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- PDB-9gs6: Crystal structure of fascin in complex with compound 4 -

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Basic information

Entry
Database: PDB / ID: 9gs6
TitleCrystal structure of fascin in complex with compound 4
ComponentsFascin
KeywordsSTRUCTURAL PROTEIN / actin bundling / small molecule inhibition
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 / positive regulation of filopodium 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 / cell-cell junction assembly / positive regulation of podosome assembly / positive regulation of filopodium assembly / podosome / establishment or maintenance of cell polarity / microvillus / actin filament bundle assembly / positive regulation of lamellipodium assembly / stress fiber / ruffle / regulation of actin cytoskeleton organization / filopodium / cell motility / actin filament binding / cell-cell junction / cell migration / lamellipodium / actin cytoskeleton / actin binding / growth cone / actin cytoskeleton organization / cell cortex / Interleukin-4 and Interleukin-13 signaling / protein-macromolecule adaptor activity / cytoskeleton / cadherin binding / RNA binding / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Fascin / Fascin, metazoans / Fascin domain / Fascin domain / Actin-crosslinking
Similarity search - Domain/homology
: / ACETATE ION / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSchuettelkopf, A.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: To be published
Title: Ultrahigh Resolution Saturation Transfer Difference (STD) NMR for Drug Discovery
Authors: Nepravishta, R. / Munoz-Garcia, J.C. / Cameron, K. / Schuettelkopf, A.W. / Parry, C. / Pennestri, M. / Pollock, K. / Konczal, J. / Pasquali, C. / Wallace, E. / Castanar, L. / Cabrita, E.J. / Angulo, J.
History
DepositionSep 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0413
Polymers54,6021
Non-polymers4392
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-3 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.250, 88.060, 98.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 54601.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FSCN1, FAN1, HSN, SNL / Plasmid: pBDDP-SPR3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q16658
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-A1IPD / N-(1-(3,4-dichlorobenzyl)-6-oxo-1,6-dihydropyridin-3-yl)-5-oxopyrrolidine-2-carboxamide / (2S)-N-[1-[(3,4-dichlorophenyl)methyl]-6-oxidanylidene-pyridin-3-yl]-5-oxidanylidene-pyrrolidine-2-carboxamide


Mass: 380.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15Cl2N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.39 Å3/Da / Density % sol: 48.53 % / Mosaicity: 0.26 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 18-22% PEG 8000, 100-130 mM MgAc2, 100 mM citric acid pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 1.97→49.73 Å / Num. obs: 37664 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.519 Å2 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.079 / Rrim(I) all: 0.205 / Net I/σ(I): 10.8 / Num. measured all: 245372
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
1.97-2.026.81.9580.927510.8932.34599.9
8.81-49.736.10.02459.74950.0120.02899.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia20.3.8.0data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→49.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.641 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 1833 4.9 %RANDOM
Rwork0.2278 ---
obs0.2298 35773 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.37 Å2 / Biso mean: 37.323 Å2 / Biso min: 20.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--1.04 Å20 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 1.97→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 29 193 4006
Biso mean--38.93 37.33 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133860
X-RAY DIFFRACTIONr_bond_other_d0.0360.0173445
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.6535231
X-RAY DIFFRACTIONr_angle_other_deg2.5111.5877961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6125483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30821.567217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59815611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3811531
X-RAY DIFFRACTIONr_chiral_restr0.1220.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024448
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02885
X-RAY DIFFRACTIONr_mcbond_it1.1522.1081939
X-RAY DIFFRACTIONr_mcbond_other1.1512.1071938
X-RAY DIFFRACTIONr_mcangle_it1.9183.1542419
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 145 -
Rwork0.352 2602 -
all-2747 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 17.2363 Å / Origin y: 11.2711 Å / Origin z: 26.1026 Å
111213212223313233
T0.096 Å2-0.0092 Å20.0141 Å2-0.2252 Å2-0.0201 Å2--0.0079 Å2
L0.7863 °2-0.0261 °20.4567 °2-0.5939 °20.0055 °2--1.0575 °2
S0.0491 Å °0.0502 Å °0.0035 Å °-0.1031 Å °0.0026 Å °-0.0134 Å °0.0525 Å °0.0203 Å °-0.0517 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9999
2X-RAY DIFFRACTION1L1 - 9999
3X-RAY DIFFRACTION1W1 - 9999
4X-RAY DIFFRACTION1X1 - 9999

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