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- EMDB-0868: Cryo-EM structure of the AtMLKL2 tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-0868
TitleCryo-EM structure of the AtMLKL2 tetramer
Map dataNone
Sample
  • Complex: Mixed lineage kinase domain-like (MLKL) protein 2
    • Protein or peptide: Protein kinase family protein
KeywordsPlant MLKLs / Cryo-EM / Tetramer / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


defense response to other organism / protein serine/threonine/tyrosine kinase activity / protein kinase activity / signal transduction / ATP binding / cytoplasm
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
Protein kinase family protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLisa M / Huang M
CitationJournal: To Be Published
Title: Cryo-EM structure of the AtMLKL3 tetramer
Authors: Lisa M / Huang M / Zhang X / Ryohei TN / Leila BK / Isabel MLS / Florence J / Viera K / Dmitry L / Jane EP / James MM / Kay H / Paul SL / Chai J / Takaki M
History
DepositionNov 13, 2019-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6lba
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0868.png

Downloads & links

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Map

FileDownload / File: emd_0868.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 200 pix.
= 261.308 Å		1.31 Å/pix.
x 200 pix.
= 261.308 Å		1.31 Å/pix.
x 200 pix.
= 261.308 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.06479044 - 0.1049937
Average (Standard dev.)0.00029341225 (±0.0037391027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 261.308 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.306541.306541.30654
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z261.308261.308261.308
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0650.1050.000

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Supplemental data

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Sample components

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Entire : Mixed lineage kinase domain-like (MLKL) protein 2

EntireName: Mixed lineage kinase domain-like (MLKL) protein 2
Components
  • Complex: Mixed lineage kinase domain-like (MLKL) protein 2
    • Protein or peptide: Protein kinase family protein

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Supramolecule #1: Mixed lineage kinase domain-like (MLKL) protein 2

SupramoleculeName: Mixed lineage kinase domain-like (MLKL) protein 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Protein kinase family protein

MacromoleculeName: Protein kinase family protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 66.682531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AAMEQFRQIG EVLGSLNALM VLQDDILINQ RQCCLLLELF SLAFNTVAEE IRQNLKLEEK HTKWRALEQP LRELTRVFKE GELYVKHCM DNSDWWGKVI NLHQNKDCVE FHIHNLFCYF SAVVEAIEAA GEISGLDPSE MERRRVVFSR KYDREWNDPK M FQWRFGKQ ...String:
AAMEQFRQIG EVLGSLNALM VLQDDILINQ RQCCLLLELF SLAFNTVAEE IRQNLKLEEK HTKWRALEQP LRELTRVFKE GELYVKHCM DNSDWWGKVI NLHQNKDCVE FHIHNLFCYF SAVVEAIEAA GEISGLDPSE MERRRVVFSR KYDREWNDPK M FQWRFGKQ YLLSRDICSR FEHSWREDRW NLVEALQEKR KSDSDDIGKT EKRLADLLLK KLTGLEQFNG KLFPSSILLG SK DYQVKKR LDADGQYKEI QWLGDSFALR HFFSDLEPLS SEISSLLALC HSNILQYLCG FYDEERKECF LVMELMHKDL QSY MKENCG PRRRYLFSIP VVIDIMLQIA RGMEYLHGND IFHGDLNPMN IHLKERSHTE GYFHAKICGF GLSSVVKAQS SSKP GTPDP VIWYAPEVLA EMEQDLNGKT PKSKLTHKAD VYSFAMVCFE LITGKVPFED SHLQGEPMTI NIRMGERPLF PFPSP KTLV SLIKRCWHSE PSQRPNFSSI CRILRYIKKF LVVNPDHGHP QMQTPLVDCW DLEARFLRKF PGDAGSHTAS VNQIPF QLT SYRVLEKEK

UniProtKB: Protein kinase family protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1527009
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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