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- PDB-7zau: Fascin-1 in complex with Nb 3E11 -

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Basic information

Entry
Database: PDB / ID: 7zau
TitleFascin-1 in complex with Nb 3E11
Components
  • Fascin
  • Nanobody 3E11
KeywordsSTRUCTURAL PROTEIN / Nanobody / actin-bundling inhibitor
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 / cell cortex / Interleukin-4 and Interleukin-13 signaling / protein-macromolecule adaptor activity / cytoskeleton / cadherin binding / RNA binding / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Fascin / Fascin, metazoans / Fascin domain / Fascin domain / Actin-crosslinking
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBurgess, S.G. / Bayliss, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC24461/A23303 United Kingdom
CitationJournal: Open Biology / Year: 2024
Title: A nanobody inhibitor of Fascin-1 actin-bundling activity and filopodia formation.
Authors: Burgess, S.G. / Paul, N.R. / Richards, M.W. / Ault, J.R. / Askenatzis, L. / Claydon, S.G. / Corbyn, R. / Machesky, L.M. / Bayliss, R.
History
DepositionMar 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fascin
B: Nanobody 3E11
C: Fascin
D: Nanobody 3E11
E: Fascin
F: Nanobody 3E11
G: Fascin
H: Nanobody 3E11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,73529
Polymers279,2118
Non-polymers1,52421
Water17,006944
1
A: Fascin
B: Nanobody 3E11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1758
Polymers69,8032
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fascin
D: Nanobody 3E11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0335
Polymers69,8032
Non-polymers2303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Fascin
F: Nanobody 3E11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,43210
Polymers69,8032
Non-polymers6298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Fascin
H: Nanobody 3E11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0956
Polymers69,8032
Non-polymers2924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.907, 210.324, 105.469
Angle α, β, γ (deg.)90.000, 91.262, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 55079.340 Da / Num. of mol.: 4
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 (E. coli) / References: UniProt: Q16658
#2: Antibody
Nanobody 3E11


Mass: 14723.501 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 944 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.02 M D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine; 0.1 M MES/imidazole pH 6.5, 10% PEG 8000, 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 7, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→105.16 Å / Num. obs: 155971 / % possible obs: 99.86 % / Redundancy: 3.3 % / Biso Wilson estimate: 46.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Rrim(I) all: 0.077 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7600 / CC1/2: 0.599 / Rpim(I) all: 0.427 / Rrim(I) all: 0.748 / % possible all: 97.9

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Processing

Software
NameVersionClassification
DIALSdata scaling
DIALSdata reduction
MOLREPphasing
Zanudadata reduction
PHENIX1.19_4085refinement
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LLP, 2X1O

3llp

2x1o


Resolution: 2.2→59.44 Å / SU ML: 0.4285 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.7365
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2904 7598 5.09 %
Rwork0.2468 141646 -
obs0.2491 149244 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.78 Å2
Refinement stepCycle: LAST / Resolution: 2.2→59.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18284 0 99 944 19327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003218782
X-RAY DIFFRACTIONf_angle_d0.670525475
X-RAY DIFFRACTIONf_chiral_restr0.04692785
X-RAY DIFFRACTIONf_plane_restr0.00393343
X-RAY DIFFRACTIONf_dihedral_angle_d11.87396512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.4812400.46714168X-RAY DIFFRACTION84.95
2.22-2.250.48512300.45824365X-RAY DIFFRACTION88.67
2.25-2.280.46252080.44934460X-RAY DIFFRACTION89.41
2.28-2.310.47612410.44274444X-RAY DIFFRACTION90.67
2.31-2.340.48292250.43134579X-RAY DIFFRACTION92.1
2.34-2.370.49312320.43844567X-RAY DIFFRACTION92.29
2.37-2.40.47082320.4194579X-RAY DIFFRACTION92.97
2.4-2.440.43892520.40124564X-RAY DIFFRACTION92.51
2.44-2.480.46042650.40164539X-RAY DIFFRACTION93.15
2.48-2.520.42742280.38024717X-RAY DIFFRACTION94.01
2.52-2.560.48182110.37044672X-RAY DIFFRACTION94.76
2.56-2.610.45342340.35894706X-RAY DIFFRACTION94.95
2.61-2.660.41642610.35184631X-RAY DIFFRACTION94.44
2.66-2.710.43462410.35244736X-RAY DIFFRACTION95.33
2.71-2.770.4052680.35074745X-RAY DIFFRACTION96.37
2.77-2.830.40622260.32314815X-RAY DIFFRACTION96.64
2.83-2.910.3482460.30054790X-RAY DIFFRACTION97.52
2.91-2.980.33362970.29164820X-RAY DIFFRACTION97.69
2.98-3.070.34252430.28594886X-RAY DIFFRACTION98.07
3.07-3.170.31222850.27754753X-RAY DIFFRACTION98.02
3.17-3.280.35152550.28294911X-RAY DIFFRACTION98.95
3.28-3.420.312650.24714906X-RAY DIFFRACTION98.99
3.42-3.570.31152940.22784877X-RAY DIFFRACTION99.1
3.57-3.760.31482580.21164909X-RAY DIFFRACTION99.44
3.76-3.990.2542710.20234913X-RAY DIFFRACTION99.31
3.99-4.30.20742730.17674891X-RAY DIFFRACTION99.61
4.3-4.740.21393180.15754913X-RAY DIFFRACTION99.58
4.74-5.420.20632610.17384927X-RAY DIFFRACTION99.39
5.42-6.830.22512650.19284943X-RAY DIFFRACTION99.64
6.83-59.440.18572730.19234920X-RAY DIFFRACTION97.94

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