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- PDB-5awu: Crystal structure of the SGIP1 mu homology domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 5awu
TitleCrystal structure of the SGIP1 mu homology domain in complex with an Eps15 fragment containing two DPF motifs (YDPFKGSDPFA)
Components
  • Epidermal growth factor receptor substrate 15
  • SH3-containing GRB2-like protein 3-interacting protein 1
KeywordsENDOCYTOSIS / Protein-protein interaction
Function / homology
Function and homology information


positive regulation of feeding behavior / Golgi to endosome transport / clathrin coat of coated pit / AP-2 adaptor complex / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / clathrin-dependent endocytosis / endocytic recycling / aggresome ...positive regulation of feeding behavior / Golgi to endosome transport / clathrin coat of coated pit / AP-2 adaptor complex / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / clathrin-dependent endocytosis / endocytic recycling / aggresome / clathrin-coated vesicle / endosomal transport / positive regulation of receptor recycling / response to dietary excess / polyubiquitin modification-dependent protein binding / energy homeostasis / clathrin-coated pit / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / phospholipid binding / EGFR downregulation / Negative regulation of MET activity / SH3 domain binding / endocytosis / positive regulation of receptor-mediated endocytosis / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / regulation of cell population proliferation / microtubule binding / early endosome membrane / postsynapse / receptor-mediated endocytosis of virus by host cell / cadherin binding / symbiont entry into host cell / apical plasma membrane / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SGIP1, mu-homology domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. ...SGIP1, mu-homology domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Epidermal growth factor receptor substrate 15 / SH3-containing GRB2-like protein 3-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShimada, A. / Yamaguchi, A. / Kohda, D.
Funding support Japan, 2items
OrganizationGrant numberCountry
MEXT/JSPSKAKENHI 20687006 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
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SH3-containing GRB2-like protein 3-interacting protein 1
B: Epidermal growth factor receptor substrate 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3506
Polymers32,0882
Non-polymers2624
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-91 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.562, 109.562, 80.094
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: 30844.158 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: Protein/peptide Epidermal growth factor receptor substrate 15 / Eps15


Mass: 1244.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42566*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, zinc acetate, sodium acetate, sodium iodide
PH range: 5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 14137 / % possible obs: 99.8 % / Redundancy: 12 % / Net I/σ(I): 9.8

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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: MOLECULAR REPLACEMENT
Starting model: 5AWR

5awr


Resolution: 2.7→37.613 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 711 5.05 %
Rwork0.2086 --
obs0.2104 14087 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→37.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 4 7 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152191
X-RAY DIFFRACTIONf_angle_d1.1822977
X-RAY DIFFRACTIONf_dihedral_angle_d14.618799
X-RAY DIFFRACTIONf_chiral_restr0.08336
X-RAY DIFFRACTIONf_plane_restr0.007385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.88580.34571450.30642530X-RAY DIFFRACTION96
2.8858-3.17610.28961440.26842635X-RAY DIFFRACTION100
3.1761-3.63540.31151430.22182668X-RAY DIFFRACTION100
3.6354-4.57890.22521370.20282707X-RAY DIFFRACTION100
4.5789-37.61680.21111420.1842836X-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)
10.3239-2.29521.58164.4139-5.4914.4473-0.08120.085-0.14480.8-0.17270.018-1.0027-0.12770.20160.83620.0711-0.04750.86040.02990.597732.761311.1085104.2806
28.18681.0611-3.15275.9631-1.23188.75420.38430.5044-0.5877-0.2647-0.46210.01810.8963-0.0975-0.03520.75780.1351-0.13060.5863-0.13210.599938.8917-2.0648106.6833
35.31914.25214.71723.88964.19974.5388-0.75450.77630.2626-1.71450.14970.5407-1.42340.59470.28020.97970.0995-0.08310.7528-0.00650.72444.1737-1.6708105.0371
47.6771-1.769-2.38944.24612.15786.8593-0.5645-2.11230.3651.250.63770.1589-0.3686-1.0984-0.16060.85060.180.12051.11250.05810.547738.51324.6357118.6947
54.49331.96870.37122.8225-2.97324.61860.20860.5601-0.0393-0.4483-0.0230.4113-0.1706-0.0974-0.26790.88160.1751-0.08560.8192-0.04280.562122.631126.033791.4565
66.1186-3.0107-0.7099.2132-1.24062.84990.4141-0.21790.35170.1295-0.2570.7454-0.5812-0.2975-0.11610.83510.1561-0.00250.8231-0.07460.541119.152235.004898.9454
74.1812-3.3831.44852.8407-2.25313.41080.24840.18-0.8403-0.2183-0.07390.70320.2741-0.577-0.08840.7104-0.1151-0.07620.7487-0.01690.606629.14387.4362103.2285
83.69473.0967-5.67833.2743-4.97938.92470.68641.05481.87111.21650.30463.5334-0.403-0.5994-0.94021.09210.41010.27551.23290.26311.287525.83687.6258116.2122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 559 through 601 )
2X-RAY DIFFRACTION2chain 'A' and (resid 602 through 625 )
3X-RAY DIFFRACTION3chain 'A' and (resid 626 through 648 )
4X-RAY DIFFRACTION4chain 'A' and (resid 649 through 678 )
5X-RAY DIFFRACTION5chain 'A' and (resid 679 through 722 )
6X-RAY DIFFRACTION6chain 'A' and (resid 723 through 794 )
7X-RAY DIFFRACTION7chain 'A' and (resid 795 through 828 )
8X-RAY DIFFRACTION8chain 'B' and (resid 644 through 654 )

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