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- PDB-6ikn: Crystal structure of the GAS7 F-BAR domain -

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Basic information

Entry
Database: PDB / ID: 6ikn
TitleCrystal structure of the GAS7 F-BAR domain
ComponentsGrowth arrest-specific protein 7
KeywordsLIPID BINDING PROTEIN / membrane deformation / phagocytosis / F-BAR domain
Function / homology
Function and homology information


actin filament bundle assembly / ruffle / actin filament polymerization / neuron projection morphogenesis / actin filament / neuron differentiation / actin filament binding / regulation of cell shape / cytoplasm
Similarity search - Function
GAS7, F-BAR domain / Unstructured linker region between on GAS7 protein / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ...GAS7, F-BAR domain / Unstructured linker region between on GAS7 protein / Fes/CIP4, and EFC/F-BAR homology domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Growth arrest-specific protein 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsHanawa-Suetsugu, K. / Itoh, Y. / Kohda, D. / Shimada, A. / Suetsugu, S.
Funding support Japan, 11items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceKAKENHI 24687014 Japan
Japan Society for the Promotion of ScienceKAKENHI 25121726 Japan
Japan Society for the Promotion of ScienceKAKENHI 17K07309 Japan
Japan Society for the Promotion of ScienceKAKENHI 26291037 Japan
Japan Society for the Promotion of ScienceKAKENHI 15H0164 Japan
Japan Society for the Promotion of ScienceKAKENHI 15H05902 Japan
Japan Society for the Promotion of ScienceKAKENHI 17H03674 Japan
Japan Society for the Promotion of ScienceKAKENHI 17H06006 Japan
Japan Society for the Promotion of ScienceNEXT program LS031 Japan
Japan Society for the Promotion of ScienceKAKENHI 16K07351 Japan
Japan Society for the Promotion of ScienceKAKENHI 23121507 Japan
CitationJournal: Nat Commun / Year: 2019
Title: Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7.
Authors: Hanawa-Suetsugu, K. / Itoh, Y. / Ab Fatah, M. / Nishimura, T. / Takemura, K. / Takeshita, K. / Kubota, S. / Miyazaki, N. / Wan Mohamad Noor, W.N.I. / Inaba, T. / Nguyen, N.T.H. / Hamada- ...Authors: Hanawa-Suetsugu, K. / Itoh, Y. / Ab Fatah, M. / Nishimura, T. / Takemura, K. / Takeshita, K. / Kubota, S. / Miyazaki, N. / Wan Mohamad Noor, W.N.I. / Inaba, T. / Nguyen, N.T.H. / Hamada-Nakahara, S. / Oono-Yakura, K. / Tachikawa, M. / Iwasaki, K. / Kohda, D. / Yamamoto, M. / Kitao, A. / Shimada, A. / Suetsugu, S.
History
DepositionOct 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth arrest-specific protein 7
B: Growth arrest-specific protein 7
C: Growth arrest-specific protein 7
D: Growth arrest-specific protein 7


Theoretical massNumber of molelcules
Total (without water)158,4724
Polymers158,4724
Non-polymers00
Water00
1
A: Growth arrest-specific protein 7
B: Growth arrest-specific protein 7


Theoretical massNumber of molelcules
Total (without water)79,2362
Polymers79,2362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-75 kcal/mol
Surface area33300 Å2
MethodPISA
2
C: Growth arrest-specific protein 7
D: Growth arrest-specific protein 7


Theoretical massNumber of molelcules
Total (without water)79,2362
Polymers79,2362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-75 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.264, 87.281, 88.793
Angle α, β, γ (deg.)80.98, 74.72, 79.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Growth arrest-specific protein 7 / GAS-7


Mass: 39618.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gas7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60780*PLUS
Has protein modificationY
Sequence detailsThe authors state the reference sequence is GenBank XM_006532202.1 and that residues 146-165 are ...The authors state the reference sequence is GenBank XM_006532202.1 and that residues 146-165 are expression tags.

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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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: PEG 4000, PEG 8000, ammonium sulfate, 80 mM HEPES-NaOH (pH 7.5), MES (pH 6.5)
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 30444 / % possible obs: 99.1 % / Redundancy: 6.4 % / CC1/2: 0.97 / Net I/σ(I): 7
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 1515 / CC1/2: 0.49

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3→32.029 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.45
RfactorNum. reflection% reflection
Rfree0.2547 1501 5.04 %
Rwork0.194 --
obs0.197 29801 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→32.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10017 0 0 0 10017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410181
X-RAY DIFFRACTIONf_angle_d0.93413660
X-RAY DIFFRACTIONf_dihedral_angle_d16.5734032
X-RAY DIFFRACTIONf_chiral_restr0.0371473
X-RAY DIFFRACTIONf_plane_restr0.0051778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.09680.32441350.28752520X-RAY DIFFRACTION97
3.0968-3.20740.32221350.25212550X-RAY DIFFRACTION99
3.2074-3.33560.29411290.25432610X-RAY DIFFRACTION99
3.3356-3.48730.29041280.23622592X-RAY DIFFRACTION99
3.4873-3.67090.28221510.20772543X-RAY DIFFRACTION99
3.6709-3.90050.25881360.19082577X-RAY DIFFRACTION99
3.9005-4.20110.24111440.18192585X-RAY DIFFRACTION99
4.2011-4.62270.23981450.1642571X-RAY DIFFRACTION99
4.6227-5.2890.21411330.16312592X-RAY DIFFRACTION99
5.289-6.65380.27271390.20772599X-RAY DIFFRACTION100
6.6538-32.0310.20291260.15282561X-RAY DIFFRACTION98
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)
12.0003-0.45531.90710.9492-0.18211.8676-0.22751.80810.0059-0.28570.3270.4352-0.0269-1.268-0.0340.4314-0.0105-0.10330.91190.0880.331725.397710.2387-1.5928
26.0671-3.99462.26442.4973-1.09581.1496-0.6864-0.88290.07350.47620.5891-0.1637-0.2119-0.28470.04420.37190.06210.02810.37180.04910.361859.8166-12.825521.0967
33.9568-4.46243.795.1955-2.76884.9955-0.0701-0.88780.20220.18470.25880.59350.5855-0.0857-0.05160.49790.0866-0.05210.50120.09680.496922.369211.416216.3927
43.1922-1.97080.35872.6762-0.59980.5696-0.0857-0.17111.2403-0.05630.1103-0.40880.0134-0.10360.0090.45780.0087-0.02730.3177-0.05970.277930.981810.89412.2067
53.272-4.22731.53094.6673-0.84282.4946-0.02750.16180.55310.2828-0.2423-0.3398-0.0910.44580.28590.25890.0513-0.01080.39870.05370.4635106.4005-40.483729.1652
61.7731-2.001-0.13595.5216-2.17286.12160.18040.15160.5871-0.1366-0.3516-0.92290.64460.48380.20750.44420.0357-0.07480.5455-0.04260.656115.3196-52.456436.5186
74.745-5.80194.80546.4713-4.72843.4705-0.4891-0.9321-1.05050.17390.75360.4193-0.2708-0.3557-0.18580.38050.08920.03540.36710.07780.483581.5209-39.678726.3935
87.0023-5.35241.54037.3855-1.74411.9730.144-0.3902-0.343-0.53650.03030.22520.1833-0.0988-0.04640.3443-0.0155-0.00310.34720.04050.262268.5843-28.371114.443
96.9627-4.99941.54936.7847-2.79793.13760.0075-0.4163-0.3262-0.1355-0.09790.18490.6190.4481-0.03410.77180.1909-0.06090.58650.0570.4875118.2051-74.73739.3434
107.4444-6.38362.07215.6192-1.87230.81060.2044-0.03340.0403-0.307-0.12-0.12510.24310.12760.02170.45070.0486-0.03420.3308-0.02970.307190.4063-40.628219.8835
117.8314-2.0559-1.60955.40433.56032.5463-0.7895-2.47720.04931.42560.59150.7364-0.4001-1.36690.21220.70040.07080.19931.020.03380.5516-0.6341-36.8745.1663
125.88563.7972-1.89782.6874-1.26811.0827-0.46480.9160.0042-0.27640.54520.05040.0303-0.1602-0.05730.4108-0.08310.03390.4382-0.03970.361133.4518-13.7336-17.1379
133.64164.1733-1.4563.6322-1.88151.9660.29641.51790.0086-0.56740.33130.6646-0.3118-0.23570.02220.4402-0.16760.11920.7372-0.0340.682-7.3978-38.6356-11.7282
141.0204-0.1736-0.1051.6578-1.25580.97560.05220.1308-0.1176-0.30410.28811.6050.3676-0.7982-0.08150.843-0.10040.00971.28870.01661.1862-43.9782-51.0846-0.2617
155.27413.3016-1.03612.5572-0.77420.4625-0.17430.1959-0.7196-0.13570.1187-0.3420.0728-0.020.14160.4187-0.07030.06770.2793-0.16690.263932.638-20.643-14.0008
165.61823.2784-3.19316.952-6.60319.5567-0.1882-0.0396-0.0247-0.07760.1149-0.4682-0.2505-0.04390.02280.6115-0.1170.18590.765-0.39650.617390.3125.4986-30.544
176.22198.1959-5.9218.913-4.72013.74330.1383-0.04340.4286-0.1281-0.00670.0223-0.13230.1458-0.23760.4678-0.13180.02230.49510.0510.382955.497712.9143-22.2272
188.09117.4562-1.44559.1202-0.89620.36340.44840.05420.20190.5315-0.23990.1355-0.05460.1805-0.29070.3525-0.0150.03830.4760.07550.230536.6279-4.1994-8.9593
192.5848-0.2628-1.47755.8806-2.89112.00330.65970.14972.8135-0.0668-0.142-0.8731-3.05860.4245-0.8885-0.0029-0.35020.38911.03650.31521.233759.214820.4319-15.5052
202.94391.064-0.08183.8953-0.78211.75010.3260.75540.6758-0.0556-0.13970.3281-0.66880.0263-0.10231.0976-0.25770.43630.7175-0.05361.086894.587347.2568-34.8253
218.50966.597-2.66555.9011-2.13881.40970.6514-0.19210.41880.6325-0.253-0.0848-0.5910.2786-0.23030.5444-0.11540.1430.4569-0.13670.498363.943712.4997-14.8126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 171 through 192 )
2X-RAY DIFFRACTION2chain 'A' and (resid 193 through 308 )
3X-RAY DIFFRACTION3chain 'A' and (resid 309 through 351 )
4X-RAY DIFFRACTION4chain 'A' and (resid 352 through 440 )
5X-RAY DIFFRACTION5chain 'A' and (resid 441 through 475 )
6X-RAY DIFFRACTION6chain 'B' and (resid 172 through 218 )
7X-RAY DIFFRACTION7chain 'B' and (resid 219 through 259 )
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 310 )
9X-RAY DIFFRACTION9chain 'B' and (resid 311 through 360 )
10X-RAY DIFFRACTION10chain 'B' and (resid 361 through 475 )
11X-RAY DIFFRACTION11chain 'C' and (resid 172 through 192 )
12X-RAY DIFFRACTION12chain 'C' and (resid 193 through 308 )
13X-RAY DIFFRACTION13chain 'C' and (resid 309 through 355 )
14X-RAY DIFFRACTION14chain 'C' and (resid 356 through 363 )
15X-RAY DIFFRACTION15chain 'C' and (resid 364 through 475 )
16X-RAY DIFFRACTION16chain 'D' and (resid 172 through 218 )
17X-RAY DIFFRACTION17chain 'D' and (resid 219 through 259 )
18X-RAY DIFFRACTION18chain 'D' and (resid 260 through 299 )
19X-RAY DIFFRACTION19chain 'D' and (resid 300 through 310 )
20X-RAY DIFFRACTION20chain 'D' and (resid 311 through 362 )
21X-RAY DIFFRACTION21chain 'D' and (resid 363 through 475 )

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