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- PDB-4yc7: Crystal structure of human FMNL2 GBD-FH3 Domains bound to Cdc42-GppNHp -

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Basic information

Entry
Database: PDB / ID: 4yc7
TitleCrystal structure of human FMNL2 GBD-FH3 Domains bound to Cdc42-GppNHp
Components
  • Cell division control protein 42 homolog
  • Formin-like protein 2
KeywordsSIGNALING PROTEIN / Armadillo repeat / Rho GTPase / cell cycle
Function / homology
Function and homology information


GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination ...GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / GTP-dependent protein binding / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / embryonic heart tube development / regulation of cell morphogenesis / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / cortical actin cytoskeleton organization / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / nuclear migration / small GTPase-mediated signal transduction / Myogenesis / positive regulation of cytokinesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / RHOC GTPase cycle / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / cytoskeleton organization / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of substrate adhesion-dependent cell spreading / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / actin filament organization / EGFR downregulation / small monomeric GTPase / integrin-mediated signaling pathway / MAPK6/MAPK4 signaling / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / filopodium / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / G beta:gamma signalling through CDC42 / actin filament binding / mitotic spindle / ubiquitin protein ligase activity / apical part of cell / intracellular protein localization / cell migration / cell-cell junction / regulation of cell shape / Factors involved in megakaryocyte development and platelet production / G protein activity / actin cytoskeleton organization
Similarity search - Function
Formin-like protein, animal / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Cdc42 / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain ...Formin-like protein, animal / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Cdc42 / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Small GTPase Rho / Small GTPase Rho domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cell division control protein 42 homolog / Formin-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKuhn, S. / Geyer, M.
CitationJournal: Nat Commun / Year: 2015
Title: The structure of FMNL2-Cdc42 yields insights into the mechanism of lamellipodia and filopodia formation.
Authors: Kuhn, S. / Erdmann, C. / Kage, F. / Block, J. / Schwenkmezger, L. / Steffen, A. / Rottner, K. / Geyer, M.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
B: Formin-like protein 2
A: Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6564
Polymers64,1092
Non-polymers5472
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-19 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.094, 91.094, 144.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Formin-like protein 2 / Formin homology 2 domain-containing protein 2 / FMNL2


Mass: 44081.191 Da / Num. of mol.: 1 / Fragment: UNP residues 1-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FMNL2, FHOD2, KIAA1902 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96PY5
#2: Protein Cell division control protein 42 homolog / G25K GTP-binding protein / Cdc42


Mass: 20027.961 Da / Num. of mol.: 1 / Fragment: UNP residues 1-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / References: UniProt: P60953
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 mM Tris/HCl (pH 8.0), 14% (v/v) PEG 3350, 0.25 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→43.4 Å / Num. obs: 22213 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.9
Reflection shellHighest resolution: 2.5 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4.4 / Num. measured obs: 4521 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
PHENIXphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB accession code 3EG5, Chain A

3eg5


Resolution: 2.5→43.4 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1110 5.12 %
Rwork0.1935 --
obs0.1964 21696 99.99 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.781 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1795 Å20 Å20 Å2
2--2.1795 Å20 Å2
3---2.6871 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 33 63 3903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083911
X-RAY DIFFRACTIONf_angle_d1.1335296
X-RAY DIFFRACTIONf_dihedral_angle_d16.5551480
X-RAY DIFFRACTIONf_chiral_restr0.083598
X-RAY DIFFRACTIONf_plane_restr0.004677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.6140.40471440.3682520X-RAY DIFFRACTION100
2.614-2.75180.38341340.34672515X-RAY DIFFRACTION100
2.7518-2.92410.30971340.25862518X-RAY DIFFRACTION100
2.9241-3.14980.30731550.23392518X-RAY DIFFRACTION100
3.1498-3.46670.25561460.18752549X-RAY DIFFRACTION100
3.4667-3.96810.27021270.18032586X-RAY DIFFRACTION100
3.9681-4.99820.1891180.14762624X-RAY DIFFRACTION100
4.9982-43.44050.2251520.17732756X-RAY DIFFRACTION100
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)
11.0179-0.2645-0.07550.43720.27970.56850.3604-0.2526-0.59710.52370.1933-0.62180.80220.56210.00050.6968-0.0414-0.11190.69220.06440.450519.11749.0769-14.9933
21.43220.9878-0.60361.77790.02681.2092-0.14240.243-0.1281-0.20710.09390.00290.2306-0.0313-0.00020.3260.03960.08040.4552-0.06840.381411.862111.4267-46.214
30.98041.2436-0.57621.58270.08630.5553-0.14190.2447-0.0208-0.16620.09730.1032-0.10730.2191-00.27510.0051-0.01660.41850.00520.319419.985929.8387-42.2741
40.44420.59130.43640.55360.44660.58510.22760.16330.9214-0.03410.03780.0268-0.45990.45220.00020.53-0.05840.04940.44720.10650.560123.605846.5485-38.4926
50.8661-0.6803-0.19260.51210.05510.0793-0.07680.0095-0.14840.4669-0.009-0.2081-0.12640.15710.00010.3174-0.03840.00060.4542-0.05970.24750.849120.2109-10.6491
60.1797-0.0964-0.17410.3386-0.10650.2335-0.3016-0.7533-0.18810.0858-0.0529-0.2403-0.0010.4198-0.00010.39260.00050.03350.54670.06260.3881-4.170310.6294-8.8145
70.3015-0.26430.00170.29460.13960.40370.01660.2773-0.29460.6005-0.0199-0.2352-0.17480.1434-0.00020.40.0237-0.00830.5192-0.00190.43039.842813.6475-20.3581
80.29080.2605-0.09180.40160.33290.3225-0.0669-0.09790.1998-0.2490.1727-0.2067-0.08470.116-0.00010.30490.02470.03960.4989-0.03480.42291.657321.1847-26.5547
91.13370.3643-0.41760.2318-0.37020.49270.35280.10550.1767-0.024-0.40290.458-0.0296-0.4656-0.00370.38990.06710.09480.4896-0.05250.4639-3.107830.494-21.783
100.1039-0.0274-0.01960.1726-0.27490.3564-0.11220.3040.4517-0.9953-0.2560.5838-0.0183-0.0038-0.00010.41520.098-0.04720.56870.01940.582-6.77730.7928-30.2499
110.0647-0.08070.0160.2244-0.20460.206-0.1424-0.08150.59230.1533-0.170.7218-0.2435-0.3499-0.0030.3388-0.04460.08740.4714-0.15080.4912-9.180424.5851-18.8619
120.4480.84470.48242.68792.30362.1408-0.30350.09810.5532-0.7623-0.40311.0664-1.0165-0.2774-0.08180.2491-0.07490.20460.6944-0.11670.5371-12.053215.0099-15.7053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 32:75)
2X-RAY DIFFRACTION2chain 'B' and (resseq 76:219)
3X-RAY DIFFRACTION3chain 'B' and (resseq 220:329)
4X-RAY DIFFRACTION4chain 'B' and (resseq 330:377)
5X-RAY DIFFRACTION5chain 'A' and (resseq -1:36)
6X-RAY DIFFRACTION6chain 'A' and (resseq 37:58)
7X-RAY DIFFRACTION7chain 'A' and (resseq 59:76)
8X-RAY DIFFRACTION8chain 'A' and (resseq 77:104)
9X-RAY DIFFRACTION9chain 'A' and (resseq 105:131)
10X-RAY DIFFRACTION10chain 'A' and (resseq 132:148)
11X-RAY DIFFRACTION11chain 'A' and (resseq 149:164)
12X-RAY DIFFRACTION12chain 'A' and (resseq 165:177)

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