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

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Basic information

Entry
Database: PDB / ID: 5elq
TitleCrystal structure of the SNX27 PDZ domain bound to the C-terminal DGKzeta PDZ binding motif
Components
  • GLU-ASP-GLN-GLU-THR-ALA-VAL
  • Sorting nexin-27
KeywordsPROTEIN TRANSPORT / Endosome / PDZ domain / sorting nexin
Function / homology
Function and homology information


alkylglycerol kinase / alkylglycerol kinase activity / lipid phosphorylation / glycerolipid metabolic process / diacylglycerol metabolic process / postsynaptic early endosome / diacylglycerol kinase (ATP) / lipid kinase activity / ATP-dependent diacylglycerol kinase activity / establishment of protein localization to plasma membrane ...alkylglycerol kinase / alkylglycerol kinase activity / lipid phosphorylation / glycerolipid metabolic process / diacylglycerol metabolic process / postsynaptic early endosome / diacylglycerol kinase (ATP) / lipid kinase activity / ATP-dependent diacylglycerol kinase activity / establishment of protein localization to plasma membrane / phosphatidic acid biosynthetic process / positive regulation of AMPA glutamate receptor clustering / response to methamphetamine hydrochloride / neurotransmitter receptor transport to plasma membrane / WASH complex / postsynaptic recycling endosome / Effects of PIP2 hydrolysis / retromer complex / endosome to plasma membrane protein transport / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / endosomal transport / negative regulation of T cell receptor signaling pathway / endosome to lysosome transport / immunological synapse / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / mitotic G1 DNA damage checkpoint signaling / phosphatidylinositol binding / intracellular protein transport / cellular response to nerve growth factor stimulus / Schaffer collateral - CA1 synapse / platelet activation / calcium-dependent protein binding / kinase activity / cell migration / nervous system development / lamellipodium / early endosome membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / early endosome / postsynapse / endosome / intracellular signal transduction / nuclear speck / glutamatergic synapse / signal transduction / ATP binding / metal ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Diacylglycerol kinase / Diacylglycerol kinase, accessory domain / Diacylglycerol kinase accessory domain / Diacylglycerol kinase accessory domain (presumed) / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / Diacylglycerol kinase, catalytic domain ...: / : / Diacylglycerol kinase / Diacylglycerol kinase, accessory domain / Diacylglycerol kinase accessory domain / Diacylglycerol kinase accessory domain (presumed) / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Phorbol esters/diacylglycerol binding domain (C1 domain) / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Diacylglycerol kinase zeta / Sorting nexin-27
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsCollins, B.M. / Clairfeuille, T.
Funding support Australia, 1items
OrganizationGrant numberCountry
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 5, 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
P: GLU-ASP-GLN-GLU-THR-ALA-VAL
B: Sorting nexin-27
C: GLU-ASP-GLN-GLU-THR-ALA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8138
Polymers23,0364
Non-polymers7774
Water4,720262
1
A: Sorting nexin-27
P: GLU-ASP-GLN-GLU-THR-ALA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7123
Polymers11,5182
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-4 kcal/mol
Surface area6680 Å2
MethodPISA
2
B: Sorting nexin-27
C: GLU-ASP-GLN-GLU-THR-ALA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1015
Polymers11,5182
Non-polymers5833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-2 kcal/mol
Surface area5970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.940, 54.120, 74.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

21A-409-

HOH

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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.: 2 / 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-ASP-GLN-GLU-THR-ALA-VAL


Mass: 947.966 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13574*PLUS
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 2.0 M Ammonium citrate, 5% PEG400

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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: 1.1→14.9 Å / Num. obs: 80541 / % possible obs: 99.8 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.5
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3.3 / % possible all: 99.6

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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: 1.1→14.9 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1803 3934 5.03 %
Rwork0.1628 --
obs0.1636 78149 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 52 262 1834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081586
X-RAY DIFFRACTIONf_angle_d1.2712118
X-RAY DIFFRACTIONf_dihedral_angle_d16.192618
X-RAY DIFFRACTIONf_chiral_restr0.073242
X-RAY DIFFRACTIONf_plane_restr0.007278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11340.2491240.24662426X-RAY DIFFRACTION90
1.1134-1.12750.22651500.23772470X-RAY DIFFRACTION92
1.1275-1.14230.25911460.23482515X-RAY DIFFRACTION93
1.1423-1.1580.23861160.21522538X-RAY DIFFRACTION94
1.158-1.17450.2281220.2122540X-RAY DIFFRACTION94
1.1745-1.1920.24621600.20072519X-RAY DIFFRACTION94
1.192-1.21070.20671260.20682549X-RAY DIFFRACTION94
1.2107-1.23050.20261420.19622562X-RAY DIFFRACTION95
1.2305-1.25170.19181280.19782581X-RAY DIFFRACTION95
1.2517-1.27450.21391400.19252597X-RAY DIFFRACTION96
1.2745-1.2990.21571420.18812614X-RAY DIFFRACTION97
1.299-1.32550.20911310.18122685X-RAY DIFFRACTION97
1.3255-1.35430.19771490.17332619X-RAY DIFFRACTION97
1.3543-1.38570.17581490.16952634X-RAY DIFFRACTION98
1.3857-1.42040.20711440.17182621X-RAY DIFFRACTION98
1.4204-1.45870.15681270.16482711X-RAY DIFFRACTION98
1.4587-1.50160.17291510.16022664X-RAY DIFFRACTION99
1.5016-1.550.15811390.1492701X-RAY DIFFRACTION98
1.55-1.60540.16841460.1562685X-RAY DIFFRACTION99
1.6054-1.66960.16211370.14862729X-RAY DIFFRACTION99
1.6696-1.74550.18051500.14882739X-RAY DIFFRACTION99
1.7455-1.83730.15451520.15112706X-RAY DIFFRACTION99
1.8373-1.95220.15041320.13862755X-RAY DIFFRACTION100
1.9522-2.10260.15911310.13282761X-RAY DIFFRACTION100
2.1026-2.31350.16211500.13082785X-RAY DIFFRACTION100
2.3135-2.64660.15641600.14872762X-RAY DIFFRACTION100
2.6466-3.32830.19111410.15652832X-RAY DIFFRACTION100
3.3283-14.93610.17551490.16512915X-RAY DIFFRACTION99
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)
12.9803-1.20850.31332.28150.43712.58050.05240.2479-0.18810.0057-0.06650.03010.2449-0.0523-0.0320.0636-0.0134-0.00470.068-0.00610.068852.90529.671756.6284
21.73440.41082.50953.8384-3.46748.1911-0.111-0.13360.0670.29580.01690.0274-0.53150.00380.1110.09370.02330.01410.0897-0.02920.074253.802222.800574.5444
35.98671.7087-1.20597.32430.75716.99110.1077-0.0605-0.505-0.1528-0.16050.84220.3886-0.74360.02490.1174-0.0337-0.01530.1662-0.00510.176950.54149.710378.973
41.84680.46271.67061.54771.91975.04050.10910.0086-0.150.0689-0.08680.02490.247-0.1952-0.0110.063-0.007-0.00610.0762-0.00030.075747.400610.004460.4929
51.89732.1109-0.54637.5206-2.0354.3892-0.0442-0.1478-0.00890.27650.10560.16120.182-0.0739-0.02410.0677-0.0036-0.0060.06510.00020.037654.980210.749168.353
61.677-0.5785-0.09910.55890.124.03540.0729-0.01340.07390.03180.0283-0.0272-0.07960.1072-0.08660.0567-0.00930.00490.0618-0.01240.068259.134517.615965.5651
73.92941.3981-3.29813.7046-2.41267.6663-0.02490.3238-0.11670.00970.0957-0.00170.2159-0.1924-0.01470.0431-0.0024-0.02420.0788-0.02640.066458.21129.584259.1476
85.59420.93630.58856.6148-0.13846.1160.0113-0.23790.5120.2699-0.05390.1382-0.4368-0.15420.02970.09250.0052-0.00350.0838-0.00580.121649.13622.970261.7309
92.93731.01130.66182.30940.07882.02780.0327-0.1241-0.1209-0.0289-0.0040.03980.1924-0.0627-0.0290.06510.0088-0.010.04540.00460.065569.43459.096993.2818
101.39120.4762.242.51783.05518.3388-0.16380.11640.1071-0.2841-0.03290.0302-0.6759-0.20280.15190.1591-0.0136-0.00540.08850.02780.091668.500122.760975.9854
112.6612-2.1316-0.62533.0593-1.24457.79660.0628-0.0662-0.44640.1118-0.0658-0.79810.53460.88310.06130.13380.0314-0.00440.1601-0.00060.197371.931710.103170.7542
121.03420.14430.27121.3635-1.04312.54650.0421-0.017-0.099-0.0204-0.0792-0.06490.0990.14020.03110.05110.0013-0.00870.03180.00090.057574.283710.395590.1358
137.02194.9871-5.47755.1828-3.32984.73280.0327-0.3011-0.36730.0544-0.2587-0.4570.52160.41110.1170.11810.0204-0.02250.07250.01770.09876.79226.884887.6866
142.0885-2.9114-1.92756.83742.0844.8319-0.0140.1020.0396-0.29580.0831-0.12570.1771-0.0168-0.00980.07460.0012-0.00770.04590.0030.0467.44910.45881.543
152.19770.67620.20871.2525-0.23524.06040.0365-0.02330.0443-0.03170.01860.0227-0.1203-0.2235-0.03940.04930.0156-0.00150.05790.01070.056763.229817.172584.6811
164.1501-1.3385-3.26733.51572.44598.1448-0.0168-0.2972-0.09810.01180.10930.0160.26690.04590.0410.0474-0.0014-0.0270.06850.02790.068364.13739.026490.733
173.5774-0.49490.17475.9175-0.19883.2926-0.0370.17390.4118-0.18360.0236-0.0583-0.28880.0698-0.01470.0936-0.0039-0.01810.05280.00770.106573.435522.473888.6636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 104 )
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 121 )
7X-RAY DIFFRACTION7chain 'A' and (resid 122 through 134 )
8X-RAY DIFFRACTION8chain 'P' and (resid 201 through 207 )
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 58 )
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 67 )
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 75 )
12X-RAY DIFFRACTION12chain 'B' and (resid 76 through 93 )
13X-RAY DIFFRACTION13chain 'B' and (resid 94 through 99 )
14X-RAY DIFFRACTION14chain 'B' and (resid 100 through 104 )
15X-RAY DIFFRACTION15chain 'B' and (resid 105 through 121 )
16X-RAY DIFFRACTION16chain 'B' and (resid 122 through 134 )
17X-RAY DIFFRACTION17chain 'C' and (resid 201 through 207 )

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