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- PDB-4gzu: Crystal structure of the DH-PH-PH domain of FARP2 -

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Basic information

Entry
Database: PDB / ID: 4gzu
TitleCrystal structure of the DH-PH-PH domain of FARP2
ComponentsFERM, RhoGEF and pleckstrin domain-containing protein 2
KeywordsSIGNALING PROTEIN / FARP2 / DHPH / GEF / guanine nucleotide exchange factor
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 / osteoclast differentiation ...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 / osteoclast differentiation / guanyl-nucleotide exchange factor activity / actin cytoskeleton organization / cytoskeleton / cell adhesion / cytosol / cytoplasm
Similarity search - Function
FARP1/FARP2/FRMD7, FERM domain C-lobe / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain ...FARP1/FARP2/FRMD7, FERM domain C-lobe / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Ezrin/radixin/moesin-like / 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 / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
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 / molecular replacement / Resolution: 3.2 Å
AuthorsHe, X. / Zhang, X.
CitationJournal: Structure / Year: 2013
Title: Structural Basis for Autoinhibition of the Guanine Nucleotide Exchange Factor FARP2.
Authors: He, X. / Kuo, Y.C. / Rosche, T.J. / Zhang, X.
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,1412
Polymers116,1412
Non-polymers00
Water34219
1
A: FERM, RhoGEF and pleckstrin domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)58,0701
Polymers58,0701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FERM, RhoGEF and pleckstrin domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)58,0701
Polymers58,0701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)184.394, 85.248, 103.451
Angle α, β, γ (deg.)90.000, 118.760, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 58070.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Farp2, Kiaa0793 / Plasmid: modified pET28a with a preScission protease site / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91VS8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE SEQUENCE MATCHES NCBI NUCLEOTIDE ID BC009153, IN WHICH RESIDUE 821 IS A LEUCINE.

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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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM MMT, 0.2 M LiSO4, 20% PEG3350, pH 7.0, vapor diffusion, hanging drop, temperature 293K

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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
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 23394 / Num. obs: 23322 / % possible obs: 99.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.111 / Χ2: 1.752 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.264.10.7511751.331199.9
3.26-3.314.10.54511631.2841100
3.31-3.384.10.46111471.3291100
3.38-3.454.10.40611441.3961100
3.45-3.524.20.3311921.4941100
3.52-3.64.20.29111491.3381100
3.6-3.694.10.26111571.5661100
3.69-3.794.20.24911611.475199.7
3.79-3.914.20.19711821.567199.8
3.91-4.034.10.15511311.633199.6
4.03-4.184.10.14711641.738199.7
4.18-4.344.10.11611461.872199.5
4.34-4.544.10.10211802.073199.7
4.54-4.784.10.08811732.088199.3
4.78-5.084.10.08811492.256199.6
5.08-5.474.10.09211632.289199.8
5.47-6.024.10.09311822.22199.9
6.02-6.8940.07611752.15199.7
6.89-8.673.90.0511892.04199.9
8.67-503.80.03512001.983197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4GYV, 1FHW, and 2D9Y

4gyv

1fhw

2d9y


Resolution: 3.2→45.343 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7596 / SU ML: 0.84 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 1118 5.03 %RANDOM
Rwork0.2322 ---
obs0.2346 22223 92.44 %-
all-23394 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.683 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso max: 215.05 Å2 / Biso mean: 103.3605 Å2 / Biso min: 5 Å2
Baniso -1Baniso -2Baniso -3
1-8.3819 Å20 Å2-20.9781 Å2
2--3.691 Å20 Å2
3----12.073 Å2
Refinement stepCycle: LAST / Resolution: 3.2→45.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6705 0 0 19 6724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076858
X-RAY DIFFRACTIONf_angle_d1.0059311
X-RAY DIFFRACTIONf_chiral_restr0.0641073
X-RAY DIFFRACTIONf_plane_restr0.0041158
X-RAY DIFFRACTIONf_dihedral_angle_d14.5242363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.31580.3642980.29061884198267
3.3158-3.49060.31831390.27552544268390
3.4906-3.70920.34361430.25332684282795
3.7092-3.99540.291420.2282708285095
3.9954-4.39720.27531450.19942746289197
4.3972-5.03270.22671470.1782799294698
5.0327-6.3380.24881500.24572853300399
6.338-45.34770.27861540.24682887304199
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)
14.9585-1.5829-0.64982.8898-0.1213.5218-0.08440.2309-0.15740.36420.1096-0.39080.92360.5295-0.05170.8110.2275-0.08290.58970.01990.578432.6882-30.070620.3832
24.85290.82531.06556.9175-0.10315.0876-0.2060.50940.2605-0.0624-0.06060.12770.02730.54640.18040.42590.141-0.01890.56060.06440.414113.5277-9.9512-1.3901
31.74950.4613-0.75132.4262-0.31963.5919-0.07540.4530.25890.1145-0.0293-0.25840.16581.06810.13870.5438-0.02050.0491.11170.17880.712540.2093-12.794910.6698
41.6106-0.5968-0.37323.31292.58884.311-0.0016-0.09230.435-1.2534-0.35110.2995-1.3546-0.8320.19691.68580.4172-0.38430.704-0.12520.7116-7.158637.4994-36.7582
52.70290.0476-1.5155.32050.94045.80640.13010.0312-0.0875-0.1822-0.3616-0.18780.01340.59060.230.6098-0.0173-0.16840.54060.15550.56546.122417.3627-12.3792
63.12110.96330.07272.1186-0.08868.7482-0.04940.4946-0.2866-0.7403-0.3592-0.1901-0.07210.87730.33941.01520.24140.01710.8351-0.00910.68633.783120.4863-41.8568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND RESID 535:746A535 - 1026
2X-RAY DIFFRACTION2CHAIN A AND RESID 747:868A535 - 1026
3X-RAY DIFFRACTION3CHAIN A AND RESID 907:1026A535 - 1026
4X-RAY DIFFRACTION4CHAIN B AND RESID 537:746B537 - 1025
5X-RAY DIFFRACTION5CHAIN B AND RESID 747:868B537 - 1025
6X-RAY DIFFRACTION6CHAIN B AND RESID 907:1025B537 - 1025

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