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- EMDB-3671: Open dimer of human ATM (Ataxia telangiectasia mutated) -

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Entry
Database: EMDB / ID: 3671
TitleOpen dimer of human ATM (Ataxia telangiectasia mutated)
Map dataOpen dimer of human ATM (Ataxia telangiectasia mutated)
SampleDimeric human ATM (Ataxia telangiectasia mutated) kinase
  • human ATM (Ataxia Telangiectasia mutated)
Function/homologySerine/threonine-protein kinase ATM / regulation of cellular response to gamma radiation / regulation of microglial cell activation / positive regulation of DNA catabolic process / signal transduction involved in mitotic G2 DNA damage checkpoint / positive regulation of telomerase catalytic core complex assembly / establishment of RNA localization to telomere / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / positive regulation of telomere maintenance via telomere lengthening ...Serine/threonine-protein kinase ATM / regulation of cellular response to gamma radiation / regulation of microglial cell activation / positive regulation of DNA catabolic process / signal transduction involved in mitotic G2 DNA damage checkpoint / positive regulation of telomerase catalytic core complex assembly / establishment of RNA localization to telomere / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / positive regulation of telomere maintenance via telomere lengthening / DNA-dependent protein kinase activity / cellular response to nitrosative stress / Sensing of DNA Double Strand Breaks / positive regulation of DNA damage response, signal transduction by p53 class mediator / establishment of protein-containing complex localization to telomere / negative regulation of telomere capping / pre-B cell allelic exclusion / meiotic telomere clustering / negative regulation of TORC1 signaling / cellular response to X-ray / immunoglobulin production / histone mRNA catabolic process / lipoprotein catabolic process / female meiotic nuclear division / male meiotic nuclear division / V(D)J recombination / PIK-related kinase, FAT / oocyte development / regulation of telomere maintenance via telomerase / peptidyl-serine autophosphorylation / FAT domain profile. / FATC domain profile. / PIK-related kinase / FATC domain / positive regulation of histone phosphorylation / reciprocal meiotic recombination / DNA repair complex / FAT domain / FATC domain / strand displacement / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Homologous DNA Pairing and Strand Exchange / DNA double-strand break processing / Resolution of D-loop Structures through Holliday Junction Intermediates / somitogenesis / response to ionizing radiation / mitotic spindle assembly checkpoint / HDR through Single Strand Annealing (SSA) / DNA synthesis involved in DNA repair / DNA damage induced protein phosphorylation / TP53 Regulates Transcription of Caspase Activators and Caspases / Phosphatidylinositol 3- and 4-kinases signature 1. / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of B cell proliferation / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases family profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / Phosphatidylinositol 3-/4-kinase, catalytic domain / determination of adult lifespan / replicative senescence / Regulation of HSF1-mediated heat shock response / histone phosphorylation / regulation of autophagy / ovarian follicle development / Nonhomologous End-Joining (NHEJ) / post-embryonic development / positive regulation of telomere maintenance via telomerase / telomere maintenance / TP53 Regulates Transcription of DNA Repair Genes / Phosphatidylinositol 3- and 4-kinase / 1-phosphatidylinositol-3-kinase activity / double-strand break repair via nonhomologous end joining / Autodegradation of the E3 ubiquitin ligase COP1 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / thymus development / HDR through Homologous Recombination (HRR) / Stabilization of p53 / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / cellular response to gamma radiation / Regulation of TP53 Activity through Methylation / brain development / regulation of cellular response to heat / Meiotic recombination / spindle / positive regulation of neuron apoptotic process / neuron apoptotic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cell cycle arrest / intrinsic apoptotic signaling pathway in response to DNA damage / Regulation of TP53 Degradation / Processing of DNA double-strand break ends / protein N-terminus binding / heart development / Armadillo-type fold / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
Function and homology information
SourceHomo sapiens / / human
MethodCryo EM / single particle reconstruction / 11.5 Å resolution
AuthorsBaretic D / Pollard HK / Fisher DI / Johnson CM / Santhanam B / Truman CM / Kouba T / Fersht AR / Phillips C / Pollard HK / Fisher DI
CitationJournal: Sci Adv / Year: 2017
Title: Structures of closed and open conformations of dimeric human ATM.
Authors: Domagoj Baretić / Hannah K Pollard / David I Fisher / Christopher M Johnson / Balaji Santhanam / Caroline M Truman / Tomas Kouba / Alan R Fersht / Christopher Phillips / Roger L Williams
Abstract: ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, ...ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, insulin signaling, and neurogenesis. Our electron cryomicroscopy (cryo-EM) suggests that human ATM is in a dynamic equilibrium between closed and open dimers. In the closed state, the PIKK regulatory domain blocks the peptide substrate-binding site, suggesting that this conformation may represent an inactive or basally active enzyme. The active site is held in this closed conformation by interaction with a long helical hairpin in the TRD3 (tetratricopeptide repeats domain 3) domain of the symmetry-related molecule. The open dimer has two protomers with only a limited contact interface, and it lacks the intermolecular interactions that block the peptide-binding site in the closed dimer. This suggests that the open conformation may be more active. The ATM structure shows the detailed topology of the regulator-interacting N-terminal helical solenoid. The ATM conformational dynamics shown by the structures represent an important step in understanding the enzyme regulation.
DateDeposition: Apr 13, 2017 / Header (metadata) release: May 17, 2017 / Map release: May 17, 2017 / Last update: Feb 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
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3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_3671.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.43 Å/pix.
= 429. Å
300 pix
1.43 Å/pix.
= 429. Å
300 pix
1.43 Å/pix.
= 429. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.43 Å
Density
Contour Level:0.01 (by author), 0.01 (movie #1):
Minimum - Maximum-0.016301412 - 0.05805342
Average (Standard dev.)1.9439296E-5 (0.0028006977)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
CellA=B=C: 428.99997 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z429.000429.000429.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0160.0580.000

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Supplemental data

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Sample components

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Entire Dimeric human ATM (Ataxia telangiectasia mutated) kinase

EntireName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Details: ATM was produced and imaged with the FLAG tag at the N-terminus
Number of components: 2
MassExperimental: 705 kDa

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Component #1: cellular-component, Dimeric human ATM (Ataxia telangiectasia muta...

Cellular-componentName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Details: ATM was produced and imaged with the FLAG tag at the N-terminus
Recombinant expression: No
MassExperimental: 705 kDa
SourceSpecies: Homo sapiens / / human
Source (engineered)Expression System: Homo sapiens / / human / Cell of expression system: Expi293F

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Component #2: protein, human ATM (Ataxia Telangiectasia mutated)

ProteinName: human ATM (Ataxia Telangiectasia mutated) / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens / / human / Vector: pDEST12.2-OriP

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: Cryo EM
Sample solutionSpecimen conc.: 0.6 mg/ml / pH: 8
Vitrification #1Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %
Details: 3 uL of sample/grid blotted for 12 s before plunge-freezing
Vitrification #2Cryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.1 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 97902 X (nominal), 35714 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500 - 4000 nm / Energy filter: GIF / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80.15 - K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2720

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 17816
3D reconstructionSoftware: RELION / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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