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- PDB-4ydh: The structure of human FMNL1 N-terminal domains bound to Cdc42 -

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Basic information

Entry
Database: PDB / ID: 4ydh
TitleThe structure of human FMNL1 N-terminal domains bound to Cdc42
Components
  • Cell division control protein 42 homolog
  • Formin-like protein 1
KeywordsSIGNALING PROTEIN / actin cytoskeleton / GTPase / formin
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / substrate-dependent cell migration / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction ...small GTPase binding => GO:0031267 / substrate-dependent cell migration / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / bleb / positive regulation of pseudopodium assembly / profilin binding / Inactivation of CDC42 and RAC1 / cardiac conduction system development / GTP-dependent protein binding / actin filament severing / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / thioesterase binding / embryonic heart tube development / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / adherens junction organization / GTPase activating protein binding / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / cortical actin cytoskeleton organization / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / establishment or maintenance of cell polarity / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / RAC3 GTPase cycle / spindle midzone / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / G protein activity / positive regulation of DNA replication / secretory granule / filopodium / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / EGFR downregulation / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / protein localization / G beta:gamma signalling through CDC42 / cytoplasmic ribonucleoprotein granule
Similarity search - Function
Formin-like protein 1 / Formin-like protein, animal / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Cdc42 / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain ...Formin-like protein 1 / Formin-like protein, animal / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Cdc42 / 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 family 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 / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Formin-like protein 1 / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsKuhn, S. / Anand, K. / 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 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formin-like protein 1
B: Cell division control protein 42 homolog
C: Formin-like protein 1
D: Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,7758
Polymers138,6824
Non-polymers1,0934
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-68 kcal/mol
Surface area48670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.600, 102.100, 170.600
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 Formin-like protein 1 / CLL-associated antigen KW-13 / Leukocyte formin


Mass: 49313.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FMNL1, C17orf1, C17orf1B, FMNL / Production host: Escherichia coli (E. coli) / References: UniProt: O95466
#2: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 20027.961 Da / Num. of mol.: 2
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 / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 17% (v/v) PEG 3350, 0.16 M tri-ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 15654 / % possible obs: 99.4 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 11.8
Reflection shellResolution: 3.8→50 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YC7

4yc7


Resolution: 3.8→47.698 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2809 782 5 %
Rwork0.2079 --
obs0.2114 15648 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→47.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7498 0 66 0 7564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057713
X-RAY DIFFRACTIONf_angle_d1.17610559
X-RAY DIFFRACTIONf_dihedral_angle_d14.9752605
X-RAY DIFFRACTIONf_chiral_restr0.0431249
X-RAY DIFFRACTIONf_plane_restr0.0051374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8002-4.03810.31711270.26852416X-RAY DIFFRACTION100
4.0381-4.34970.29781290.23392455X-RAY DIFFRACTION100
4.3497-4.78710.30311280.20422422X-RAY DIFFRACTION100
4.7871-5.47890.27251300.2052475X-RAY DIFFRACTION100
5.4789-6.89950.28911310.24582485X-RAY DIFFRACTION100
6.8995-47.70150.25361370.16732613X-RAY DIFFRACTION100

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