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

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Basic information

Entry
Database: PDB / ID: 5awt
TitleCrystal structure of the SGIP1 mu homology domain in complex with an Eps15 fragment containing two DPF motifs (YDPFGGDPFKG)
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 / ubiquitin-dependent endocytosis / Golgi to endosome transport / clathrin coat of coated pit / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / vesicle organization / clathrin coat assembly / clathrin-dependent endocytosis ...positive regulation of feeding behavior / ubiquitin-dependent endocytosis / Golgi to endosome transport / clathrin coat of coated pit / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / vesicle organization / clathrin coat assembly / clathrin-dependent endocytosis / endocytic recycling / clathrin-coated vesicle / aggresome / endosomal transport / ciliary membrane / response to dietary excess / positive regulation of receptor recycling / polyubiquitin modification-dependent protein binding / synaptic vesicle endocytosis / energy homeostasis / receptor-mediated endocytosis of virus by host cell / clathrin-coated pit / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / ubiquitin binding / EGFR downregulation / Negative regulation of MET activity / phospholipid binding / positive regulation of receptor-mediated endocytosis / SH3 domain binding / endocytosis / Cargo recognition for clathrin-mediated endocytosis / presynapse / regulation of cell population proliferation / Clathrin-mediated endocytosis / regulation of protein localization / early endosome membrane / microtubule binding / apical plasma membrane / cadherin binding / intracellular membrane-bounded organelle / calcium ion binding / symbiont entry into host cell / glutamatergic synapse / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SGIP1, mu-homology domain / Muniscin C-terminal / Muniscin C-terminal mu homology domain / EH domain / 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 / EH domain / 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: 2.702 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
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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)32,4378
Polymers32,0442
Non-polymers3926
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.716, 107.716, 79.978
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: 1200.277 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.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66.02 %
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: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13428 / % possible obs: 100 % / Redundancy: 14.1 % / Net I/σ(I): 26.8

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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: 2.702→41.265 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 661 4.93 %
Rwork0.1884 --
obs0.1906 13396 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.702→41.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 6 35 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122191
X-RAY DIFFRACTIONf_angle_d1.4482978
X-RAY DIFFRACTIONf_dihedral_angle_d15.129800
X-RAY DIFFRACTIONf_chiral_restr0.093335
X-RAY DIFFRACTIONf_plane_restr0.008386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7024-2.9110.25251430.24892469X-RAY DIFFRACTION100
2.911-3.20380.29931250.23152494X-RAY DIFFRACTION100
3.2038-3.66710.26491290.20392511X-RAY DIFFRACTION100
3.6671-4.61920.24121480.17062545X-RAY DIFFRACTION100
4.6192-41.26980.19721160.17522716X-RAY DIFFRACTION100
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)
13.3556-2.04941.44656.5796-4.53228.2095-0.088-0.2919-0.34880.4592-0.2704-0.1239-0.20310.00830.3950.25280.03650.03030.3885-0.01970.267431.9311.755103.083
26.34670.64020.39567.4855-1.78738.50850.07710.5895-0.2898-0.5189-0.192-0.0921.09080.5580.04890.45720.1779-0.050.3475-0.03410.487439.659-1.784107.256
35.4047-1.1007-0.6124.8810.64193.729-0.2849-1.75280.22371.23450.30480.4426-0.2776-0.0915-0.12210.55380.12350.10510.86890.10320.405438.4731.938119.789
43.7811-0.08430.24784.4563-1.34023.58220.12110.3851-0.1751-0.7370.02350.6648-0.1233-0.0951-0.12060.57990.1362-0.08530.4685-0.05460.342324.62724.79291.379
54.6126-0.9568-0.34596.0437-0.61983.36780.127-0.24080.49170.545-0.15331.1554-0.8621-0.38590.00170.64140.1967-0.03470.5361-0.0520.472118.533434.992198.5151
61.9672-3.39351.28463.2588-2.62474.48990.2126-0.1851-0.59590.08510.0611.01870.1374-0.406-0.24420.3383-0.0866-0.07060.42320.08120.470728.34497.4838103.0902
79.0885-0.75624.36966.09366.37859.6060.3231-0.96930.31120.556-0.7970.67210.7717-0.50150.24141.05230.08630.29040.77110.21910.837925.40987.3119116.1961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 558 through 599 )
2X-RAY DIFFRACTION2chain 'A' and (resid 600 through 643 )
3X-RAY DIFFRACTION3chain 'A' and (resid 644 through 673 )
4X-RAY DIFFRACTION4chain 'A' and (resid 674 through 717 )
5X-RAY DIFFRACTION5chain 'A' and (resid 718 through 789 )
6X-RAY DIFFRACTION6chain 'A' and (resid 790 through 823 )
7X-RAY DIFFRACTION7chain 'B' and (resid 639 through 648 )

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