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- PDB-4gxb: Structure of the SNX17 atypical FERM domain bound to the NPxY mot... -

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Basic information

Entry
Database: PDB / ID: 4gxb
TitleStructure of the SNX17 atypical FERM domain bound to the NPxY motif of P-selectin
Components
  • P-selectin
  • Sorting nexin-17
KeywordsPROTEIN TRANSPORT/CELL ADHESION / FERM domain / PROTEIN TRANSPORT-CELL ADHESION complex
Function / homology
Function and homology information


regulation of cellular extravasation / regulation of integrin activation / : / fucose binding / cardiac septum development / sialic acid binding / oligosaccharide binding / positive regulation of leukocyte tethering or rolling / Cell surface interactions at the vascular wall / Platelet degranulation ...regulation of cellular extravasation / regulation of integrin activation / : / fucose binding / cardiac septum development / sialic acid binding / oligosaccharide binding / positive regulation of leukocyte tethering or rolling / Cell surface interactions at the vascular wall / Platelet degranulation / platelet alpha granule membrane / leukocyte tethering or rolling / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / cholesterol catabolic process / coronary vasculature development / endocytic recycling / positive regulation of platelet activation / cellular response to interleukin-6 / low-density lipoprotein particle receptor binding / aorta development / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / endosomal transport / leukocyte cell-cell adhesion / leukocyte migration / plasma membrane => GO:0005886 / : / regulation of endocytosis / positive regulation of cell adhesion / receptor-mediated endocytosis / phosphatidylinositol binding / kidney development / lipopolysaccharide binding / intracellular protein transport / cell-cell adhesion / calcium-dependent protein binding / heparin binding / cytoplasmic vesicle / early endosome / endosome membrane / endosome / inflammatory response / external side of plasma membrane / signaling receptor binding / intracellular membrane-bounded organelle / calcium ion binding / Golgi apparatus / signal transduction / protein-containing complex / extracellular space / membrane / cytosol
Similarity search - Function
Acyl-CoA Binding Protein - #60 / Sorting nexin-17 / SNX17, atypical FERM-like domain / Sorting nexin-17/31, FERM domain / : / : / Sorting Nexin 17 FERM C-terminal domain / Sortin nexin 17/31, FERM domain, F2 lobe / Sortin nexin 17/27/31, FERM domain, F1 lobe / Selectin superfamily ...Acyl-CoA Binding Protein - #60 / Sorting nexin-17 / SNX17, atypical FERM-like domain / Sorting nexin-17/31, FERM domain / : / : / Sorting Nexin 17 FERM C-terminal domain / Sortin nexin 17/31, FERM domain, F2 lobe / Sortin nexin 17/27/31, FERM domain, F1 lobe / Selectin superfamily / Selectin, C-type lectin-like domain / SNX17/27/31 / Ras-associating (RA) domain profile. / Acyl-CoA Binding Protein / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / C-type lectin-like/link domain superfamily / PH-domain like / EGF-like domain / C-type lectin fold / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
P-selectin / Sorting nexin-17
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsGhai, R. / Bugarcic, A. / Liu, H. / Norwood, S.J. / Li, S.S. / Teasdale, R.D. / Collins, B.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for endosomal trafficking of diverse transmembrane cargos by PX-FERM proteins.
Authors: Ghai, R. / Bugarcic, A. / Liu, H. / Norwood, S.J. / Skeldal, S. / Coulson, E.J. / Li, S.S. / Teasdale, R.D. / Collins, B.M.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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-17
B: P-selectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3663
Polymers36,2742
Non-polymers921
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-10 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.754, 93.754, 91.308
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-598-

HOH

21A-799-

HOH

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Components

#1: Protein Sorting nexin-17 / / SNX17


Mass: 31950.572 Da / Num. of mol.: 1 / Fragment: FERM domain, UNP residues 111-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15036
#2: Protein/peptide P-selectin /


Mass: 4323.804 Da / Num. of mol.: 1 / Fragment: intracellular domain, UNP residues 735-768
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Selp / Production host: Escherichia coli (E. coli) / References: UniProt: Q01102
#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.: 371 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M sodium acetate, 0.2M magnesium chloride, 15% PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX110.95369
SYNCHROTRONAustralian Synchrotron MX120.99184
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDApr 11, 2011
ADSC QUANTUM 210r2CCDApr 11, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.991841
ReflectionResolution: 1.8→46.9 Å / Num. all: 43434 / Num. obs: 43434 / % possible obs: 100 % / Observed criterion σ(I): 3.2 / Redundancy: 22 % / Biso Wilson estimate: 19.99 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 18.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→40.597 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8825 / SU ML: 0.21 / σ(F): 0.03 / Phase error: 18.94 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2038 1945 4.59 %
Rwork0.1772 --
obs0.1785 42407 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.313 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 83.78 Å2 / Biso mean: 26.2759 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.558 Å20 Å2-0 Å2
2--0.558 Å20 Å2
3----1.116 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 6 371 2603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062289
X-RAY DIFFRACTIONf_angle_d0.9473098
X-RAY DIFFRACTIONf_chiral_restr0.069355
X-RAY DIFFRACTIONf_plane_restr0.004393
X-RAY DIFFRACTIONf_dihedral_angle_d12.236867
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7997-1.8640.22821710.20883751392291
1.864-1.93860.24431860.19743869405595
1.9386-2.02680.22421880.18263960414897
2.0268-2.13370.21881960.17064026422298
2.1337-2.26740.22931960.17344049424599
2.2674-2.44240.20132030.18074063426699
2.4424-2.68810.221940.17654101429599
2.6881-3.0770.20361970.17894133433099
3.077-3.87620.19532020.1641954397100
3.8762-40.6070.17342120.174343154527100

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