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- PDB-7ct1: Crystal structure of Snx27 FERM domain in complex with a DLF motif -

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Basic information

Entry
Database: PDB / ID: 7ct1
TitleCrystal structure of Snx27 FERM domain in complex with a DLF motif
ComponentsFusion protein Sorting nexin-27 and DLF motif
KeywordsTRANSPORT PROTEIN / Complex / snx27 / snx1
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 / 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 ...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 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.947 Å
AuthorsHu, W. / Da, J. / Sun, Q.
CitationJournal: To Be Published
Title: Crystal structure of Snx27 FERM domain in complex with a DLF motif
Authors: Hu, W. / Jia, D. / Sun, Q.
History
DepositionAug 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion protein Sorting nexin-27 and DLF motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5603
Polymers33,3761
Non-polymers1842
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-0 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.194, 72.941, 103.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fusion protein Sorting nexin-27 and DLF motif


Mass: 33375.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: SNX27, KIAA0488, My014 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96L92
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.09 M NPS 0.1 M Buffer System 3 pH8.5 50 % v/v Precipitant Mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.947→59.72 Å / Num. obs: 24036 / % possible obs: 96.8 % / Redundancy: 10.7 % / CC1/2: 0.999 / Net I/σ(I): 23.8
Reflection shellResolution: 1.95→2.05 Å / Num. unique obs: 3158 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.947→22.276 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.89 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2222 1183 4.94 %
Rwork0.1717 --
obs0.1741 23957 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.85 Å2 / Biso mean: 46.4014 Å2 / Biso min: 22.7 Å2
Refinement stepCycle: final / Resolution: 1.947→22.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 12 153 2354
Biso mean--75.3 50.52 -
Num. residues----263
Refinement TLS params.Method: refined / Origin x: 15.1667 Å / Origin y: 34.7715 Å / Origin z: 36.7214 Å
111213212223313233
T0.2615 Å20.0353 Å20.01 Å2-0.2449 Å20.0214 Å2--0.2441 Å2
L1.2364 °2-0.0311 °2-0.024 °2-1.4371 °2-0.0162 °2--0.6484 °2
S-0.0624 Å °-0.0736 Å °-0.0774 Å °0.1865 Å °0.0728 Å °-0.0191 Å °-0.0668 Å °-0.0358 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA274 - 602
2X-RAY DIFFRACTION1allS1 - 154

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