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- PDB-6i10: CRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 2 -

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Basic information

Entry
Database: PDB / ID: 6i10
TitleCRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 2
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 / 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 / actin cytoskeleton / cell migration / 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 / cytoplasm / cytosol
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
ACETATE ION / Chem-GZK / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchuettelkopf, A.W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Structure-based design, synthesis and biological evaluation of a novel series of isoquinolone and pyrazolo[4,3-c]pyridine inhibitors of fascin 1 as potential anti-metastatic agents.
Authors: Francis, S. / Croft, D. / Schuttelkopf, A.W. / Parry, C. / Pugliese, A. / Cameron, K. / Claydon, S. / Drysdale, M. / Gardner, C. / Gohlke, A. / Goodwin, G. / Gray, C.H. / Konczal, J. / ...Authors: Francis, S. / Croft, D. / Schuttelkopf, A.W. / Parry, C. / Pugliese, A. / Cameron, K. / Claydon, S. / Drysdale, M. / Gardner, C. / Gohlke, A. / Goodwin, G. / Gray, C.H. / Konczal, J. / McDonald, L. / Mezna, M. / Pannifer, A. / Paul, N.R. / Machesky, L. / McKinnon, H. / Bower, J.
History
DepositionOct 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2606
Polymers54,6021
Non-polymers6595
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint11 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.667, 91.839, 97.062
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-GZK / 1-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-5-[(3,4-dichlorophenyl)methyl]pyrazolo[3,4-d]pyrimidin-4-one


Mass: 413.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14Cl2N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.13 % / Mosaicity: 0.665 °
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.1→48.53 Å / Num. obs: 32836 / % possible obs: 99.7 % / Redundancy: 3.68 % / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.101 / Χ2: 1 / Net I/σ(I): 5.9 / Num. measured all: 121862 / Scaling rejects: 915
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsΧ2Diffraction-ID% possible all
2.1-2.182.750.4711.81.2198.1
2.18-2.263.740.47421.15199.9
2.26-2.373.810.4372.21.14199.9
2.37-2.493.820.4022.41.131100
2.49-2.653.830.3382.81.081100
2.65-2.853.820.2663.41.04199.9
2.85-3.143.80.1784.70.98199.9
3.14-3.593.810.1037.80.86199.9
3.59-4.523.790.05613.50.75199.9
4.52-48.533.630.047170.73199.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
d*TREK9.7 W8RSSIdata scaling
PDB_EXTRACT3.22data extraction
d*TREK9.7 W8RSSIdata reduction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P53

3p53


Resolution: 2.1→48.53 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 22.079 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.219
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1718 5.2 %RANDOM
Rwork0.2499 ---
obs0.2519 31006 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.87 Å2 / Biso mean: 44.03 Å2 / Biso min: 28.66 Å2
Baniso -1Baniso -2Baniso -3
1--4.65 Å20 Å20 Å2
2---1.16 Å20 Å2
3---5.81 Å2
Refinement stepCycle: final / Resolution: 2.1→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3777 0 42 98 3917
Biso mean--46.19 43.04 -
Num. residues----483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0143906
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173385
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.6695281
X-RAY DIFFRACTIONr_angle_other_deg1.661.667943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2115484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.35321.396222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59115638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9951533
X-RAY DIFFRACTIONr_chiral_restr0.1090.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024489
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02761
X-RAY DIFFRACTIONr_mcbond_it0.8580.8261937
X-RAY DIFFRACTIONr_mcbond_other0.8570.8251935
X-RAY DIFFRACTIONr_mcangle_it1.4781.2342420
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 107 -
Rwork0.376 2217 -
all-2324 -
obs--97.44 %
Refinement TLS params.Method: refined / Origin x: -14.489 Å / Origin y: 11.97 Å / Origin z: -23.689 Å
111213212223313233
T0.5247 Å2-0.0182 Å20.0317 Å2-0.4886 Å2-0.0115 Å2--0.0057 Å2
L1.5887 °2-0.2121 °20.8491 °2-0.2945 °2-0.1924 °2--1.521 °2
S0.0502 Å °0.0355 Å °-0.0489 Å °-0.0093 Å °-0.0036 Å °-0.0116 Å °0.0653 Å °0.045 Å °-0.0467 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 493
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION1A601 - 698
4X-RAY DIFFRACTION1A502 - 505

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