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- PDB-4gp0: The crystal structure of human fascin 1 R149A K150A R151A mutant -

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Basic information

Entry
Database: PDB / ID: 4gp0
TitleThe crystal structure of human fascin 1 R149A K150A R151A 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 / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)111,95352
Polymers108,7432
Non-polymers3,20950
Water6,107339
1
A: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,36418
Polymers54,3721
Non-polymers99317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,58834
Polymers54,3721
Non-polymers2,21733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Fascin
B: Fascin
hetero molecules

A: Fascin
B: Fascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,905104
Polymers217,4864
Non-polymers6,419100
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area21570 Å2
ΔGint-585 kcal/mol
Surface area75050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.907, 71.218, 109.735
Angle α, β, γ (deg.)90.00, 130.28, 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: 54371.547 Da / Num. of mol.: 2 / Mutation: R149A K150A R151A
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 , 6 types, 389 molecules

#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.: 29 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 43.88 %
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: 2.5→30 Å / Num. obs: 33193 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.86
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 2.21 / Num. unique all: 1645 / % possible all: 99.3

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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: 2.5→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 19.336 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24914 1682 5.1 %RANDOM
Rwork0.20002 ---
obs0.20255 31499 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.762 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å2-1.74 Å2
2--0.16 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7460 0 135 339 7934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.027718
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.94510425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42923.587368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.986151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0791559
X-RAY DIFFRACTIONr_chiral_restr0.0770.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215891
LS refinement shellResolution: 2.487→2.551 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 113 -
Rwork0.278 2172 -
obs--96.9 %
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)
11.5458-1.542-0.05452.86010.44471.58860.01630.1193-0.08190.0597-0.20270.1683-0.0465-0.20510.18640.0112-0.001-0.01230.0918-0.03910.06241.83280.2169-23.861
20.59420.1453-0.07771.5616-0.07490.6427-0.08010.03730.0434-0.12170.0394-0.04780.07010.0130.04060.0620.01270.00940.0850.02220.013558.825-24.5135-34.428
31.6715-0.7925-0.2952.8074-0.08643.1185-0.0489-0.10710.08670.2029-0.0241-0.0622-0.03990.2040.0730.0639-0.0107-0.00530.08640.01590.010957.2617-26.7625-13.528
41.3664-0.52520.07262.51850.41061.85230.0456-0.015-0.13450.0853-0.0077-0.07310.06240.0648-0.03780.0456-0.0211-0.02490.0571-0.00740.059622.1737-22.10791.8703
50.55110.17660.44330.95850.87321.3024-0.00940.03810.0162-0.1229-0.02860.0174-0.23250.02160.0380.0911-0.00970.0110.0799-0.01970.060915.8846-17.3399-3.393
60.67980.2190.132.52150.60340.48930.04670.0497-0.0621-0.1404-0.09240.119-0.0955-0.07620.04570.05140.0415-0.01590.1084-0.04410.03637.8473-32.7517-21.3436
72.55070.9537-0.53352.23990.1392.8632-0.0306-0.0465-0.5450.2225-0.0290.11620.4709-0.30260.05950.1185-0.0382-0.00250.04240.00530.21817.8119-61.2052-17.1113
82.32210.4338-0.30251.2088-0.00681.06420.00780.04450.0178-0.0657-0.041-0.1354-0.01780.13080.03310.06940.0423-0.02020.054-0.00660.077128.577-40.3908-22.0665
93.21360.84330.96494.65190.25792.95670.1503-0.2589-0.18510.4337-0.06-0.26820.2939-0.0653-0.09030.12520.0216-0.05280.04010.00690.036428.4417-47.4607-12.3403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 142
2X-RAY DIFFRACTION2A143 - 395
3X-RAY DIFFRACTION3A396 - 493
4X-RAY DIFFRACTION4B8 - 77
5X-RAY DIFFRACTION5B78 - 155
6X-RAY DIFFRACTION6B156 - 304
7X-RAY DIFFRACTION7B305 - 376
8X-RAY DIFFRACTION8B377 - 451
9X-RAY DIFFRACTION9B452 - 493

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