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- PDB-3dyu: Crystal structure of Snx9PX-BAR (230-595), H32 -

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Basic information

Entry
Database: PDB / ID: 3dyu
TitleCrystal structure of Snx9PX-BAR (230-595), H32
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 / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology ...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 / 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 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 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Sorting nexin-9


Theoretical massNumber of molelcules
Total (without water)127,2743
Polymers127,2743
Non-polymers00
Water00
1
A: Sorting nexin-9
B: Sorting nexin-9


Theoretical massNumber of molelcules
Total (without water)84,8492
Polymers84,8492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-47.3 kcal/mol
Surface area37870 Å2
MethodPISA
2
C: Sorting nexin-9

C: Sorting nexin-9


Theoretical massNumber of molelcules
Total (without water)84,8492
Polymers84,8492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area6410 Å2
ΔGint-47.6 kcal/mol
Surface area37500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.765, 131.765, 569.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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: 42424.609 Da / Num. of mol.: 3 / Fragment: UNP residues 230-595
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX9, SH3PX1, SH3PXD3A / Plasmid: pProExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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: 3.73 Å3/Da / Density % sol: 67.07 %
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: APS / Beamline: 24-ID-C / Wavelength: 0.9771 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 17, 2006 / Details: Mirrors
RadiationMonochromator: KOHZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9771 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. all: 15467 / Num. obs: 15467 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 129.53 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.109 / Net I/σ(I): 25.9
Reflection shellResolution: 4.1→4.25 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 3 / Rsym value: 0.483 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2RAK, 3DYT

2rak

3dyt


Resolution: 4.1→32.94 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 32734.29 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT AND NOT REFINED DUE TO VERY LOW RESOLUTION OF THE DATA COLLECTED. THE ONLY MODIFICATION PERFORMED TO THE OBTAINED MODEL FROM MOLECULAR ...Details: STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT AND NOT REFINED DUE TO VERY LOW RESOLUTION OF THE DATA COLLECTED. THE ONLY MODIFICATION PERFORMED TO THE OBTAINED MODEL FROM MOLECULAR REPLACEMENT WAS SOME RIGID BODY ADJUSTMENT OF HELICAL TIPS AND DOMAINS (RESIDUES 507-548, RESIDUES 230-390, RESIDUES 391-595) ACCORDING TO THE ELECTRON DENSITY. AUTHORS DID NOT HAVE ENOUGH DATA TO SEE THE SIDE CHAIN POSITIONS. THE CLASHES BETWEEN SIDE CHAINS OF SURFACE RESIDUES WERE REMOVED USING ALTERNATIVE ROTAMER CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.403 682 5 %RANDOM
Rwork0.388 ---
obs0.388 13767 89.2 %-
all-13767 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 102.447 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 153.1 Å2
Baniso -1Baniso -2Baniso -3
1-17.36 Å20 Å20 Å2
2--17.36 Å20 Å2
3----34.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.85 Å0.96 Å
Luzzati d res low-5 Å
Luzzati sigma a2.54 Å1.21 Å
Refinement stepCycle: LAST / Resolution: 4.1→32.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8931 0 0 0 8931
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.56
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 4.1→4.36 Å / Rfactor Rfree error: 0.061 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.573 87 4.8 %
Rwork0.461 1739 -
obs--72.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP

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