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- PDB-3dyt: Crystal structure of Snx9PX-BAR (230-595), C2221 -

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Basic information

Entry
Database: PDB / ID: 3dyt
TitleCrystal structure of Snx9PX-BAR (230-595), C2221
ComponentsSorting nexin-9
KeywordsTRANSPORT PROTEIN / 3-helix bundle / BAR domain / PX domain / Phosphoprotein / Protein transport / SH3 domain / Transport
Function / homology
Function and homology information


lipid tube assembly / plasma membrane tubulation / 1-phosphatidylinositol binding / cuticular plate / Arp2/3 complex binding / cleavage furrow formation / positive regulation of membrane protein ectodomain proteolysis / clathrin-coated vesicle / regulation of synaptic vesicle endocytosis / endosomal transport ...lipid tube assembly / plasma membrane tubulation / 1-phosphatidylinositol binding / cuticular plate / Arp2/3 complex binding / cleavage furrow formation / positive regulation of membrane protein ectodomain proteolysis / clathrin-coated vesicle / regulation of synaptic vesicle endocytosis / endosomal transport / positive regulation of actin filament polymerization / Golgi Associated Vesicle Biogenesis / mitotic cytokinesis / positive regulation of protein kinase activity / clathrin-coated pit / ruffle / receptor-mediated endocytosis / phosphatidylinositol binding / positive regulation of GTPase activity / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / endocytosis / Clathrin-mediated endocytosis / presynapse / cytoplasmic vesicle / protein-containing complex assembly / cadherin binding / ubiquitin protein ligase binding / protein homodimerization activity / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SNX9, SH3 domain / Sorting nexin-9, BAR domain / Sorting nexin-9, PX domain / Sorting nexin 9 family / Sorting nexin protein, WASP-binding domain / WASP-binding domain of Sorting nexin protein / Arfaptin homology (AH) domain/BAR domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. ...SNX9, SH3 domain / Sorting nexin-9, BAR domain / Sorting nexin-9, PX domain / Sorting nexin 9 family / Sorting nexin protein, WASP-binding domain / WASP-binding domain of Sorting nexin protein / Arfaptin homology (AH) domain/BAR domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsWang, Q. / Kaan, H.Y.K. / Sondermann, H.
CitationJournal: Structure / Year: 2008
Title: Structure and plasticity of endophilin and sorting nexin 9.
Authors: Wang, Q. / Kaan, H.Y. / Hooda, R.N. / Goh, S.L. / Sondermann, H.
History
DepositionJul 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Sorting nexin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1772
Polymers43,0811
Non-polymers961
Water2,576143
1
A: Sorting nexin-9
hetero molecules

A: Sorting nexin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3544
Polymers86,1622
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5660 Å2
ΔGint-53.6 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.000, 144.005, 103.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sorting nexin-9 / SH3 and PX domain-containing protein 1 / Protein SDP1 / SH3 and PX domain-containing protein 3A


Mass: 43081.141 Da / Num. of mol.: 1 / Fragment: UNP residues 230-595
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX9, SH3PX1, SH3PXD3A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y5X1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8M Ammonium sulfate, 0.1M Tris-HCl pH 8.5, 5% PEG 400, 0.05M MgSO4, 15% Xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2006 / Details: Mirrors
RadiationMonochromator: Horizontal focusing 5.05 degrees asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. all: 30311 / Num. obs: 30311 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 27.22 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.098 / Net I/σ(I): 20.6
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 14 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 9.6 / Num. unique all: 2984 / Rsym value: 0.316 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 2071 7.19 %Random
Rwork0.217 ---
all0.219 28804 --
obs0.219 28804 95.05 %-
Displacement parametersBiso mean: 2.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 5 143 3032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.099
X-RAY DIFFRACTIONf_dihedral_angle_d17.012
LS refinement shellResolution: 2.08→2.13 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.2447 127
Rwork0.2099 -
obs-1724

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