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- PDB-6i16: CRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 15 -

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Basic information

Entry
Database: PDB / ID: 6i16
TitleCRYSTAL STRUCTURE OF FASCIN IN COMPLEX WITH COMPOUND 15
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 / Interleukin-4 and Interleukin-13 signaling / cell cortex / protein-macromolecule adaptor activity / 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-H0B / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)55,0893
Polymers54,6021
Non-polymers4872
Water4,954275
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 area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.620, 87.300, 98.100
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-H0B / 6-[(3,4-dichlorophenyl)methyl]-~{N}-(1-methylpyrazol-4-yl)-5-oxidanylidene-1,6-naphthyridine-8-carboxamide


Mass: 428.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15Cl2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 48.25 %
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 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→60.62 Å / Num. obs: 35194 / % possible obs: 98.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 26.188 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.036 / Rrim(I) all: 0.087 / Net I/σ(I): 15.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 2.2 / Rpim(I) all: 0.338 / Rrim(I) all: 0.805 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.22data extraction
xia20.5.582data reduction
xia20.5.582data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I10

6i10


Resolution: 2→51.59 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.174 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.172
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1688 4.8 %RANDOM
Rwork0.2025 ---
obs0.2043 33451 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.59 Å2 / Biso mean: 34.837 Å2 / Biso min: 16.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--1 Å20 Å2
3----1.36 Å2
Refinement stepCycle: final / Resolution: 2→51.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 33 275 4092
Biso mean--32.92 36.99 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0143914
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173384
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.6695298
X-RAY DIFFRACTIONr_angle_other_deg1.6541.6527939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9365487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58121.396222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27115640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6811533
X-RAY DIFFRACTIONr_chiral_restr0.1140.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024523
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02769
X-RAY DIFFRACTIONr_mcbond_it1.0681.9571946
X-RAY DIFFRACTIONr_mcbond_other1.0671.9561944
X-RAY DIFFRACTIONr_mcangle_it1.7072.9282433
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 114 -
Rwork0.255 2444 -
all-2558 -
obs--97.56 %
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)
13.2205-0.15581.14322.3027-0.16392.2248-0.00570.1223-0.0674-0.07010.0175-0.26870.10960.2035-0.01180.00950.00050.01040.1012-0.02560.03864.9038.665-7.529
22.0259-0.06730.83562.40210.09333.37980.16430.1298-0.2893-0.07410.0005-0.06050.4340.1139-0.16470.08830.0014-0.03160.0595-0.04440.0639-13.711-3.59-23.66
30.9242-0.4051-0.91273.34050.47773.94020.10050.25020.1503-0.60250.0570.0721-0.593-0.1582-0.15740.24320.00540.00990.16440.01220.0998-22.1119.781-43.838
42.3937-0.76860.74492.27480.75013.97570.034400.2586-0.03320.00480.0387-0.2461-0.0934-0.03920.01950.01050.01440.048-0.01450.0539-23.94720.963-17.877
50.7791-0.02650.46680.39470.06441.05210.0343-0.0524-0.0042-0.06320.0202-0.00980.0176-0.05-0.05450.1293-0.01080.00460.135-0.00750.1133-12.51710.929-19.009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 138
2X-RAY DIFFRACTION2A139 - 260
3X-RAY DIFFRACTION3A261 - 384
4X-RAY DIFFRACTION4A385 - 493
5X-RAY DIFFRACTION5A501
6X-RAY DIFFRACTION5A601 - 875
7X-RAY DIFFRACTION5L502

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