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- PDB-6i12: CRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 5 -

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Basic information

Entry
Database: PDB / ID: 6i12
TitleCRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 5
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 / microvillus / establishment or maintenance of cell polarity / 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 / growth cone / actin binding / 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 / 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-H08 / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)55,0543
Polymers54,6021
Non-polymers4522
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.550, 87.410, 98.250
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-H08 / 2-[(4-chlorophenyl)methyl]-~{N}-(1-methylpyrazol-4-yl)-1-oxidanylidene-isoquinoline-4-carboxamide


Mass: 392.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.38 Å3/Da / Density % sol: 48.34 % / Mosaicity: 0.127 °
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: I02 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→60.55 Å / Num. obs: 63454 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 22.448 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 15.8 / Num. measured all: 409438
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.085 / Mean I/σ(I) obs: 1.7 / Rpim(I) all: 0.508 / Rrim(I) all: 1.283 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia20.3.8.0data scaling
PDB_EXTRACT3.22data extraction
xia20.3.8.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I10

6i10


Resolution: 1.65→51.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.939 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.091
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 3062 4.8 %RANDOM
Rwork0.1831 ---
obs0.1842 60322 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.36 Å2 / Biso mean: 31.222 Å2 / Biso min: 13.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2--1.3 Å20 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 1.65→51.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 32 294 4110
Biso mean--27.26 36.73 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0143922
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173397
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6695310
X-RAY DIFFRACTIONr_angle_other_deg1.5821.6527969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3185489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56421.396222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5115642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7261533
X-RAY DIFFRACTIONr_chiral_restr0.10.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024536
X-RAY DIFFRACTIONr_gen_planes_other0.010.02773
X-RAY DIFFRACTIONr_mcbond_it0.9511.5221951
X-RAY DIFFRACTIONr_mcbond_other0.9481.5221949
X-RAY DIFFRACTIONr_mcangle_it1.5232.282441
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 247 -
Rwork0.363 4382 -
all-4629 -
obs--100 %
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)
12.9435-0.16060.89462.2145-0.19822.4752-0.01820.0964-0.02250.00550.005-0.23070.08960.20380.01320.0483-0.0063-0.00770.029-0.01450.05624.9118.704-7.564
22.7096-0.00510.81931.98090.01433.12590.17590.098-0.3688-0.03540.0209-0.02870.4150.0733-0.19680.12650.0043-0.03820.0119-0.03470.1144-13.577-3.567-23.773
31.214-0.1078-0.83873.59580.25494.21940.08790.29220.1363-0.59570.07420.0468-0.5603-0.1439-0.16220.2624-0.0015-0.00310.09770.01570.1171-22.00919.814-43.9
42.5796-0.53290.68622.34720.45793.75230.0304-0.04210.2102-0.0138-0.00270.0694-0.2254-0.152-0.02770.05260.01440.00730.0121-0.01560.0767-23.95320.992-17.906
51.033-0.22050.80930.5932-0.12741.2068-0.0149-0.0111-0.0005-0.01270.04540.0239-0.0165-0.064-0.03050.173-0.01120.02640.1181-0.01890.1669-12.21311.067-18.793
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 DIFFRACTION5A502
6X-RAY DIFFRACTION5A601 - 894
7X-RAY DIFFRACTION5A501

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