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- EMDB-3669: Closed dimer (C1) of human ATM (Ataxia telangiectasia mutated) -

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Basic information

Entry
Database: EMDB / ID: 3669
TitleClosed dimer (C1) of human ATM (Ataxia telangiectasia mutated)
Map dataClosed dimer (C1) of human ATM (Ataxia telangiectasia mutated)
SampleDimeric human ATM (Ataxia telangiectasia mutated) kinase:
Serine-protein kinase ATM
Function / homologyResolution of D-loop Structures through Holliday Junction Intermediates / Armadillo-type fold / Phosphatidylinositol 3- and 4-kinases signature 1. / Telomere-length maintenance and DNA damage repair / FATC domain / TP53 Regulates Transcription of DNA Repair Genes / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Telomere-length maintenance and DNA damage repair / Phosphatidylinositol 3/4-kinase, conserved site ...Resolution of D-loop Structures through Holliday Junction Intermediates / Armadillo-type fold / Phosphatidylinositol 3- and 4-kinases signature 1. / Telomere-length maintenance and DNA damage repair / FATC domain / TP53 Regulates Transcription of DNA Repair Genes / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Telomere-length maintenance and DNA damage repair / Phosphatidylinositol 3/4-kinase, conserved site / Serine/threonine-protein kinase ATM / Phosphatidylinositol 3- and 4-kinases family profile. / PIK-related kinase / Protein kinase-like domain superfamily / Presynaptic phase of homologous DNA pairing and strand exchange / FATC domain / PIK-related kinase, FAT / Phosphatidylinositol 3-/4-kinase, catalytic domain / Processing of DNA double-strand break ends / Nonhomologous End-Joining (NHEJ) / Homologous DNA Pairing and Strand Exchange / Phosphatidylinositol 3- and 4-kinases signature 2. / FAT domain / FAT domain profile. / G2/M DNA damage checkpoint / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Sensing of DNA Double Strand Breaks / FATC domain profile. / HDR through Single Strand Annealing (SSA) / Meiotic recombination / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / HDR through Homologous Recombination (HRR) / Regulation of TP53 Activity through Methylation / DNA Damage/Telomere Stress Induced Senescence / Autodegradation of the E3 ubiquitin ligase COP1 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / Regulation of HSF1-mediated heat shock response / Regulation of TP53 Activity through Phosphorylation / TP53 Regulates Transcription of Caspase Activators and Caspases / Regulation of TP53 Degradation / signal transduction involved in mitotic G2 DNA damage checkpoint / regulation of cellular response to gamma radiation / positive regulation of DNA catabolic process / regulation of microglial cell activation / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / positive regulation of telomere maintenance via telomere lengthening / DNA-dependent protein kinase activity / cellular response to nitrosative stress / 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 / oocyte development / immunoglobulin production / lipoprotein catabolic process / histone mRNA catabolic process / male meiotic nuclear division / female meiotic nuclear division / regulation of telomere maintenance via telomerase / V(D)J recombination / positive regulation of histone phosphorylation / peptidyl-serine autophosphorylation / reciprocal meiotic recombination / DNA repair complex / DNA double-strand break processing / somitogenesis / response to ionizing radiation / mitotic spindle assembly checkpoint / DNA damage induced protein phosphorylation / negative regulation of B cell proliferation / determination of adult lifespan / replicative senescence / histone phosphorylation / ovarian follicle development / regulation of autophagy / post-embryonic development / 1-phosphatidylinositol-3-kinase activity / positive regulation of telomere maintenance via telomerase / telomere maintenance / thymus development / multicellular organism growth / double-strand break repair via homologous recombination / brain development / cellular response to gamma radiation / regulation of cellular response to heat / spindle / double-strand break repair via nonhomologous end joining / positive regulation of neuron apoptotic process / neuron apoptotic process / cell cycle arrest / intrinsic apoptotic signaling pathway in response to DNA damage / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / heart development / protein N-terminus binding
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 5.7 Å resolution
AuthorsBaretic D / Pollard HK
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
Validation ReportPDB-ID: 5np0

SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2017 / Header (metadata) release: Apr 26, 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: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5np0
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3669.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.

Voxel sizeX=Y=Z: 1.43 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.028897868 - 0.09947639
Average (Standard dev.)-1.13511205E-5 (0.0042891996)
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-0.0290.099-0.000

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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: homodimer / 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: homodimer / Recombinant expression: No
MassExperimental: 705 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pDEST12.2-OriP / Cell of expression system: HEK293

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Component #2: protein, Serine-protein kinase ATM

ProteinName: Serine-protein kinase ATM / Recombinant expression: No
MassTheoretical: 352.393969 kDa
Source (engineered)Expression System: Homo sapiens (human) / Vector: pDEST12.2-OriP / Cell of expression system: HEK293F

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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
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 % / Details: 3 uL of sample/grid blotted for 12 s

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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: 25315
3D reconstructionSoftware: RELION / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 4JSP
Output model

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