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- PDB-4gov: The crystal structure of human fascin 1 S39D mutant -

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Basic information

Entry
Database: PDB / ID: 4gov
TitleThe crystal structure of human fascin 1 S39D 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: 2.2 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)111,27532
Polymers109,2602
Non-polymers2,01630
Water10,106561
1
A: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,39712
Polymers54,6301
Non-polymers76811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,87820
Polymers54,6301
Non-polymers1,24819
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Fascin
hetero molecules

B: Fascin
hetero molecules

A: Fascin
hetero molecules

A: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,55164
Polymers218,5204
Non-polymers4,03160
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area15990 Å2
ΔGint-277 kcal/mol
Surface area74250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.250, 70.723, 111.058
Angle α, β, γ (deg.)90.00, 130.68, 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: 54629.887 Da / Num. of mol.: 2 / Mutation: S39D
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, 591 molecules

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


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 13 / 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.: 10 / 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.: 561 / 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: 44.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM 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: 2.2→30 Å / Num. obs: 48266 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 28.18
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.99 / Num. unique all: 2372 / % possible all: 99.9

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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: 2.2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.735 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23432 2438 5.1 %RANDOM
Rwork0.19609 ---
obs0.19804 45824 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.938 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.74 Å2
2---0.76 Å20 Å2
3---1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7451 0 87 561 8099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.027682
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.94210372
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245953
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36323.422374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.645151250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1661564
X-RAY DIFFRACTIONr_chiral_restr0.0720.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215888
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.194→2.251 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 166 -
Rwork0.269 2962 -
obs--90.61 %
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)
11.5048-1.533-0.79512.53691.10381.6238-0.06160.0553-0.14460.1449-0.12520.26140.0651-0.11420.18680.04760.0257-0.00630.0803-0.05150.058543.2315-0.7944-25.3623
20.82220.2917-0.69313.1688-0.07061.5302-0.12010.053-0.048-0.1732-0.0486-0.12820.2254-0.12150.16870.0770.0440.01570.1341-0.03110.032959.4662-24.4688-34.4934
31.9148-0.6991-1.10684.76961.36116.7573-0.17-0.2351-0.06260.2655-0.02260.114-0.06520.21020.19260.04390.0070.00010.05530.02120.015657.0872-27.188-14.1216
42.3022-0.6444-0.21023.39950.66252.39140.212-0.06420.09110.1094-0.1388-0.0842-0.0970.151-0.07320.0454-0.04560.01520.0804-0.00610.02221.1366-17.8151.5245
50.7276-0.47670.15832.5285-0.01190.8860.12070.0498-0.2028-0.2426-0.08330.2805-0.0213-0.0933-0.03740.05720.0696-0.05070.1389-0.03860.092210.6264-39.8472-18.8041
65.0758-0.29610.78054.7365-0.51481.72290.1782-0.0891-0.0003-0.1006-0.0728-0.48890.12960.1159-0.10540.12510.11420.01090.1292-0.0170.115929.4773-45.9674-18.2421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 151
2X-RAY DIFFRACTION2A152 - 395
3X-RAY DIFFRACTION3A396 - 493
4X-RAY DIFFRACTION4B7 - 130
5X-RAY DIFFRACTION5B131 - 419
6X-RAY DIFFRACTION6B420 - 493

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