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- EMDB-4085: The Dimeric Architecture of Checkpoint Kinases Mec1/ATR and Tel1/... -

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Basic information

Entry
Database: EMDB / ID: EMD-4085
TitleThe Dimeric Architecture of Checkpoint Kinases Mec1/ATR and Tel1/ATM Reveal a Common Structural Organization.
Map data
Sample
  • Complex: Complex of Checkpoint Kinase Mec1 with its associating protein Ddc2
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 22.5 Å
AuthorsSawicka M / Wanrooij PH / Darbari VC / Tannous E / Hailemariam S / Bose D / Makarova AV / Burgers PM / Zhang X
CitationJournal: J Biol Chem / Year: 2016
Title: The Dimeric Architecture of Checkpoint Kinases Mec1ATR and Tel1ATM Reveal a Common Structural Organization.
Authors: Marta Sawicka / Paulina H Wanrooij / Vidya C Darbari / Elias Tannous / Sarem Hailemariam / Daniel Bose / Alena V Makarova / Peter M Burgers / Xiaodong Zhang /
Abstract: The phosphatidylinositol 3-kinase-related protein kinases are key regulators controlling a wide range of cellular events. The yeast Tel1 and Mec1·Ddc2 complex (ATM and ATR-ATRIP in humans) play ...The phosphatidylinositol 3-kinase-related protein kinases are key regulators controlling a wide range of cellular events. The yeast Tel1 and Mec1·Ddc2 complex (ATM and ATR-ATRIP in humans) play pivotal roles in DNA replication, DNA damage signaling, and repair. Here, we present the first structural insight for dimers of Mec1·Ddc2 and Tel1 using single-particle electron microscopy. Both kinases reveal a head to head dimer with one major dimeric interface through the N-terminal HEAT (named after Huntingtin, elongation factor 3, protein phosphatase 2A, and yeast kinase TOR1) repeat. Their dimeric interface is significantly distinct from the interface of mTOR complex 1 dimer, which oligomerizes through two spatially separate interfaces. We also observe different structural organizations of kinase domains of Mec1 and Tel1. The kinase domains in the Mec1·Ddc2 dimer are located in close proximity to each other. However, in the Tel1 dimer they are fully separated, providing potential access of substrates to this kinase, even in its dimeric form.
History
DepositionAug 2, 2016-
Header (metadata) releaseOct 12, 2016-
Map releaseOct 12, 2016-
UpdateOct 12, 2016-
Current statusOct 12, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0153
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0153
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4085.png

Downloads & links

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Map

FileDownload / File: emd_4085.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.52 Å/pix.
x 128 pix.
= 450.56 Å		3.52 Å/pix.
x 128 pix.
= 450.56 Å		3.52 Å/pix.
x 128 pix.
= 450.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0153 / Movie #1: 0.0153
Minimum - Maximum-0.036641434 - 0.08795247
Average (Standard dev.)0.00023641532 (±0.004065771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.523.523.52
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z450.560450.560450.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.0370.0880.000

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Supplemental data

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Sample components

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Entire : Complex of Checkpoint Kinase Mec1 with its associating protein Ddc2

EntireName: Complex of Checkpoint Kinase Mec1 with its associating protein Ddc2
Components
  • Complex: Complex of Checkpoint Kinase Mec1 with its associating protein Ddc2

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Supramolecule #1: Complex of Checkpoint Kinase Mec1 with its associating protein Ddc2

SupramoleculeName: Complex of Checkpoint Kinase Mec1 with its associating protein Ddc2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 720 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.025 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
30.0 mMC8H18N2O4SHEPES
200.0 mMNaClSodium Chloride
5.0 %C3H8O3Glycerol
0.5 mMC10H16N2O8EDTA
1.0 mMC4H10O2S2DTT
StainingType: NEGATIVE / Material: 2% v/v uranyl acetate
GridModel: TAAB / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 22.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 5633
Initial angle assignmentType: COMMON LINE / Software - Name: IMAGIC (ver. V)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. V)

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