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- PDB-4z68: Hybrid structural analysis of the Arp2/3 regulator Arpin identifi... -

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Basic information

Entry
Database: PDB / ID: 4z68
TitleHybrid structural analysis of the Arp2/3 regulator Arpin identifies its acidic tail as a primary binding epitope
Components
  • GLU-ILE-ARG-GLU-GLN-GLY-ASP-GLY-ALA-GLU-ASP-GLU
  • Tankyrase-2
KeywordsPROTEIN BINDING / cell migration / Arpin / Arp 2/3 / actin polymerization
Function / homology
Function and homology information


negative regulation of lamellipodium morphogenesis / negative regulation of actin nucleation / directional locomotion / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material ...negative regulation of lamellipodium morphogenesis / negative regulation of actin nucleation / directional locomotion / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / negative regulation of cell migration / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / lamellipodium / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Arpin / Arp2/3-interacting proteins Arpin / Ankyrin repeat / : / Ankyrin repeat-containing domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. ...Arpin / Arp2/3-interacting proteins Arpin / Ankyrin repeat / : / Ankyrin repeat-containing domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Arpin / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.859 Å
AuthorsFetics, S.K. / Campanacci, V. / Dang, I. / Gautreau, A. / Cherfils, J.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Structure / Year: 2016
Title: Hybrid Structural Analysis of the Arp2/3 Regulator Arpin Identifies Its Acidic Tail as a Primary Binding Epitope.
Authors: Susan Fetics / Aurélien Thureau / Valérie Campanacci / Magali Aumont-Nicaise / Irène Dang / Alexis Gautreau / Javier Pérez / Jacqueline Cherfils /
Abstract: Arpin is a newly discovered regulator of actin polymerization at the cell leading edge, which steers cell migration by exerting a negative control on the Arp2/3 complex. Arpin proteins have an acidic ...Arpin is a newly discovered regulator of actin polymerization at the cell leading edge, which steers cell migration by exerting a negative control on the Arp2/3 complex. Arpin proteins have an acidic tail homologous to the acidic motif of the VCA domain of nucleation-promoting factors (NPFs). This tail is predicted to compete with the VCA of NPFs for binding to the Arp2/3 complex, thereby mitigating activation and/or tethering of the complex to sites of actin branching. Here, we investigated the structure of full-length Arpin using synchrotron small-angle X-ray scattering, and of its acidic tail in complex with an ankyrin repeats domain using X-ray crystallography. The data were combined in a hybrid model in which the acidic tail extends from the globular core as a linear peptide and forms a primary epitope that is readily accessible in unbound Arpin and suffices to tether Arpin to interacting proteins with high affinity.
History
DepositionApr 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tankyrase-2
E: GLU-ILE-ARG-GLU-GLN-GLY-ASP-GLY-ALA-GLU-ASP-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5344
Polymers18,3422
Non-polymers1922
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-19 kcal/mol
Surface area8180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.543, 43.806, 107.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tankyrase-2 / TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / ...TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 16993.242 Da / Num. of mol.: 1 / Fragment: ankyrin repeats domain, UNP residues 490-644
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pETG30A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta PlysS / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Protein/peptide GLU-ILE-ARG-GLU-GLN-GLY-ASP-GLY-ALA-GLU-ASP-GLU


Mass: 1348.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z6K5*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, isopropanol / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.859→40.574 Å / Num. obs: 12297 / % possible obs: 99.5 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.8
Reflection shellResolution: 1.859→1.97 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 5 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TWR

3twr


Resolution: 1.859→40.574 Å / FOM work R set: 0.8757 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 1230 10.01 %
Rwork0.1698 11063 -
obs0.1745 12293 99.45 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.009 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 84.93 Å2 / Biso mean: 20.6 Å2 / Biso min: 8.48 Å2
Baniso -1Baniso -2Baniso -3
1--4.3602 Å20 Å2-0 Å2
2--4.9973 Å2-0 Å2
3----0.637 Å2
Refinement stepCycle: final / Resolution: 1.859→40.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 10 68 1328
Biso mean--39.22 28.74 -
Num. residues----167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061307
X-RAY DIFFRACTIONf_angle_d1.0411780
X-RAY DIFFRACTIONf_chiral_restr0.067202
X-RAY DIFFRACTIONf_plane_restr0.005236
X-RAY DIFFRACTIONf_dihedral_angle_d14.675470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8591-1.93360.25161260.17031142126896
1.9336-2.02160.25451350.167712021337100
2.0216-2.12810.22271350.167912171352100
2.1281-2.26150.21021350.161212151350100
2.2615-2.43610.2111370.165912361373100
2.4361-2.68120.20451360.164912211357100
2.6812-3.0690.24771380.182812421380100
3.069-3.86620.20091390.16212531392100
3.8662-40.58410.20591490.1761335148499

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