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- PDB-9fn6: Full-length crystal structure of human Fascin 1 -

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Basic information

Entry
Database: PDB / ID: 9fn6
TitleFull-length crystal structure of human Fascin 1
ComponentsFascin
KeywordsPROTEIN BINDING / Actin-binding protein / Cancer / Metastasis
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 / cell-cell junction assembly / positive regulation of podosome assembly / podosome ...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 / cell-cell junction assembly / positive regulation of podosome assembly / podosome / positive regulation of filopodium assembly / establishment or maintenance of cell polarity / microvillus / actin filament bundle assembly / stress fiber / positive regulation of lamellipodium assembly / ruffle / filopodium / regulation of actin cytoskeleton organization / cell motility / actin filament binding / cell-cell junction / cell migration / lamellipodium / actin cytoskeleton / actin binding / actin cytoskeleton organization / growth cone / cell cortex / protein-macromolecule adaptor activity / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQuereda-Moraleda, I. / Grieco, A. / Martin-Garcia, J.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)CNS2022-135713 Spain
CitationJournal: To Be Published
Title: Full-length crystal structure of human Fascin 1
Authors: Quereda-Moraleda, I. / Grieco, A. / Martin-Garcia, J.M.
History
DepositionJun 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fascin
B: Fascin


Theoretical massNumber of molelcules
Total (without water)109,2042
Polymers109,2042
Non-polymers00
Water5,549308
1
A: Fascin


Theoretical massNumber of molelcules
Total (without water)54,6021
Polymers54,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fascin


Theoretical massNumber of molelcules
Total (without water)54,6021
Polymers54,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.566, 70.804, 122.210
Angle α, β, γ (deg.)90.00, 92.78, 90.00
Int Tables number5
Space group name H-MI121

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Components

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


Mass: 54601.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FSCN1, FAN1, HSN, SNL / Production host: Escherichia coli (E. coli) / References: UniProt: Q16658
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0,1M HEPES pH 7.5, 20% polyethylene glycol (PEG) 4000, 2% propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→43.42 Å / Num. obs: 47005 / % possible obs: 99.16 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 4.4
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.541 / Num. unique obs: 47005

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.42 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.891 / SU B: 20.218 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30435 2399 4.9 %RANDOM
Rwork0.23397 ---
obs0.23747 47005 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.66 Å2
2--0.75 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.2→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7594 0 0 308 7902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127951
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167313
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.82310779
X-RAY DIFFRACTIONr_angle_other_deg0.6281.78316830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.84751009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.537569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.823101323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.21149
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021981
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8723.5693983
X-RAY DIFFRACTIONr_mcbond_other3.8723.5693983
X-RAY DIFFRACTIONr_mcangle_it5.9446.4125009
X-RAY DIFFRACTIONr_mcangle_other5.9436.4115010
X-RAY DIFFRACTIONr_scbond_it3.8183.9093968
X-RAY DIFFRACTIONr_scbond_other3.8183.9093968
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0116.9955771
X-RAY DIFFRACTIONr_long_range_B_refined9.79537.918693
X-RAY DIFFRACTIONr_long_range_B_other9.78937.98669
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 179 -
Rwork0.307 3436 -
obs--99.75 %
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)
10.4-0.3114-0.45370.97980.23180.66710.0660.07550.0358-0.0812-0.10520.0021-0.008-0.13410.03920.09480.00830.01360.0497-0.05310.1653-35.374-43.9793.132
20.40150.29370.07340.5075-0.06680.06970.0667-0.0018-0.03530.0743-0.0491-0.0787-0.03210.0166-0.01750.19070.00770.15360.00830.01990.16710.973-26.43423.085
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 493
2X-RAY DIFFRACTION2B8 - 493

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