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- PDB-5ly5: Arcadin-1 from Pyrobaculum calidifontis -

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Basic information

Entry
Database: PDB / ID: 5ly5
TitleArcadin-1 from Pyrobaculum calidifontis
Componentsarcadin-1
KeywordsUNKNOWN FUNCTION / arcade clauster / crenactin
Function / homologyArcadin 1 / Arcadin 1 / Arcadin_1 domain-containing protein
Function and homology information
Biological speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsIzore, T. / Lowe, J.
CitationJournal: Elife / Year: 2016
Title: Crenactin forms actin-like double helical filaments regulated by arcadin-2.
Authors: Thierry Izoré / Danguole Kureisaite-Ciziene / Stephen H McLaughlin / Jan Löwe /
Abstract: The similarity of eukaryotic actin to crenactin, a filament-forming protein from the crenarchaeon supports the theory of a common origin of Crenarchaea and Eukaryotes. Monomeric structures of ...The similarity of eukaryotic actin to crenactin, a filament-forming protein from the crenarchaeon supports the theory of a common origin of Crenarchaea and Eukaryotes. Monomeric structures of crenactin and actin are similar, although their filament architectures were suggested to be different. Here we report that crenactin forms double helical filaments that show exceptional similarity to eukaryotic F-actin. With cryo-electron microscopy and helical reconstruction we solved the structure of the crenactin filament to 3.8 Å resolution. When forming double filaments, the 'hydrophobic plug' loop in crenactin rearranges. Arcadin-2, also encoded by the arcade gene cluster, binds tightly with its C-terminus to the hydrophobic groove of crenactin. Binding is reminiscent of eukaryotic actin modulators such as cofilin and thymosin β4 and arcadin-2 is a depolymeriser of crenactin filaments. Our work further supports the theory of shared ancestry of Eukaryotes and Crenarchaea.
History
DepositionSep 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: arcadin-1


Theoretical massNumber of molelcules
Total (without water)12,6321
Polymers12,6321
Non-polymers00
Water64936
1
A: arcadin-1

A: arcadin-1


Theoretical massNumber of molelcules
Total (without water)25,2652
Polymers25,2652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_777-y+2,-x+2,-z+13/61
Buried area2930 Å2
ΔGint-17 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.051, 84.051, 61.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein arcadin-1


Mass: 12632.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZVH7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 7.2 % MPD (v/v), 14 mM MgCl2, 50 mM sodium cacodylate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9095 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Net I/σ(I): 26.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 19.7 % / Rmerge(I) obs: 1.348 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.903 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.37 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23032 472 5.2 %RANDOM
Rwork0.20844 ---
obs0.20961 8598 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 55.337 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms608 0 0 36 644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019615
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.982833
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.226575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg48.73926.53826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52715118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.961152
X-RAY DIFFRACTIONr_chiral_restr0.1690.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021437
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_it6.22511.804306
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.55615.052379
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.21713.601308
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.51371.17853
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 31 -
Rwork0.305 620 -
obs--100 %

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