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- PDB-7whg: Lokiarchaeota gelsolin (2DGel) bound to two molecules of rabbit actin -

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Basic information

Entry
Database: PDB / ID: 7whg
TitleLokiarchaeota gelsolin (2DGel) bound to two molecules of rabbit actin
Components
  • Actin, alpha skeletal muscle
  • Lokiarchaeota gelsolin (2DGel)
KeywordsSTRUCTURAL PROTEIN / Asgard / gelsolin / actin / filament
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Candidatus Lokiarchaeota archaeon (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsRobinson, R.C. / Akil, C.
Funding support4items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR19S5
Japan Society for the Promotion of Science (JSPS)JP20H00476
Simons FoundationGBMF9743
Other privateMoore Foundation GBMF9743
CitationJournal: Commun Biol / Year: 2022
Title: Structural and biochemical evidence for the emergence of a calcium-regulated actin cytoskeleton prior to eukaryogenesis
Authors: Akil, C. / Tran, L.T. / Orhant-Prioux, M. / Baskaran, Y. / Senju, Y. / Takeda, S. / Chotchuang, P. / Muengsaen, D. / Schulte, A. / Manser, E. / Blanchoin, L. / Robinson, R.C.
History
DepositionDec 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
G: Lokiarchaeota gelsolin (2DGel)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,98014
Polymers121,7653
Non-polymers1,21511
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-140 kcal/mol
Surface area41070 Å2
Unit cell
Length a, b, c (Å)87.662, 72.057, 100.385
Angle α, β, γ (deg.)90.000, 92.080, 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 Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACTA1, ACTA / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Lokiarchaeota gelsolin (2DGel)


Mass: 37544.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Lokiarchaeota archaeon (archaea)
Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.4 mM Loki2DGel 0.4 mM rabbit actin 0.1 M Tris-HCl, pH 7.0 0.2 M magnesium chloride hexahydrate 10% w/v polyethylene glycol 8000 1 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→20 Å / Num. obs: 17387 / % possible obs: 100 % / Redundancy: 5.5 % / CC1/2: 0.887 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.077 / Rrim(I) all: 0.183 / Net I/σ(I): 10.5
Reflection shellResolution: 3.25→3.4 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.189 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1504 / CC1/2: 0.523 / Rpim(I) all: 0.578 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBT

3hbt


Resolution: 3.25→20 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232 --
Rwork0.175 --
obs-17387 100 %
Displacement parametersBiso mean: 68.14 Å2
Refinement stepCycle: LAST / Resolution: 3.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7544 0 63 0 7607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01117753
X-RAY DIFFRACTIONf_angle_d1.316110500
X-RAY DIFFRACTIONf_chiral_restr0.06441164
X-RAY DIFFRACTIONf_plane_restr0.00811343
X-RAY DIFFRACTIONf_dihedral_angle_d19.77712880
LS refinement shellResolution: 3.25→3.46 Å /
Rfactor% reflection
Rfree0.324 -
Rwork0.245 -
obs-99.8 %

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