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- PDB-6i18: CRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH BDP-13176 -

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Basic information

Entry
Database: PDB / ID: 6i18
TitleCRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH BDP-13176
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 / cell-cell junction / actin filament binding / 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 / 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
ACETATE ION / Chem-H0N / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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)55,4698
Polymers54,6021
Non-polymers8677
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint15 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.660, 87.810, 98.280
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 (E. coli) / Strain (production host): BL21(DE3)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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-H0N / 5-[(3,4-dichlorophenyl)methyl]-4-oxidanylidene-1-piperidin-4-yl-~{N}-pyridin-4-yl-pyrazolo[4,3-c]pyridine-7-carboxamide


Mass: 497.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22Cl2N6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.36 Å3/Da / Density % sol: 47.82 % / Mosaicity: 0.214 °
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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.49→49.35 Å / Num. obs: 84863 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.368 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Net I/σ(I): 18 / Num. measured all: 543840
Reflection shellResolution: 1.49→1.53 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.014 / Mean I/σ(I) obs: 1.7 / Rpim(I) all: 0.464 / Rrim(I) all: 1.195 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia20.4.0.0data scaling
PDB_EXTRACT3.22data extraction
xia20.4.0.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I10

6i10


Resolution: 1.49→49.35 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.176 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.068
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 4172 4.9 %RANDOM
Rwork0.1724 ---
obs0.1735 80613 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.29 Å2 / Biso mean: 26.229 Å2 / Biso min: 13.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.97 Å20 Å2
3----1.49 Å2
Refinement stepCycle: final / Resolution: 1.49→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 58 349 4191
Biso mean--28.09 34.65 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0143960
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173443
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.6735355
X-RAY DIFFRACTIONr_angle_other_deg1.6271.6688079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2235493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30121.396222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24315645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1761533
X-RAY DIFFRACTIONr_chiral_restr0.1080.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024565
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02775
X-RAY DIFFRACTIONr_mcbond_it0.9211.2751961
X-RAY DIFFRACTIONr_mcbond_other0.9121.2751959
X-RAY DIFFRACTIONr_mcangle_it1.4291.9122457
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 309 -
Rwork0.294 5864 -
all-6173 -
obs--99.9 %
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)
12.3825-0.23830.89261.68820.08892.91680.01290.06550.00350.00160.0226-0.22260.10440.2367-0.03550.02430.0027-0.00790.0243-0.01970.11745.3218.486-7.57
21.8288-0.02430.32561.8603-0.08762.28320.03050.0731-0.1612-0.05420.0236-0.01850.22390.0242-0.0540.0676-0.0087-0.00880.0086-0.02270.1118-13.567-3.58-23.437
30.57350.0056-0.25131.7072-0.12932.85-0.00150.15780.0508-0.13410.05660.0622-0.2242-0.181-0.05510.0878-0.0093-0.0060.07970.0090.1419-21.5719.919-43.715
41.8923-0.64640.69471.82650.45583.6740.0174-0.0220.16990.05250.01720.0617-0.0925-0.144-0.03450.02710.00880.01320.0117-0.01440.1176-23.30721.257-17.742
50.518-0.13760.45540.4793-0.11111.0603-0.0059-0.00850.00890.01470.03160.00160.0077-0.06-0.02570.1413-0.01420.0180.1224-0.02070.2337-12.16210.652-19.2
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 138
2X-RAY DIFFRACTION2A139 - 260
3X-RAY DIFFRACTION3A261 - 384
4X-RAY DIFFRACTION4A385 - 493
5X-RAY DIFFRACTION5A507
6X-RAY DIFFRACTION5A601 - 949
7X-RAY DIFFRACTION5A501 - 506

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