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- EMDB-9954: Cryo-EM structure of the AtMLKL3 tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-9954
TitleCryo-EM structure of the AtMLKL3 tetramer
Map data
Sample
  • Complex: Mixed lineage kinase domain-like (MLKL) protein
    • Protein or peptide: F22L4.1 protein
KeywordsPlant MLKLs / Cryo-EM / Tetramer / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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
DepositionJun 20, 2019-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 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: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ka4
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9954.png

Downloads & links

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Map

FileDownload / File: emd_9954.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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 AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.06984771 - 0.14855513
Average (Standard dev.)0.0002475999 (±0.0044590244)
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
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0700.1490.000

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Supplemental data

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Sample components

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

EntireName: Mixed lineage kinase domain-like (MLKL) protein
Components
  • Complex: Mixed lineage kinase domain-like (MLKL) protein
    • Protein or peptide: F22L4.1 protein

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

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

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Macromolecule #1: F22L4.1 protein

MacromoleculeName: F22L4.1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 80.046188 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MDQFREIGEV LGSIRALMVF KDSIQINQRQ CSLLLDLFTA AYESISVSMR SNLRFKEKNT KWKILEQPLR ELLWVVREGE AYVRMSLEP KLGFWAKAIV LHSNRDCTEL HIHNLLSCLP IIVEAIETAS EVSGWDEEEM SKKRLVHSNK YMKQWNDSQM F TWKFGREY ...String:
MDQFREIGEV LGSIRALMVF KDSIQINQRQ CSLLLDLFTA AYESISVSMR SNLRFKEKNT KWKILEQPLR ELLWVVREGE AYVRMSLEP KLGFWAKAIV LHSNRDCTEL HIHNLLSCLP IIVEAIETAS EVSGWDEEEM SKKRLVHSNK YMKQWNDSQM F TWKFGREY LVTEDFCNRF ESAWTEDRWI LIKELQEKKQ SGSSKHERKM ADFLLKHLGD GNESPKLFPS SLLDNTKDYQ VK KRLGNGS QYKEITWLGE SFALRHFFGD IDALLPQITP LLSLSHPNIV YYLCGFTDEE KKECFLVMEL MRKTLGMHIK EVC GPRKKN TLSLPVAVDL MLQIALGMEY LHSKRIYHGE LNPSNILVKP RSNQSGDGYL LGKIFGFGLN SVKGFSSKSA SLTS QNENF PFIWYSPEVL EEQEQSGTAG SLKYSDKSDV YSFGMVSFEL LTGKVPFEDS HLQGDKMSRN IRAGERPLFP FNSPK FITN LTKRCWHADP NQRPTFSSIS RILRYIKRFL ALNPECYSSS QQDPSIAPTV DYCEIETKLL QKLSWESTEL TKVSQV PFQ MFAYRVVERA KTCEKDNLRE PSESGSEWAS CSEDEGGAGS DEQLSYAKER RLSCSSNDVG MSKKQVSNLL KRASSLK PI QKPAFGFCSG TTPRGRSRHP PLSPCGGQSM RANSESQLIL ISPRIRRSNS GHASDSELS

UniProtKB: F22L4.1 protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 983779
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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