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- PDB-3g9g: Crystal Structure of the N-terminal EFC/F-BAR domain of Syp1 -

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Basic information

Entry
Database: PDB / ID: 3g9g
TitleCrystal Structure of the N-terminal EFC/F-BAR domain of Syp1
ComponentsSuppressor of yeast profilin deletion
KeywordsENDOCYTOSIS / Syp1 / BAR domain / FCH / adaptor / Phosphoprotein
Function / homology
Function and homology information


endocytic patch / Syp1 complex / Clathrin-mediated endocytosis / mating projection base / budding cell bud growth / septin cytoskeleton organization / cellular bud neck septin ring / unidimensional cell growth / actin cortical patch assembly / prospore membrane ...endocytic patch / Syp1 complex / Clathrin-mediated endocytosis / mating projection base / budding cell bud growth / septin cytoskeleton organization / cellular bud neck septin ring / unidimensional cell growth / actin cortical patch assembly / prospore membrane / cellular bud tip / cellular bud neck / mating projection tip / enzyme inhibitor activity / cell division site / positive regulation of endocytosis / endocytic vesicle / endocytosis / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Arfaptin homology (AH) domain/BAR domain / Mu homology domain / Mu homology domain (MHD) profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Suppressor of yeast profilin deletion
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsReider, A. / Barker, S. / Mishra, S. / Im, Y.J. / Maldonado-Baez, L. / Hurley, J. / Traub, L. / Wendland, B.
CitationJournal: Embo J. / Year: 2009
Title: Syp1 is a conserved endocytic adaptor that contains domains involved in cargo selection and membrane tubulation.
Authors: Reider, A. / Barker, S.L. / Mishra, S.K. / Im, Y.J. / Maldonado-Baez, L. / Hurley, J.H. / Traub, L.M. / Wendland, B.
History
DepositionFeb 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: Suppressor of yeast profilin deletion


Theoretical massNumber of molelcules
Total (without water)33,4871
Polymers33,4871
Non-polymers00
Water3,657203
1
A: Suppressor of yeast profilin deletion

A: Suppressor of yeast profilin deletion


Theoretical massNumber of molelcules
Total (without water)66,9752
Polymers66,9752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+11
Buried area7960 Å2
ΔGint-68 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.940, 97.950, 138.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Suppressor of yeast profilin deletion


Mass: 33487.336 Da / Num. of mol.: 1 / Fragment: The N-terminal EFC/F-BAR domain, residues 1-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SYP1, YCR030C, YCR30C/YCR29C / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25623
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M NaCitrate pH 5.6, 0.2M Ammonium acetate, 20% PEG-3350, 3% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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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: Apr 22, 2008 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 14793 / Num. obs: 14372 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 6.7 % / Biso Wilson estimate: 32.5 Å2 / Rsym value: 0.14
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 1390 / Rsym value: 0.441 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→28.37 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3502163.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 652 5 %RANDOM
Rwork0.189 ---
all0.191 13646 --
obs0.189 12994 89.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.9141 Å2 / ksol: 0.327197 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--2.63 Å20 Å2
3----3.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 0 203 2285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
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: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 93 5 %
Rwork0.19 1758 -
obs--78.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater_rep.top

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