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

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Basic information

Entry
Database: PDB / ID: 5ema
TitleCrystal structure of the SNX27 PDZ domain bound to the phosphorylated C-terminal LRRC3B PDZ binding motif
Components
  • ASP-ASP-ILE-SEP-THR-VAL-VAL
  • Sorting nexin-27
KeywordsPROTEIN TRANSPORT / Endosome / PDZ domain / sorting nexin
Function / homology
Function and homology information


response to methamphetamine hydrochloride / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / WASH complex / endosome to plasma membrane protein transport / retromer complex / phosphatidylinositol-3-phosphate binding / endocytic recycling / endosomal transport / regulation of postsynaptic membrane neurotransmitter receptor levels ...response to methamphetamine hydrochloride / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / WASH complex / endosome to plasma membrane protein transport / retromer complex / phosphatidylinositol-3-phosphate binding / endocytic recycling / endosomal transport / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / ionotropic glutamate receptor binding / extracellular matrix / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / intracellular protein transport / Schaffer collateral - CA1 synapse / nervous system development / early endosome membrane / membrane => GO:0016020 / early endosome / endosome / glutamatergic synapse / signal transduction / extracellular space / cytosol
Similarity search - Function
SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Leucine rich repeat N-terminal domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain ...SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Leucine rich repeat N-terminal domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Sorting nexin-27 / Leucine-rich repeat-containing protein 3B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsCollins, B.M. / Clairfeuille, T.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1041929 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

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Assembly

Deposited unit
A: Sorting nexin-27
B: ASP-ASP-ILE-SEP-THR-VAL-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5873
Polymers11,4952
Non-polymers921
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area5850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.171, 48.490, 56.229
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 ASP-ASP-ILE-SEP-THR-VAL-VAL


Mass: 924.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96PB8*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 2 M ammonium sulphate and 0.1 M sodium acetate (pH 4.6)
PH range: 4.6

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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: 1.32→48.5 Å / Num. obs: 23850 / % possible obs: 96.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.9
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.5 / % possible all: 86.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z8J

4z8j


Resolution: 1.32→36.721 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1788 2000 8.4 %
Rwork0.1618 --
obs0.1632 23811 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→36.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms772 0 6 150 928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01803
X-RAY DIFFRACTIONf_angle_d1.4311088
X-RAY DIFFRACTIONf_dihedral_angle_d13.506303
X-RAY DIFFRACTIONf_chiral_restr0.078127
X-RAY DIFFRACTIONf_plane_restr0.005145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3161-1.3490.25321300.23771422X-RAY DIFFRACTION89
1.349-1.38540.24181390.18861504X-RAY DIFFRACTION95
1.3854-1.42620.21641400.19491529X-RAY DIFFRACTION96
1.4262-1.47230.21161380.17961517X-RAY DIFFRACTION96
1.4723-1.52490.21811440.16921556X-RAY DIFFRACTION97
1.5249-1.58590.16631400.161533X-RAY DIFFRACTION97
1.5859-1.65810.18451420.15541555X-RAY DIFFRACTION97
1.6581-1.74550.17981430.15521559X-RAY DIFFRACTION97
1.7455-1.85490.17541460.15541594X-RAY DIFFRACTION97
1.8549-1.99810.15061450.14641570X-RAY DIFFRACTION98
1.9981-2.19910.17881460.13841596X-RAY DIFFRACTION98
2.1991-2.51730.15161470.14391608X-RAY DIFFRACTION99
2.5173-3.17130.18781510.16731638X-RAY DIFFRACTION99
3.1713-36.73570.17421490.17171630X-RAY DIFFRACTION93

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