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- PDB-4fzs: Structure of human SNX1 BAR domain -

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Basic information

Entry
Database: PDB / ID: 4fzs
TitleStructure of human SNX1 BAR domain
ComponentsSorting nexin-1
KeywordsPROTEIN TRANSPORT / BAR / membrane remodeling
Function / homology
Function and homology information


retromer, tubulation complex / lamellipodium morphogenesis / leptin receptor binding / early endosome to Golgi transport / retromer complex / transferrin receptor binding / retrograde transport, endosome to Golgi / epidermal growth factor receptor binding / phosphatidylinositol binding / intracellular protein transport ...retromer, tubulation complex / lamellipodium morphogenesis / leptin receptor binding / early endosome to Golgi transport / retromer complex / transferrin receptor binding / retrograde transport, endosome to Golgi / epidermal growth factor receptor binding / phosphatidylinositol binding / intracellular protein transport / insulin receptor binding / receptor internalization / lamellipodium / early endosome membrane / vesicle / lysosome / endosome membrane / endosome / cadherin binding / protein heterodimerization activity / intracellular membrane-bounded organelle / Golgi apparatus / protein homodimerization activity / protein-containing complex / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Sorting nexin, N-terminal / Sorting nexin-1 / Sorting Nexin 1, PX domain / Sorting nexin, N-terminal domain / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Arfaptin homology (AH) domain/BAR domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain ...Sorting nexin, N-terminal / Sorting nexin-1 / Sorting Nexin 1, PX domain / Sorting nexin, N-terminal domain / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Arfaptin homology (AH) domain/BAR domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
Authorsvan Weering, J.R.T. / Sessions, R.B. / Traer, C.J. / Kloer, D.P. / Bhatia, V.K. / Stamou, D. / Hurley, J.H. / Cullen, P.J.
CitationJournal: To be Published
Title: Molecular insight into vesicle-to-tubule membrane remodeling by SNX-BAR proteins
Authors: van Weering, J.R.T. / Sessions, R.B. / Traer, C.J. / Kloer, D.P. / Bhatia, V.K. / Stamou, D. / Hurley, J.H. / Cullen, P.J.
History
DepositionJul 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-1
B: Sorting nexin-1


Theoretical massNumber of molelcules
Total (without water)53,0522
Polymers53,0522
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-41 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.990, 118.090, 61.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Sorting nexin-1 /


Mass: 26526.121 Da / Num. of mol.: 2 / Fragment: BAR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13596

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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: 59.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 1-3% PEG 20K, 0.1 M Tris pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 16580 / Num. obs: 15254 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 74.89 Å2
Reflection shellResolution: 2.8→3 Å / % possible all: 91.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 2.8→19.76 Å / Cor.coef. Fo:Fc: 0.9137 / Cor.coef. Fo:Fc free: 0.8912 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 719 4.71 %RANDOM
Rwork0.2282 ---
obs0.2296 15253 --
Displacement parametersBiso mean: 85.38 Å2
Baniso -1Baniso -2Baniso -3
1--28.0507 Å20 Å20 Å2
2---0.4105 Å20 Å2
3---28.4612 Å2
Refine analyzeLuzzati coordinate error obs: 0.479 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 0 0 3341
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013403HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.184576HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1280SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes116HARMONIC2
X-RAY DIFFRACTIONt_gen_planes467HARMONIC5
X-RAY DIFFRACTIONt_it3403HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion23.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion429SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3800SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 115 4.29 %
Rwork0.2655 2566 -
all0.2676 2681 -

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