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- PDB-6ka4: Cryo-EM structure of the AtMLKL3 tetramer -

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Basic information

Entry
Database: PDB / ID: 6ka4
TitleCryo-EM structure of the AtMLKL3 tetramer
ComponentsF22L4.1 protein
KeywordsMEMBRANE PROTEIN / Plant MLKLs / Cryo-EM / Tetramer
Function / homology
Function and homology information


protein kinase activity / ATP binding / membrane
Similarity search - Function
Domain of unknown function DUF1221 / Protein of unknown function (DUF1221) / : / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLisa, M. / Huang, M. / Zhang, X. / Ryohei, T.N. / Leila, B.K. / Isabel, M.L.S. / Florence, J. / Viera, K. / Dmitry, L. / Jane, E.P. ...Lisa, M. / Huang, M. / Zhang, X. / Ryohei, T.N. / Leila, B.K. / Isabel, M.L.S. / Florence, J. / Viera, K. / Dmitry, L. / Jane, E.P. / James, M.M. / Kay, H. / Paul, S.L. / Chai, J. / Takaki, M.
CitationJournal: To Be Published
Title: Cryo-EM structure of the AtMLKL3 tetramer
Authors: Lisa, M. / Huang, M. / Zhang, X. / Ryohei, T.N. / Leila, B.K. / Isabel, M.L.S. / Florence, J. / Viera, K. / Dmitry, L. / Jane, E.P. / James, M.M. / Kay, H. / Paul, S.L. / Chai, J. / Takaki, M.
History
DepositionJun 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-9954
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Structure viewerMolecule:
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Assembly

Deposited unit
A: F22L4.1 protein
D: F22L4.1 protein
B: F22L4.1 protein
C: F22L4.1 protein


Theoretical massNumber of molelcules
Total (without water)320,1854
Polymers320,1854
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9540 Å2
ΔGint-43 kcal/mol
Surface area89060 Å2

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Components

#1: Protein
F22L4.1 protein


Mass: 80046.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F22L4.1, At1g01453
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9LMN2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mixed lineage kinase domain-like (MLKL) protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.5625 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 983779 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00717884
ELECTRON MICROSCOPYf_angle_d0.6924096
ELECTRON MICROSCOPYf_dihedral_angle_d19.1292300
ELECTRON MICROSCOPYf_chiral_restr0.0452612
ELECTRON MICROSCOPYf_plane_restr0.0063032

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