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- PDB-2rak: PI(3)P bound PX-BAR membrane remodeling unit of Sorting Nexin 9 -

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Basic information

Entry
Database: PDB / ID: 2rak
TitlePI(3)P bound 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 / 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
Chem-PIB / Sorting nexin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8512
Polymers45,2971
Non-polymers5541
Water00
1
A: Sorting nexin-9
hetero molecules

A: Sorting nexin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7034
Polymers90,5942
Non-polymers1,1092
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.059, 144.177, 118.245
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: 45297.027 Da / Num. of mol.: 1 / 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
#2: Chemical ChemComp-PIB / 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE / D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATED (+)-SN-1,2-DI-O-BUTANOYLGLYCERYL,3-O-PHOSPHO


Mass: 554.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32O16P2

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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: 3.01 Å3/Da / Density % sol: 59.19 %
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: 0.97955 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97955 Å / Relative weight: 1
ReflectionResolution: 3→19.89 Å / Num. obs: 12284 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 69.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.3
Reflection shellResolution: 3→3.1 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.372 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.89 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 4203491.47 / 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
Rfree0.293 565 5 %RANDOM
Rwork0.233 ---
all0.2331 11267 --
obs0.2331 11267 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.024 Å2 / ksol: 0.268283 e/Å3
Displacement parametersBiso mean: 62.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 22 0 3124
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 93 5 %
Rwork0.3 1759 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2pib-small-par.txtpib-small-top.txt

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