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- PDB-7whf: Heimdallarchaeota gelsolin (2DGel) bound to rabbit actin -

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Basic information

Entry
Database: PDB / ID: 7whf
TitleHeimdallarchaeota gelsolin (2DGel) bound to rabbit actin
Components
  • Actin, alpha skeletal muscle
  • Heimdallarchaeota Gelsolin domain-containing protein 2DGel
KeywordsSTRUCTURAL PROTEIN / Asgard / gelsolin / actin / filament
Function / homology
Function and homology information


actin filament severing / barbed-end actin filament capping / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly ...actin filament severing / barbed-end actin filament capping / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate 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 / actin filament binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. ...Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Gelsolin-like domain-containing protein / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
G: Heimdallarchaeota Gelsolin domain-containing protein 2DGel
B: Actin, alpha skeletal muscle
C: Heimdallarchaeota Gelsolin domain-containing protein 2DGel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,18426
Polymers148,2644
Non-polymers1,92022
Water9,962553
1
A: Actin, alpha skeletal muscle
G: Heimdallarchaeota Gelsolin domain-containing protein 2DGel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,00012
Polymers74,1322
Non-polymers86810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-112 kcal/mol
Surface area24840 Å2
MethodPISA
2
B: Actin, alpha skeletal muscle
C: Heimdallarchaeota Gelsolin domain-containing protein 2DGel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,18414
Polymers74,1322
Non-polymers1,05212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-110 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.261, 100.353, 171.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules ABGC

#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 Heimdallarchaeota Gelsolin domain-containing protein 2DGel


Mass: 32021.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Heimdallarchaeota archaeon LC_3 (archaea)
Gene: HeimC3_12500 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9NVH4

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Non-polymers , 4 types, 575 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.4 mM Heimdallarchaeota 2DGel 0.4 mM rabbit actin 1 mM CaCl2 0.1 M HEPES pH 7.0 10% w/v polyethylene glycol 6000

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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 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 63053 / % possible obs: 95.3 % / Redundancy: 5.9 % / CC1/2: 0.954 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.027 / Rrim(I) all: 0.067 / Net I/σ(I): 24.7
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1312 / CC1/2: 0.827 / Rpim(I) all: 0.286 / Rrim(I) all: 0.714

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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: 2.1→19.79 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216 --
Rwork0.165 --
obs-63045 81.3 %
Displacement parametersBiso mean: 39.69 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9111 0 92 553 9756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01319424
X-RAY DIFFRACTIONf_angle_d1.374412788
X-RAY DIFFRACTIONf_chiral_restr0.08831405
X-RAY DIFFRACTIONf_plane_restr0.00851647
X-RAY DIFFRACTIONf_dihedral_angle_d23.04133520
LS refinement shellResolution: 2.1→2.176 Å /
RfactorNum. reflection
Rfree0.269 165
Rwork0.202 3313

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