7085 Å / Relative weight: 1
ReflectionResolution: 0.85→31.265 Å / Num. obs: 90806 / % possible obs: 98.7 % / Redundancy: 14 % / Net I/σ(I): 25.9
Reflection shellResolution: 0.85→0.86 Å / Redundancy: 13.9 % / Rmerge(I) obs: 2.06 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z8J

4z8j


Resolution: 0.85→10.2 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.275 / SU ML: 0.008 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13567 2000 2.2 %RANDOM
Rwork0.1237 ---
obs0.12397 88390 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.849 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 0.85→10.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms781 0 0 182 963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.019840
X-RAY DIFFRACTIONr_bond_other_d0.010.02843
X-RAY DIFFRACTIONr_angle_refined_deg2.0891.9871148
X-RAY DIFFRACTIONr_angle_other_deg0.88831936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.725116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.10123.51437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1815150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.853159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02972
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02185
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr14.81731683
X-RAY DIFFRACTIONr_sphericity_free38.747519
X-RAY DIFFRACTIONr_sphericity_bonded12.23451831
LS refinement shellResolution: 0.85→0.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 146 -
Rwork0.222 6440 -
obs--99.91 %

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