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- PDB-4gyv: Crystal structure of the DH domain of FARP2 -

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Basic information

Entry
Database: PDB / ID: 4gyv
TitleCrystal structure of the DH domain of FARP2
ComponentsFERM, RhoGEF and pleckstrin domain-containing protein 2
KeywordsSIGNALING PROTEIN / FARP2 / DH / 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 / 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 / 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 ...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 / FERM central domain / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / FERM/acyl-CoA-binding protein superfamily / 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 / Up-down Bundle / 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 / SAD / Resolution: 2.9 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 5, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
C: FERM, RhoGEF and pleckstrin domain-containing protein 2
D: FERM, RhoGEF and pleckstrin domain-containing protein 2
E: FERM, RhoGEF and pleckstrin domain-containing protein 2
F: FERM, RhoGEF and pleckstrin domain-containing protein 2
G: FERM, RhoGEF and pleckstrin domain-containing protein 2
H: FERM, RhoGEF and pleckstrin domain-containing protein 2
I: FERM, RhoGEF and pleckstrin domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)232,1129
Polymers232,1129
Non-polymers00
Water30617
1
A: FERM, RhoGEF and pleckstrin domain-containing protein 2
F: FERM, RhoGEF and pleckstrin domain-containing protein 2
G: FERM, RhoGEF and pleckstrin domain-containing protein 2

A: FERM, RhoGEF and pleckstrin domain-containing protein 2
F: FERM, RhoGEF and pleckstrin domain-containing protein 2
G: FERM, RhoGEF and pleckstrin domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)154,7416
Polymers154,7416
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_456-x-1,y,-z+3/21
Buried area13420 Å2
ΔGint-69 kcal/mol
Surface area54750 Å2
MethodPISA
2
B: FERM, RhoGEF and pleckstrin domain-containing protein 2
C: FERM, RhoGEF and pleckstrin domain-containing protein 2
D: FERM, RhoGEF and pleckstrin domain-containing protein 2
E: FERM, RhoGEF and pleckstrin domain-containing protein 2
H: FERM, RhoGEF and pleckstrin domain-containing protein 2
I: FERM, RhoGEF and pleckstrin domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)154,7416
Polymers154,7416
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13430 Å2
ΔGint-67 kcal/mol
Surface area54360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.193, 209.991, 325.009
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 25790.172 Da / Num. of mol.: 9
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 / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4.45 Å3/Da / Density % sol: 72.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, 1.5 M LiSO4, 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: 0.979345 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2010
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979345 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 91702 / Num. obs: 91636 / % possible obs: 99.9 % / Redundancy: 10 % / Rmerge(I) obs: 0.084 / Χ2: 2.154 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-310.10.79690610.9431100
3-3.1210.10.53891070.9511100
3.12-3.2710.10.32490900.9841100
3.27-3.4410.10.19690741.0171100
3.44-3.6510.10.12391261.1281100
3.65-3.9410.10.08591261.2951100
3.94-4.33100.06791761.6241100
4.33-4.96100.06491602.7751100
4.96-6.249.80.08192564.6651100
6.24-509.30.05394606.436199.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→48.575 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8553 / SU ML: 0.32 / Phase error: 21.65 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1988 2.24 %random
Rwork0.1778 ---
obs0.1787 88708 96.57 %-
all-91702 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 230.34 Å2 / Biso mean: 90.4346 Å2 / Biso min: 31.66 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15716 0 0 17 15733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916066
X-RAY DIFFRACTIONf_angle_d1.17421804
X-RAY DIFFRACTIONf_chiral_restr0.0782482
X-RAY DIFFRACTIONf_plane_restr0.0052789
X-RAY DIFFRACTIONf_dihedral_angle_d16.2785881
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.97240.28311260.23825542566888
2.9724-3.05280.26361290.23925881601092
3.0528-3.14260.24751360.23635972610894
3.1426-3.2440.3031360.2276115625196
3.244-3.35990.2851440.20676188633297
3.3599-3.49440.26841480.20216140628897
3.4944-3.65340.23981440.17736230637497
3.6534-3.84590.17631430.16246197634098
3.8459-4.08680.23961460.16276296644298
4.0868-4.40210.22791440.16016340648499
4.4021-4.84470.20031480.14286366651499
4.8447-5.54490.21781470.15986395654299
5.5449-6.98270.26681440.210264666610100
6.9827-48.58220.16581530.16676592674598
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)
14.457-0.4681-1.25112.50020.68644.39510.2046-0.4468-0.10350.19280.0147-0.10780.28550.077-0.14980.4006-0.0447-0.02330.31180.0880.4832-58.8797-123.2258256.4449
23.4631-1.1102-1.28083.56870.74614.32380.18120.1977-0.0279-0.50240.01180.2020.0208-0.2748-0.14710.4076-0.0513-0.08840.3372-0.01640.4953-47.1314-60.0698285.3395
32.6551-0.39650.19924.52991.67674.6803-0.0691-0.3036-0.16510.32650.29470.13320.2406-0.1135-0.16160.32630.00040.06950.40360.06210.5187-45.2564-63.2897310.5396
42.5426-0.30511.46162.6787-0.41473.6439-0.042-0.1127-0.08660.5031-0.2075-0.0005-0.341-0.13060.17610.4779-0.1225-0.02450.7944-0.2150.5216-16.5752-64.3609334.1389
52.473-1.12781.21243.5992-2.20556.24230.24130.1788-0.2685-0.6055-0.52240.14091.7091-0.10520.29970.8848-0.2190.08750.6771-0.19340.6413-12.196-88.2533329.9325
62.45410.37440.84642.33521.06843.6008-0.3311-0.2447-0.06560.3480.0634-0.0036-0.1266-0.32030.18780.8488-0.08610.17410.427-0.13290.5271-43.4225-99.1013279.9932
74.26120.1432.49212.2030.13716.517-0.18510.7719-0.22820.0173-0.0774-0.17491.03461.47990.27710.9110.21690.21050.627-0.00940.6222-20.5011-107.0867275.9036
82.3898-0.33930.05052.6377-1.59544.6652-0.06020.5111-0.0297-0.1009-0.18010.10790.31020.26480.240.6634-0.23450.20870.6919-0.07440.5896-33.7787-34.653261.7301
92.7883-1.13831.40063.5733-2.44236.8454-0.5507-0.13960.05490.81590.23710.2021-0.9071-1.73260.29440.5868-0.00860.12951.0418-0.20750.6464-52.2349-18.8359265.9081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA532 - 747
2X-RAY DIFFRACTION2CHAIN BB532 - 747
3X-RAY DIFFRACTION3CHAIN CC532 - 747
4X-RAY DIFFRACTION4CHAIN DD532 - 747
5X-RAY DIFFRACTION5CHAIN EE532 - 746
6X-RAY DIFFRACTION6CHAIN FF532 - 747
7X-RAY DIFFRACTION7CHAIN GG532 - 746
8X-RAY DIFFRACTION8CHAIN HH532 - 747
9X-RAY DIFFRACTION9CHAIN II532 - 746

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