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- PDB-5em9: Crystal structure of the SNX27 PDZ domain bound to the phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 5em9
TitleCrystal structure of the SNX27 PDZ domain bound to the phosphorylated C-terminal 5HT4(a)R PDZ binding motif
Components
  • SEP-LEU-GLU-SER-CYS-PHE
  • Sorting nexin-27
KeywordsPROTEIN TRANSPORT / Endosome / PDZ domain / sorting nexin
Function / homology
Function and homology information


serotonin receptor activity / large intestinal transit / response to methamphetamine hydrochloride / establishment of protein localization to plasma membrane / regulation of appetite / positive regulation of AMPA glutamate receptor clustering / WASH complex / endosome to plasma membrane protein transport / Serotonin receptors / maintenance of gastrointestinal epithelium ...serotonin receptor activity / large intestinal transit / response to methamphetamine hydrochloride / establishment of protein localization to plasma membrane / regulation of appetite / positive regulation of AMPA glutamate receptor clustering / WASH complex / endosome to plasma membrane protein transport / Serotonin receptors / maintenance of gastrointestinal epithelium / mucus secretion / retromer complex / G protein-coupled serotonin receptor activity / phosphatidylinositol-3-phosphate binding / endocytic recycling / neurotransmitter receptor activity / endosomal transport / regulation of postsynaptic membrane neurotransmitter receptor levels / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / immunological synapse / ionotropic glutamate receptor binding / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / intracellular protein transport / Schaffer collateral - CA1 synapse / nervous system development / chemical synaptic transmission / G alpha (s) signalling events / early endosome membrane / early endosome / endosome / G protein-coupled receptor signaling pathway / dendrite / glutamatergic synapse / synapse / signal transduction / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
5-Hydroxytryptamine 4 receptor / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / 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. ...5-Hydroxytryptamine 4 receptor / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / 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 / Serpentine type 7TM GPCR chemoreceptor Srsx / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
5-hydroxytryptamine receptor 4 / Sorting nexin-27
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCollins, B.M. / Clairfeuille, T.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1061574 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1058734 Australia
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, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: Sorting nexin-27
B: SEP-LEU-GLU-SER-CYS-PHE


Theoretical massNumber of molelcules
Total (without water)11,5612
Polymers11,5612
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.219, 48.753, 57.059
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 SEP-LEU-GLU-SER-CYS-PHE


Mass: 990.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13639*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5 / Details: 40% PEG 400, 20% PEG8000, 0.1 M acetate (pH 4.5) / PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→37.2 Å / Num. obs: 14298 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 14.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.97 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z8J

4z8j


Resolution: 1.6→37.066 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1977 715 5.03 %
Rwork0.1686 --
obs0.1701 14225 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→37.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms767 0 0 109 876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011792
X-RAY DIFFRACTIONf_angle_d1.3061074
X-RAY DIFFRACTIONf_dihedral_angle_d11.648303
X-RAY DIFFRACTIONf_chiral_restr0.052125
X-RAY DIFFRACTIONf_plane_restr0.006142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.72360.3121380.24222642X-RAY DIFFRACTION100
1.7236-1.8970.27951460.22052650X-RAY DIFFRACTION100
1.897-2.17150.2041450.17242672X-RAY DIFFRACTION100
2.1715-2.73570.1841560.16612687X-RAY DIFFRACTION100
2.7357-37.07540.17321300.15052859X-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)
10.2220.2118-0.18730.71690.12630.3304-0.01170.022-0.0848-0.0242-0.018-0.0885-0.032-0.01330.00080.14060.00020.01920.1547-0.02760.1514-2.27695.543-8.8884
20.42190.13120.06911.88630.28950.05060.1312-0.10.082-0.074-0.20760.21230.15130.4737-0.050.21730.0490.0280.30730.04050.1644-8.03932.14916.4703
30.8750.6304-0.28540.74220.12760.4811-0.0549-0.0609-0.0080.02110.0116-0.1189-0.0064-0.0144-0.00040.14360.00740.00840.1286-0.01240.1387-2.35015.321-8.0522
40.5659-0.571-0.13980.97810.37480.1729-0.02130.0180.1721-0.35470.1274-0.42220.3499-0.0050.08710.1912-0.0220.02080.15640.01520.18381.9219.8032-9.3981
50.16060.00620.09350.007-0.00240.060.26120.3833-0.4742-0.214-0.2086-0.0290.0692-0.1740.00630.19640.00080.02620.2118-0.06370.1816-6.22791.8093-16.0282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 133 )
5X-RAY DIFFRACTION5chain 'B' and (resid 382 through 387 )

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