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- PDB-5awr: Crystal structure of the SGIP1 mu homology domain in the P4212 sp... -

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Basic information

Entry
Database: PDB / ID: 5awr
TitleCrystal structure of the SGIP1 mu homology domain in the P4212 space group
ComponentsSH3-containing GRB2-like protein 3-interacting protein 1
KeywordsENDOCYTOSIS / Protein-protein interaction
Function / homology
Function and homology information


positive regulation of feeding behavior / AP-2 adaptor complex / clathrin-dependent endocytosis / clathrin-coated vesicle / response to dietary excess / energy homeostasis / clathrin-coated pit / actin filament polymerization / actin filament / phospholipid binding ...positive regulation of feeding behavior / AP-2 adaptor complex / clathrin-dependent endocytosis / clathrin-coated vesicle / response to dietary excess / energy homeostasis / clathrin-coated pit / actin filament polymerization / actin filament / phospholipid binding / positive regulation of receptor-mediated endocytosis / SH3 domain binding / actin filament binding / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / microtubule binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SGIP1, mu-homology domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile.
Similarity search - Domain/homology
SH3-containing GRB2-like protein 3-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.502 Å
AuthorsShimada, A. / Yamaguchi, A. / Kohda, D.
Funding support Japan, 3items
OrganizationGrant numberCountry
MEXT/JSPSKAKENHI 20687006 Japan
MEXT/JSPSKAKENHI 24687014 Japan
MEXT/JSPSKAKENHI 25121726 Japan
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 mu homology domain.
Authors: Shimada, A. / Yamaguchi, A. / Kohda, D.
History
DepositionJul 8, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3-containing GRB2-like protein 3-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3875
Polymers31,1261
Non-polymers2624
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.826, 109.826, 79.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein SH3-containing GRB2-like protein 3-interacting protein 1 / Endophilin-3-interacting protein


Mass: 31125.525 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 552-828
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SGIP1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQI5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.85 Å3/Da / Density % sol: 68.06 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: PEG 3350, zinc acetate, sodium acetate, sodium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97912 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17337 / % possible obs: 99.9 % / Redundancy: 32.4 % / Net I/σ(I): 25.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.502→38.829 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 28.34 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2473 1642 5.13 %
Rwork0.1991 --
obs0.2014 17337 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→38.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 4 38 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082114
X-RAY DIFFRACTIONf_angle_d1.142876
X-RAY DIFFRACTIONf_dihedral_angle_d15.047774
X-RAY DIFFRACTIONf_chiral_restr0.075328
X-RAY DIFFRACTIONf_plane_restr0.006372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.502-2.57570.35611600.33612491X-RAY DIFFRACTION99
2.5757-2.65880.33841380.30432569X-RAY DIFFRACTION100
2.6588-2.75380.30771410.26862499X-RAY DIFFRACTION100
2.7538-2.8640.37371390.25252521X-RAY DIFFRACTION100
2.864-2.99430.29661440.21722528X-RAY DIFFRACTION100
2.9943-3.15210.23481310.2372542X-RAY DIFFRACTION100
3.1521-3.34950.24061290.23342529X-RAY DIFFRACTION100
3.3495-3.60790.25671470.20652535X-RAY DIFFRACTION100
3.6079-3.97070.25891340.18852539X-RAY DIFFRACTION100
3.9707-4.54450.23211330.17052529X-RAY DIFFRACTION100
4.5445-5.72270.18151250.15442552X-RAY DIFFRACTION100
5.7227-38.8340.24071210.19582534X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.55042.0452-1.27692.3761-1.90143.59010.1045-0.44870.5690.220.1880.4215-0.4441-0.2323-0.27860.54990.01920.01520.3792-0.03240.38195.401775.729326.925
27.39371.3891-4.34463.0591-1.54488.3717-0.38851.1196-0.1014-0.6260.3372-0.0214-0.0443-0.57680.06120.638-0.2028-0.03170.6156-0.04480.45251.213367.041821.5269
32.71630.8259-1.29764.5433-0.64752.02970.4639-0.7040.58511.16590.11280.1398-0.8924-0.3454-0.51930.7512-0.05530.06880.7801-0.11040.5154.34271.08238.0052
49.32790.9586-0.74263.1702-0.86812.84690.0120.75010.8116-0.23660.20880.1999-0.22190.311-0.20190.6407-0.1119-0.02150.61080.08330.430425.995387.080611.3464
56.29752.106-0.33213.68410.33593.1876-0.1066-0.11930.84530.28830.0647-0.5583-0.48590.62770.05710.7142-0.2228-0.01930.62630.02640.57936.805991.152518.3309
69.05133.0961-2.73752.9801-1.08972.81030.0143-0.28190.91760.0960.21020.59-0.47730.0968-0.19790.54720.03920.01860.38490.06070.41059.996681.444222.7794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 557 through 616 )
2X-RAY DIFFRACTION2chain 'A' and (resid 617 through 648 )
3X-RAY DIFFRACTION3chain 'A' and (resid 649 through 678 )
4X-RAY DIFFRACTION4chain 'A' and (resid 679 through 722 )
5X-RAY DIFFRACTION5chain 'A' and (resid 723 through 787 )
6X-RAY DIFFRACTION6chain 'A' and (resid 788 through 828 )

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