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- PDB-2rai: The PX-BAR membrane remodeling unit of Sorting Nexin 9 -

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Basic information

Entry
Database: PDB / ID: 2rai
TitleThe PX-BAR membrane remodeling unit of Sorting Nexin 9
ComponentsSorting nexin-9
KeywordsSTRUCTURAL PROTEIN / sorting nexin / membrane transport / PX domain / BAR domain / tubulation
Function / homology
Function and homology information


lipid tube assembly / cuticular plate / plasma membrane tubulation / 1-phosphatidylinositol binding / 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 / cuticular plate / plasma membrane tubulation / 1-phosphatidylinositol binding / Arp2/3 complex binding / cleavage furrow formation / positive regulation of membrane protein ectodomain proteolysis / clathrin-coated vesicle / regulation of synaptic vesicle endocytosis / endosomal transport / Golgi Associated Vesicle Biogenesis / positive regulation of actin filament polymerization / mitotic cytokinesis / positive regulation of protein kinase activity / clathrin-coated pit / ruffle / receptor-mediated endocytosis / phosphatidylinositol binding / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / positive regulation of GTPase activity / endocytosis / presynapse / Clathrin-mediated endocytosis / 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: 3.2 Å
AuthorsPylypenko, O. / Lundmark, R. / Rasmuson, E. / Carlsson, S.R. / Rak, A.
CitationJournal: Embo J. / Year: 2007
Title: The PX-BAR membrane-remodeling unit of sorting nexin 9
Authors: Pylypenko, O. / Lundmark, R. / Rasmuson, E. / Carlsson, S.R. / Rak, A.
History
DepositionSep 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-9
B: Sorting nexin-9


Theoretical massNumber of molelcules
Total (without water)91,9072
Polymers91,9072
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.632, 117.550, 145.814
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-9 / / SH3 and PX domain-containing protein 1 / Protein SDP1 / SH3 and PX domain-containing protein 3A


Mass: 45953.547 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, residues 214-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX9, SH3PX1, SH3PXD3A / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q9Y5X1

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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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.3M Ammonium tartrate dibasic, 0.1M BIS-TRIS propane, pH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97952 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 3.2→19.9 Å / Num. all: 35702 / Num. obs: 35702 / % possible obs: 99.2 % / Redundancy: 7.7 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.5

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Processing

Software
NameClassification
XDSdata scaling
CNSrefinement
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→19.76 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 3253538.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 955 5 %RANDOM
Rwork0.233 ---
all0.2331 19093 --
obs0.2331 19093 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.255989 e/Å3
Displacement parametersBiso mean: 60.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 3.2→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5919 0 0 0 5919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 157 5 %
Rwork0.269 2975 -
obs--99.8 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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