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- PDB-4gp3: The crystal structure of human fascin 1 K358A mutant -

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Basic information

Entry
Database: PDB / ID: 4gp3
TitleThe crystal structure of human fascin 1 K358A 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 / 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 / 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
BROMIDE ION / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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

Downloads & links

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Assembly

Deposited unit
A: Fascin
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,93034
Polymers109,0882
Non-polymers1,84232
Water7,188399
1
A: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,23712
Polymers54,5441
Non-polymers69311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,69322
Polymers54,5441
Non-polymers1,14921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-163 kcal/mol
Surface area39260 Å2
MethodPISA
4
B: Fascin
hetero molecules

B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,38544
Polymers109,0882
Non-polymers2,29842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7270 Å2
ΔGint-199 kcal/mol
Surface area38860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.906, 70.737, 110.513
Angle α, β, γ (deg.)90.00, 130.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 54543.777 Da / Num. of mol.: 2 / Mutation: K358A
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
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
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: 2.25→30 Å / Num. obs: 44686 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 18.53
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 2.53 / Num. unique all: 2199 / % possible all: 99.8

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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: 2.25→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 15.202 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25238 2245 5 %RANDOM
Rwork0.20281 ---
obs0.20535 42318 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.371 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å20 Å2-2.32 Å2
2--2.5 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7495 0 67 399 7961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.027706
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9410416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68123.387372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.916151258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2021564
X-RAY DIFFRACTIONr_chiral_restr0.0770.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215924
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 147 -
Rwork0.293 2833 -
obs--93.39 %
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)
12.16181.6083-0.31673.1584-0.64271.6282-0.0364-0.0684-0.1579-0.1461-0.1801-0.2792-0.0620.23960.21660.0386-0.0009-0.02210.12020.05290.0757-42.47437.055224.2924
20.7486-0.3159-0.36323.0031-0.17181.1585-0.0743-0.03870.00010.1509-0.07750.05490.13350.04320.15180.0794-0.04060.00790.1517-0.0040.0324-59.182313.294835.7335
31.31930.6151-1.0343.6739-0.63244.8742-0.0280.24780.0128-0.3049-0.0224-0.0303-0.0217-0.23210.05040.0633-0.0091-0.01060.0965-0.02330.034-57.09110.985615.1952
41.67420.02990.15762.2803-0.82243.05110.20030.0984-0.1069-0.0823-0.15390.10730.0658-0.2154-0.04640.06410.0192-0.01960.1009-0.01090.059-22.771715.3019-1.6551
50.9939-0.33350.25351.4279-0.8081.75920.0182-0.05920.11540.04230.0006-0.0376-0.2449-0.0737-0.01870.0851-0.02210.01020.0686-0.02340.0559-14.498818.83185.8895
61.47950.1603-0.23821.8140.19151.14550.0599-0.1250.03410.0881-0.0048-0.0431-0.17250.0016-0.05520.1144-0.059-0.02810.13230.01390.0225-8.823713.057919.5942
74.32480.53891.27033.6960.552.9520.30850.0128-0.53850.2007-0.1422-0.37220.28310.297-0.16630.0808-0.0273-0.1290.16020.0560.2768-5.297-15.630420.8835
80.2463-0.0585-0.06197.86152.37397.372-0.0490.1199-0.5696-0.1089-0.1165-0.66710.65830.57350.16550.19910.0411-0.03730.2092-0.20541.4464-7.568-23.50414.858
93.41190.29060.74162.6718-0.72041.17880.1954-0.1108-0.16190.0348-0.12030.17290.1516-0.1374-0.07510.1041-0.1067-0.02690.11710.02050.0426-26.8317-7.993518.6899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 146
2X-RAY DIFFRACTION2A147 - 376
3X-RAY DIFFRACTION3A377 - 493
4X-RAY DIFFRACTION4B8 - 78
5X-RAY DIFFRACTION5B79 - 162
6X-RAY DIFFRACTION6B163 - 262
7X-RAY DIFFRACTION7B263 - 313
8X-RAY DIFFRACTION8B314 - 363
9X-RAY DIFFRACTION9B364 - 493

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