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- PDB-4goy: The crystal structure of human fascin 1 K41A mutant -

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Basic information

Entry
Database: PDB / ID: 4goy
TitleThe crystal structure of human fascin 1 K41A mutant
ComponentsFascin
KeywordsPROTEIN BINDING / beta-trefoil / actin bundling protein / cancer / metastasis / cell migration / Actin-binding / Phosphoprotein / Actin
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 / cell migration / actin cytoskeleton / 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
BROMIDE ION / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYang, S.Y. / Huang, F.K. / Huang, J. / Chen, S. / Jakoncic, J. / Leo-Macias, A. / Diaz-Avalos, R. / Chen, L. / Zhang, J.J. / Huang, X.Y.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Molecular mechanism of fascin function in filopodial formation.
Authors: Yang, S. / Huang, F.K. / Huang, J. / Chen, S. / Jakoncic, J. / Leo-Macias, A. / Diaz-Avalos, R. / Chen, L. / Zhang, J.J. / Huang, X.Y.
History
DepositionAug 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fascin
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,78827
Polymers109,0882
Non-polymers1,70125
Water8,125451
1
A: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,20211
Polymers54,5441
Non-polymers65810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,58716
Polymers54,5441
Non-polymers1,04315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-103 kcal/mol
Surface area39530 Å2
MethodPISA
4
B: Fascin
hetero molecules

B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,17332
Polymers109,0882
Non-polymers2,08630
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5760 Å2
ΔGint-119 kcal/mol
Surface area39480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.138, 70.595, 110.979
Angle α, β, γ (deg.)90.00, 130.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 54543.773 Da / Num. of mol.: 2 / Mutation: K41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAN1, FSCN1, HSN, SNL / Plasmid: pGEX4T-Fascin1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q16658

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Non-polymers , 5 types, 476 molecules

#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Hepes, 16% PEG 4000, 1% isopropanol , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 25, 2010
RadiationMonochromator: Si 111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 42281 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.71
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.51 / Num. unique all: 2086 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LLP

3llp


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 16.024 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.467 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24501 2129 5 %RANDOM
Rwork0.20134 ---
obs0.20357 40142 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.797 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.81 Å2
2---0.03 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7475 0 62 451 7988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.027683
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9410382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78823.423371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.946151252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8961563
X-RAY DIFFRACTIONr_chiral_restr0.0860.21126
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215903
LS refinement shellResolution: 2.291→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 117 -
Rwork0.281 2570 -
obs--87.81 %
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)
11.14541.5355-0.82562.7135-1.20011.7539-0.04860-0.0574-0.1239-0.035-0.15220.113-0.00620.08360.0481-0.0267-0.01550.06490.03710.0671-47.3209-0.971326.9489
21.0910.19640.10974.23460.26371.518-0.03050.07750.26060.0597-0.0040.2266-0.1469-0.18790.03450.0433-0.0356-0.01060.13770.03760.0843-62.7511-4.063634.0238
31.8361-0.6963-0.81382.4831-2.04049.9236-0.3404-0.261-0.24230.1765-0.16910.09950.74780.7570.50950.16850.04450.08110.11020.05250.0604-56.2621-37.527937.0389
41.61870.5158-0.90934.7665-1.48366.7722-0.09450.22220.0094-0.1622-0.0372-0.1197-0.168-0.15750.13170.0295-0.0064-0.00430.038-0.00470.0192-56.4235-24.073414.5004
51.8880.49950.30952.2995-0.84582.77950.28080.1071-0.0593-0.1973-0.22910.13190.0843-0.1904-0.05170.09030.0499-0.00420.11-0.02680.0682-22.8371-19.8262-1.4838
61.0261-0.43480.29911.8616-1.02652.27550.1036-0.0250.15330.0662-0.0896-0.1058-0.2419-0.0384-0.0140.0589-0.01980.02760.0582-0.01740.0615-14.763-15.99495.7688
71.11660.59010.52963.0604-0.02761.05450.1093-0.0848-0.09290.3154-0.1032-0.3066-0.15160.0837-0.0060.0976-0.0911-0.04290.14290.04240.0579-7.7426-28.209221.3015
81.23680.4556-1.29915.7330.1834.3367-0.02850.1416-0.50910.0335-0.0692-1.01080.41440.2270.09780.05640.0296-0.05590.1328-0.03160.4187-6.806-54.930914.5031
92.7398-0.87770.37263.7716-0.44861.02880.13380.0028-0.03520.1296-0.12490.25220.085-0.1284-0.00890.1046-0.10640.00820.1210.00160.0731-26.3607-43.124918.7724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 189
2X-RAY DIFFRACTION2A190 - 266
3X-RAY DIFFRACTION3A267 - 385
4X-RAY DIFFRACTION4A386 - 493
5X-RAY DIFFRACTION5B8 - 77
6X-RAY DIFFRACTION6B78 - 162
7X-RAY DIFFRACTION7B163 - 289
8X-RAY DIFFRACTION8B290 - 362
9X-RAY DIFFRACTION9B363 - 493

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