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- PDB-1dfc: CRYSTAL STRUCTURE OF HUMAN FASCIN, AN ACTIN-CROSSLINKING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1dfc
TitleCRYSTAL STRUCTURE OF HUMAN FASCIN, AN ACTIN-CROSSLINKING PROTEIN
ComponentsFASCIN
KeywordsSTRUCTURAL PROTEIN / BETA-TREFOIL FOLD FOR ALL FOUR DOMAINS / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / podosome / positive regulation of podosome assembly / cell-cell junction assembly ...microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / podosome / positive regulation of podosome assembly / cell-cell junction assembly / positive regulation of filopodium assembly / establishment or maintenance of cell polarity / actin filament bundle assembly / microvillus / positive regulation of lamellipodium assembly / stress fiber / ruffle / filopodium / cell motility / regulation of actin cytoskeleton organization / cell-cell junction / actin filament binding / actin cytoskeleton / cell migration / lamellipodium / protein-macromolecule adaptor activity / actin binding / cell cortex / actin cytoskeleton organization / growth cone / Interleukin-4 and Interleukin-13 signaling / cytoskeleton / cadherin binding / RNA binding / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Fascin / Fascin, metazoans / Fascin domain / Fascin domain / Actin-crosslinking / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.9 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Ono, S. / Matsumura, F. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Structure, evolutionary conservation, and conformational dynamics of Homo sapiens fascin-1, an F-actin crosslinking protein.
Authors: Sedeh, R.S. / Fedorov, A.A. / Fedorov, E.V. / Ono, S. / Matsumura, F. / Almo, S.C. / Bathe, M.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: Identification of an Actin Binding Region and a Protein Kinase C Phosphorylation Site on Human Fascin
Authors: Ono, S. / Yamakita, Y. / Yamashiro, S. / Matsudaira, P.T. / Gnarra, J.R. / Obinata, T. / Matsumura, F.
History
DepositionNov 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: FASCIN
B: FASCIN


Theoretical massNumber of molelcules
Total (without water)109,2042
Polymers109,2042
Non-polymers00
Water00
1
A: FASCIN


Theoretical massNumber of molelcules
Total (without water)54,6021
Polymers54,6021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FASCIN


Theoretical massNumber of molelcules
Total (without water)54,6021
Polymers54,6021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.426, 71.689, 116.924
Angle α, β, γ (deg.)90.00, 132.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FASCIN / ACTIN BUNDLING PROTEIN


Mass: 54601.879 Da / Num. of mol.: 2 / Fragment: FULL-LENGTH PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q16658

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, hepes, dtt, sodium azide , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
310 mM1dropNaCl
430 mM1dropKCl
50.1 mMEDTA1drop
61 mMdithiothreitol1drop
720 %PEG40001reservoir
80.1 MHEPES1reservoirpH7.5
91 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 19, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→23.03 Å / Num. obs: 19147 / % possible obs: 84.2 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.1
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 21421 / % possible obs: 94.2 % / Rmerge(I) obs: 0.048

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Processing

Software
NameVersionClassification
PHASES-95model building
DMmodel building
CNSrefinement
XDSdata reduction
XSCALEdata scaling
PHASESV. 95phasing
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 2.9→8 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.268 945 5.2 %RANDOM
Rwork0.184 ---
obs0.184 18070 83.6 %-
Solvent computationBsol: 63.17 Å2 / ksol: 0.247 e/Å3
Refine analyzeLuzzati coordinate error free: 0.343 Å
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7427 0 0 0 7427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.39
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.147
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.2572
X-RAY DIFFRACTIONc_scbond_it4.3092
X-RAY DIFFRACTIONc_scangle_it7.1232.5
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 25 Å / Num. reflection obs: 20541 / Rfactor obs: 0.184 / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.39
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.147

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