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- PDB-6d2k: Crystal structure of the FERM domain of mouse FARP2 -

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Basic information

Entry
Database: PDB / ID: 6d2k
TitleCrystal structure of the FERM domain of mouse FARP2
ComponentsFERM, ARHGEF and pleckstrin domain-containing protein 2
KeywordsSIGNALING PROTEIN / membrane targeting
Function / homology
Function and homology information


regulation of integrin activation / hair cycle process / RAC1 GTPase cycle / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / podosome assembly / neuron remodeling / Rac protein signal transduction / semaphorin-plexin signaling pathway / cytoskeletal protein binding / guanyl-nucleotide exchange factor activity ...regulation of integrin activation / hair cycle process / RAC1 GTPase cycle / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / podosome assembly / neuron remodeling / Rac protein signal transduction / semaphorin-plexin signaling pathway / cytoskeletal protein binding / guanyl-nucleotide exchange factor activity / osteoclast differentiation / actin cytoskeleton organization / cytoskeleton / cell adhesion / cytosol / cytoplasm
Similarity search - Function
FARP1/FARP2/FRMD7, FERM domain C-lobe / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain ...FARP1/FARP2/FRMD7, FERM domain C-lobe / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / FERM central domain / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FERM, ARHGEF and pleckstrin domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHe, X. / Zhang, X.
Funding support United States, China, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088197 United States
Welch FoundationI-1702 United States
National Natural Science Foundation of China (NSFC)#31500605 China
CitationJournal: Sci Rep / Year: 2018
Title: Structural analyses of FERM domain-mediated membrane localization of FARP1.
Authors: Kuo, Y.C. / He, X. / Coleman, A.J. / Chen, Y.J. / Dasari, P. / Liou, J. / Biederer, T. / Zhang, X.
History
DepositionApr 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERM, ARHGEF and pleckstrin domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)34,1981
Polymers34,1981
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.418, 72.762, 94.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FERM, ARHGEF and pleckstrin domain-containing protein 2 / / FERM domain including RhoGEF / FIR / FERM / RhoGEF and pleckstrin domain-containing protein 2


Mass: 34198.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Farp2, Kiaa0793 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q91VS8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 1.98 Å3/Da / Density % sol: 37.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Sodium acetate trihydrate, 12 % PEG 3350 (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.55→36.38 Å / Num. obs: 37895 / % possible obs: 99.7 % / Redundancy: 5.4 % / Net I/σ(I): 34.02

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HE7
Resolution: 1.55→36.38 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2242 1916 5.06 %
Rwork0.1966 --
obs0.198 37895 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 60.297 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4402 Å20 Å2-0 Å2
2--6.3799 Å20 Å2
3----5.9397 Å2
Refinement stepCycle: LAST / Resolution: 1.55→36.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 0 290 2667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062445
X-RAY DIFFRACTIONf_angle_d1.0313308
X-RAY DIFFRACTIONf_dihedral_angle_d19.782922
X-RAY DIFFRACTIONf_chiral_restr0.071362
X-RAY DIFFRACTIONf_plane_restr0.004420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5512-1.590.24241230.2492187X-RAY DIFFRACTION82
1.59-1.6330.31691220.23192307X-RAY DIFFRACTION86
1.633-1.68110.25431300.22252368X-RAY DIFFRACTION89
1.6811-1.73530.2811260.21622454X-RAY DIFFRACTION91
1.7353-1.79730.27091340.21322494X-RAY DIFFRACTION93
1.7973-1.86930.23561330.20592535X-RAY DIFFRACTION94
1.8693-1.95440.24661400.19712591X-RAY DIFFRACTION97
1.9544-2.05740.21031400.18782626X-RAY DIFFRACTION98
2.0574-2.18630.21261420.18052662X-RAY DIFFRACTION98
2.1863-2.35510.20691390.18072688X-RAY DIFFRACTION99
2.3551-2.5920.22171430.19912702X-RAY DIFFRACTION99
2.592-2.96690.21541430.19392729X-RAY DIFFRACTION99
2.9669-3.73740.23691450.18122762X-RAY DIFFRACTION100
3.7374-36.3910.19471560.19442874X-RAY DIFFRACTION98

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