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- PDB-5aws: Crystal structure of the SGIP1 mu homology domain in the P1 space... -

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Basic information

Entry
Database: PDB / ID: 5aws
TitleCrystal structure of the SGIP1 mu homology domain in the P1 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 / MOLECULAR REPLACEMENT / Resolution: 2.001 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_label_seq_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: SH3-containing GRB2-like protein 3-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,47314
Polymers61,6882
Non-polymers78512
Water3,387188
1
A: SH3-containing GRB2-like protein 3-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3028
Polymers30,8441
Non-polymers4587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SH3-containing GRB2-like protein 3-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1716
Polymers30,8441
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.552, 53.634, 75.199
Angle α, β, γ (deg.)101.87, 86.91, 95.61
Int Tables number1
Space group name H-MP1

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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.: 2 / 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.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
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: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34307 / % possible obs: 89.1 % / Redundancy: 3.9 % / Net I/σ(I): 15

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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: 2.001→39.054 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2412 1714 5.01 %
Rwork0.1986 --
obs0.2007 34226 88.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→39.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4175 0 12 188 4375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084270
X-RAY DIFFRACTIONf_angle_d1.3855813
X-RAY DIFFRACTIONf_dihedral_angle_d13.2611565
X-RAY DIFFRACTIONf_chiral_restr0.097662
X-RAY DIFFRACTIONf_plane_restr0.007754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0014-2.06020.3643840.28991699X-RAY DIFFRACTION55
2.0602-2.12670.32941060.27032066X-RAY DIFFRACTION68
2.1267-2.20270.28811190.2612510X-RAY DIFFRACTION81
2.2027-2.29090.26271350.25232761X-RAY DIFFRACTION92
2.2909-2.39520.33641420.25312988X-RAY DIFFRACTION97
2.3952-2.52140.3491640.23462986X-RAY DIFFRACTION97
2.5214-2.67940.30761460.22512997X-RAY DIFFRACTION98
2.6794-2.88620.2661850.21662939X-RAY DIFFRACTION98
2.8862-3.17650.2681660.21482966X-RAY DIFFRACTION98
3.1765-3.63590.22941530.192917X-RAY DIFFRACTION96
3.6359-4.57970.21231510.17282826X-RAY DIFFRACTION92
4.5797-39.06130.19411630.17082857X-RAY DIFFRACTION94
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)
13.1586-0.1112-0.86722.77890.07594.39410.29440.92130.2724-0.3872-0.2047-0.0834-0.2903-0.04960.04960.28940.05020.01020.45690.08320.274410.915136.5813-47.9307
24.1233-0.41270.0234.485-0.0594.77470.30330.6162-0.20.1892-0.43030.057-0.0062-0.170.17070.20720.0629-0.02410.4708-0.05990.269914.27726.434-45.297
36.0781.3599-0.37675.94121.85619.47120.55220.8103-0.2738-0.773-0.67770.3675-0.0483-0.00710.13790.4670.0368-0.03430.573-0.10980.24929.78829.004-56.732
47.7907-4.22011.20618.3334-1.06754.03380.00580.06410.5574-0.231-0.0260.6179-1.2034-0.8740.15360.49360.0976-0.03420.3607-0.03330.4002-3.19543.043-51.744
52.4184-0.43370.01123.66330.94247.2902-0.2863-0.62550.19010.18780.373-0.1231-0.2305-0.063-0.0950.30260.028-0.10040.3893-0.03450.298811.757839.1481-15.4807
62.0086-1.07140.39810.56990.43546.0989-0.0946-0.08670.42320.07950.0957-0.234-0.77120.2324-0.0720.3842-0.0879-0.030.2654-0.00420.361713.351939.4945-27.8347
73.9227-0.30912.98113.60730.55212.43270.156-0.2242-0.56550.7977-0.253-0.009-0.1748-0.11310.14490.4237-0.0443-0.03950.2777-0.10040.4363-1.689513.4991-41.3184
85.52831.64220.69935.421-0.33067.76030.1545-0.2744-0.45060.65540.13210.24340.1667-0.1527-0.18720.34090.0045-0.0440.27450.04040.35952.425215.717-34.6194
95.3243-0.39752.83262.3046-0.20074.6120.22050.3993-0.1157-0.0977-0.19810.09180.1235-0.0558-0.06750.34480.0419-0.00060.4813-0.19310.3315-13.418615.047-70.0857
103.8872-0.82783.73482.345-1.60477.08210.46940.1518-0.70110.249-0.21520.00820.60430.2753-0.32250.3745-0.0419-0.02160.2688-0.07430.4623-2.92759.5362-48.0682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 554 through 615 )
2X-RAY DIFFRACTION2chain 'A' and (resid 616 through 628 )
3X-RAY DIFFRACTION3chain 'A' and (resid 629 through 657 )
4X-RAY DIFFRACTION4chain 'A' and (resid 658 through 673 )
5X-RAY DIFFRACTION5chain 'A' and (resid 674 through 751 )
6X-RAY DIFFRACTION6chain 'A' and (resid 752 through 823 )
7X-RAY DIFFRACTION7chain 'B' and (resid 558 through 606 )
8X-RAY DIFFRACTION8chain 'B' and (resid 607 through 673 )
9X-RAY DIFFRACTION9chain 'B' and (resid 674 through 782 )
10X-RAY DIFFRACTION10chain 'B' and (resid 783 through 823 )

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