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- PDB-4p2a: Structure of mouse VPS26A bound to rat SNX27 PDZ domain -

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Basic information

Entry
Database: PDB / ID: 4p2a
TitleStructure of mouse VPS26A bound to rat SNX27 PDZ domain
Components
  • Sorting nexin-27
  • Vacuolar protein sorting-associated protein 26AVacuole
KeywordsTRANSPORT PROTEIN / retromer / sorting nexin
Function / homology
Function and homology information


response to methamphetamine hydrochloride / WNT ligand biogenesis and trafficking / tubular endosome / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / retromer, cargo-selective complex / WASH complex / endosome to plasma membrane protein transport / retromer complex / phosphatidylinositol-3-phosphate binding ...response to methamphetamine hydrochloride / WNT ligand biogenesis and trafficking / tubular endosome / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / retromer, cargo-selective complex / WASH complex / endosome to plasma membrane protein transport / retromer complex / phosphatidylinositol-3-phosphate binding / endocytic recycling / retrograde transport, endosome to Golgi / endosomal transport / regulation of postsynaptic membrane neurotransmitter receptor levels / 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 / early endosome membrane / vesicle / lysosome / early endosome / endosome membrane / endosome / glutamatergic synapse / signal transduction / cytosol
Similarity search - Function
SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Immunoglobulin-like - #640 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain ...SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Immunoglobulin-like - #640 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Arrestin-like, C-terminal / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Vacuolar protein sorting-associated protein 26A / Sorting nexin-27
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsClairfeuille, T. / Gallon, M. / Mas, C. / Ghai, R. / Teasdale, R. / Cullen, P. / Collins, B.
Funding support Australia, 3items
OrganizationGrant numberCountry
ARCDP120103930 Australia
NHMRCAPP1058734 Australia
ARCFT100100027 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: A unique PDZ domain and arrestin-like fold interaction reveals mechanistic details of endocytic recycling by SNX27-retromer.
Authors: Gallon, M. / Clairfeuille, T. / Steinberg, F. / Mas, C. / Ghai, R. / Sessions, R.B. / Teasdale, R.D. / Collins, B.M. / Cullen, P.J.
History
DepositionMar 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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: Vacuolar protein sorting-associated protein 26A
B: Sorting nexin-27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3434
Polymers48,9422
Non-polymers4012
Water63135
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-35 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.810, 113.810, 94.771
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number149
Space group name H-MP312
DetailsMutational analysis indicates the biological assembly is represented by the contents of the asymmetric unit

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Components

#1: Protein Vacuolar protein sorting-associated protein 26A / Vacuole / H58 protein / H beta 58 / Vesicle protein sorting 26A / mVPS26 / VPS26A


Mass: 38372.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps26a, Vps26 / Production host: Escherichia coli (E. coli) / References: UniProt: P40336
#2: Protein Sorting nexin-27 / / MAP-responsive gene protein / Methamphetamine-responsive transcript 1 protein / PDZ-protein Mrt1


Mass: 10569.952 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4 M NaCl, 0.1 M Na Citrate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.7→68.3 Å / Num. obs: 19434 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.8
Reflection shellRmerge(I) obs: 0.964 / Mean I/σ(I) obs: 2.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3DQO and 2FAU.

3dqo

2fau


Resolution: 2.7→56.905 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 28.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2585 1949 10.03 %
Rwork0.2149 --
obs0.2193 19433 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→56.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 2 35 3109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113124
X-RAY DIFFRACTIONf_angle_d1.3574209
X-RAY DIFFRACTIONf_dihedral_angle_d20.3951189
X-RAY DIFFRACTIONf_chiral_restr0.051472
X-RAY DIFFRACTIONf_plane_restr0.007542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76750.41151360.33491224X-RAY DIFFRACTION100
2.7675-2.84230.38141370.31831239X-RAY DIFFRACTION100
2.8423-2.9260.35341400.28771220X-RAY DIFFRACTION100
2.926-3.02040.35211320.28941256X-RAY DIFFRACTION100
3.0204-3.12840.31551370.27141226X-RAY DIFFRACTION100
3.1284-3.25360.32761480.26741255X-RAY DIFFRACTION100
3.2536-3.40170.27591390.2421239X-RAY DIFFRACTION100
3.4017-3.5810.26441310.2181251X-RAY DIFFRACTION100
3.581-3.80530.2651400.191255X-RAY DIFFRACTION100
3.8053-4.0990.20721350.18341247X-RAY DIFFRACTION100
4.099-4.51140.23171390.16051256X-RAY DIFFRACTION100
4.5114-5.16380.18111470.15951243X-RAY DIFFRACTION100
5.1638-6.50440.23171400.22161267X-RAY DIFFRACTION100
6.5044-56.91760.26981480.22641306X-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)
17.88530.35562.40193.24020.36633.01680.0227-1.2674-1.37550.4444-0.05480.58970.3522-0.6216-0.01220.60660.03250.24640.75060.27270.8629-2.9827.707521.7334
24.6018-3.37194.54964.7351-3.08638.18030.2477-0.5257-0.4010.14830.2926-0.23370.5723-0.091-0.51140.54620.0067-0.00190.52920.23350.892432.050519.851534.7094
32.128-2.4135-3.50542.13960.5962.2178-0.3241-0.52330.73970.7950.40380.1997-0.7722-0.2395-0.03281.0257-0.0810.0050.56970.10220.680828.551256.79448.7004
46.0749-0.15832.74049.0653-1.49429.00450.1637-0.5966-0.13160.8940.24520.60970.1886-0.407-0.29670.54690.04880.15880.43190.18420.508123.073642.797317.3728
55.6182-0.33122.84149.1067-1.47738.7072-0.17050.25320.57280.29590.0023-0.3162-0.6890.47140.2080.49840.00410.05680.37340.14090.522129.022551.786610.3545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 151 )
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 300 )
3X-RAY DIFFRACTION3chain 'B' and (resid 39 through 58 )
4X-RAY DIFFRACTION4chain 'B' and (resid 59 through 84 )
5X-RAY DIFFRACTION5chain 'B' and (resid 85 through 135 )

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