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- PDB-4has: Crystal structure of PX domain of human sorting nexin SNX27 -

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Basic information

Entry
Database: PDB / ID: 4has
TitleCrystal structure of PX domain of human sorting nexin SNX27
ComponentsSorting nexin-27
KeywordsPROTEIN TRANSPORT / Structural Genomics / Structural Genomics Consortium / SGC / PX Domain
Function / homology
Function and homology information


establishment of natural killer cell polarity / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / endosomal transport / endosome to lysosome transport / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / phosphatidylinositol binding / intracellular protein transport ...establishment of natural killer cell polarity / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / endosomal transport / endosome to lysosome transport / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / phosphatidylinositol binding / intracellular protein transport / Schaffer collateral - CA1 synapse / early endosome membrane / early endosome / endosome / intracellular membrane-bounded organelle / glutamatergic synapse / signal transduction / cytosol
Similarity search - Function
SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Phox-like domain / PX Domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. ...SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Phox-like domain / PX Domain / 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 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Sorting nexin-27
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsFroese, D.S. / Krojer, T. / Strain-Damerell, C. / Allerston, C. / Kiyani, W. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Bountra, C. / Edwards, A. ...Froese, D.S. / Krojer, T. / Strain-Damerell, C. / Allerston, C. / Kiyani, W. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Bountra, C. / Edwards, A. / Yue, W.W. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of PX domain of human sorting nexin SNX27
Authors: Froese, D.S. / Krojer, T. / Strain-Damerell, C. / Allerston, C. / Kiyani, W. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Bountra, C. / Edwards, A. / Yue, W.W. / Structural Genomics Consortium (SGC)
History
DepositionSep 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-27
B: Sorting nexin-27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8044
Polymers31,5502
Non-polymers2542
Water4,882271
1
A: Sorting nexin-27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0293
Polymers15,7751
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sorting nexin-27


Theoretical massNumber of molelcules
Total (without water)15,7751
Polymers15,7751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.580, 47.820, 96.550
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


Mass: 15774.845 Da / Num. of mol.: 2 / Fragment: PX domain (UNP residues 156-265)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX27, KIAA0488, My014 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96L92
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 1.74 Å3/Da / Density % sol: 29.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% PEG 3.3k, 0.1M citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→33.97 Å / Num. all: 23145 / Num. obs: 23145 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 15.1
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 2.9 / % possible all: 95.9

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1065)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→33.974 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1175 5.12 %random THROUGHOUT
Rwork0.1633 ---
obs0.1653 22956 98.5 %-
all-22956 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→33.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 17 271 1977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071772
X-RAY DIFFRACTIONf_angle_d1.0132398
X-RAY DIFFRACTIONf_dihedral_angle_d15.217669
X-RAY DIFFRACTIONf_chiral_restr0.07250
X-RAY DIFFRACTIONf_plane_restr0.005317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.81920.30181410.2312626X-RAY DIFFRACTION97
1.8192-1.91510.23371440.18422642X-RAY DIFFRACTION97
1.9151-2.03510.22331570.1792652X-RAY DIFFRACTION98
2.0351-2.19220.22261450.15662682X-RAY DIFFRACTION98
2.1922-2.41270.19461630.15852692X-RAY DIFFRACTION99
2.4127-2.76170.24291330.16922762X-RAY DIFFRACTION99
2.7617-3.47890.19211510.15282776X-RAY DIFFRACTION100
3.4789-33.980.16381410.15492949X-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)
11.7813-0.06470.5033.00210.26082.80460.0741-0.1842-0.168-0.03120.10170.30620.1573-0.39640.00880.083-0.0292-0.01580.09460.02590.0691-2.7567-19.4164-17.954
21.170.65650.73282.10370.6741.9665-0.0266-0.04540.1077-0.00950.00250.0242-0.0851-0.111-0.04050.08140.0080.01380.06140.01960.07420.9511-8.9319-8.6844
32.7015-0.89872.29031.8108-1.08483.87450.04610.18690.1972-0.1938-0.0183-0.07490.01040.0393-0.00570.0912-0.01170.02620.07230.01460.07530.2183-9.5858-21.735
43.83592.0029-1.21062.24932.01556.1796-0.0341-0.0286-0.93770.2186-0.1711-0.63540.49510.041-0.25810.12640.0362-0.05250.09470.00760.16611.6362-13.2777-2.4496
57.6212.092-0.62115.304-0.33562.8926-0.1724-0.2215-0.32720.20440.44660.1608-0.0675-0.4362-0.05550.1316-0.0148-0.00640.06270.02490.06490.6146-17.9075-4.5041
67.43050.89661.76743.4051-0.2583.2602-0.22370.0053-0.17720.28020.325-0.0070.2640.4605-0.1790.12730.0457-0.00470.1368-0.00690.0661-5.908-38.703511.5736
73.3848-0.10942.44813.20041.83816.2066-0.3429-0.17740.0197-0.14760.4332-0.3474-0.40550.3801-0.10790.06370.01570.03060.1088-0.02880.0909-3.6319-36.79511.5875
82.03660.7617-1.02812.6787-1.43753.6909-0.08570.18290.0236-0.24570.0473-0.14590.0348-0.22680.0280.07720.01230.03650.1132-0.00670.1034-3.7249-35.6134-2.1914
97.01623.52522.49962.56431.14591.7248-0.01760.7588-0.4603-0.4620.1368-0.2174-0.07810.3474-0.03050.14330.04380.01880.2306-0.03250.1333-11.4551-28.8784-5.3698
101.4773-0.3346-0.53523.18242.43994.4517-0.018-0.1325-0.04290.1172-0.04220.14640.0431-0.18440.11570.04760.01130.01860.06310.02510.0975-12.0645-30.09926.8257
115.5566-1.23341.32453.8491-0.4494.3643-0.10930.3438-0.3489-0.15370.0565-0.09360.02660.02520.03960.1518-0.01710.06250.1234-0.04720.1518-4.5891-42.6564-6.0232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 171 through 198 )
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 229 )
3X-RAY DIFFRACTION3chain 'A' and (resid 230 through 257 )
4X-RAY DIFFRACTION4chain 'A' and (resid 258 through 264 )
5X-RAY DIFFRACTION5chain 'A' and (resid 265 through 274 )
6X-RAY DIFFRACTION6chain 'B' and (resid 172 through 186 )
7X-RAY DIFFRACTION7chain 'B' and (resid 187 through 196 )
8X-RAY DIFFRACTION8chain 'B' and (resid 197 through 224 )
9X-RAY DIFFRACTION9chain 'B' and (resid 225 through 229 )
10X-RAY DIFFRACTION10chain 'B' and (resid 230 through 256 )
11X-RAY DIFFRACTION11chain 'B' and (resid 257 through 274 )

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