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- PDB-3p53: Structure of fascin -

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Basic information

Entry
Database: PDB / ID: 3p53
TitleStructure of fascin
ComponentsFascin
KeywordsSTRUCTURAL PROTEIN / BETA-TREFOIL DOMAIN
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 / microvillus / actin filament bundle assembly / positive regulation of lamellipodium assembly / stress fiber / ruffle / filopodium / cell motility / regulation of actin cytoskeleton organization / actin filament binding / cell-cell junction / cell migration / actin cytoskeleton / lamellipodium / protein-macromolecule adaptor activity / actin binding / cell cortex / growth cone / actin cytoskeleton organization / 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 / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJansen, S. / Dominguez, R.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Mechanism of actin filament bundling by fascin.
Authors: Jansen, S. / Collins, A. / Yang, C. / Rebowski, G. / Svitkina, T. / Dominguez, R.
History
DepositionOct 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Apr 16, 2014Group: Other
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fascin
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,33117
Polymers109,7362
Non-polymers2,59515
Water7,134396
1
A: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4989
Polymers54,8681
Non-polymers1,6308
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8338
Polymers54,8681
Non-polymers9657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.693, 71.010, 112.736
Angle α, β, γ (deg.)90.00, 131.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fascin / / Singed-like protein / 55 kDa actin-bundling protein / p55


Mass: 54868.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAN1, FSCN1, HSN, Human, SNL / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16658

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Non-polymers , 5 types, 411 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% PEG 3350, 0.2 M Lithium Acetate, 1mM DTT, 4% glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 0.9795, 0.9798, 1.0
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
30.97981
ReflectionResolution: 2→30.7 Å / Num. all: 65070 / Num. obs: 63704 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.6 / % possible all: 87.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→30.661 Å / SU ML: 0.28 / σ(F): 1.44 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 1985 3.12 %RANDOM
Rwork0.1781 ---
obs0.1794 63704 97.89 %-
all-65070 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.485 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9863 Å20 Å2-5.5098 Å2
2--2.3684 Å20 Å2
3----5.3547 Å2
Refinement stepCycle: LAST / Resolution: 2→30.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7579 0 127 396 8102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077959
X-RAY DIFFRACTIONf_angle_d1.00310748
X-RAY DIFFRACTIONf_dihedral_angle_d14.9912960
X-RAY DIFFRACTIONf_chiral_restr0.0691152
X-RAY DIFFRACTIONf_plane_restr0.0041401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.34411230.27713796X-RAY DIFFRACTION84
2.05-2.10540.33871320.24654119X-RAY DIFFRACTION93
2.1054-2.16740.29571390.23094314X-RAY DIFFRACTION97
2.1674-2.23730.26111420.20114432X-RAY DIFFRACTION99
2.2373-2.31720.2431430.19784465X-RAY DIFFRACTION99
2.3172-2.410.25591430.19734440X-RAY DIFFRACTION100
2.41-2.51960.28451450.19124509X-RAY DIFFRACTION100
2.5196-2.65240.25291430.18934457X-RAY DIFFRACTION100
2.6524-2.81850.25561450.17974505X-RAY DIFFRACTION100
2.8185-3.03590.23261450.17984506X-RAY DIFFRACTION100
3.0359-3.34110.22641450.17184493X-RAY DIFFRACTION100
3.3411-3.82380.21521450.16524526X-RAY DIFFRACTION100
3.8238-4.81450.14831460.1424537X-RAY DIFFRACTION100
4.8145-30.66430.20531490.18044620X-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)
10.6054-0.048-0.26281.19660.22040.4958-0.05340.0166-0.06090.061-0.05240.1209-0.05840.04230.07380.15590.027-0.02810.1145-0.00060.089625.8752-32.97128.2381
20.75890.11820.1831.4553-0.41251.43690.11350.0514-0.10280.057-0.1921-0.1071-0.02090.1760.05590.0261-0.02190.00590.12280.01410.096564.0394-50.157214.1282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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