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Closed dimer of human ATM (Ataxia telangiectasia mutated)

by single particle reconstruction, at 5.7 A resolution

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#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-3669, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 5np0
TitleClosed dimer of human ATM (Ataxia telangiectasia mutated)
DescriptorSerine-protein kinase ATM (E.C.2.7.11.1)
KeywordsSIGNALING PROTEIN, PIKK, kinase, DNA-repair, HEAT-repeats
AuthorsBaretic, D., Pollard, H.K., Fisher, D.I., Johnson, C.M., Santhanam, B., Truman, C.M., Kouba, T., Fersht, A.R., Phillips, C., Williams, R.L.
DateDeposition: 2017-04-13, Release: 2017-05-17
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-3669, Imaged by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-3669

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Article
Citation - primary
ArticleSci Adv, Vol. 3, Issue 5, Page e1700933-e1700933, Year 2017
TitleStructures of closed and open conformations of dimeric human ATM.
AuthorsDomagoj 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
Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, Cambridge CB4 0WG, UK.
LinksPubMed: 28508083, DOI: 10.1126/sciadv.1700933, PMC: PMC5425235
Components
ID 1 : Ataxia telangiectasia mutated,A-T mutated
DescriptionSerine-protein kinase ATM
Typepolypeptide(L)
Formula weight352393.969 Da
Number of molecules2
ID1
Ec2.7.11.1
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: Human, HEK293F, ATM, ID:9606, Homo sapiens
Host: Human, HEK293F, ID:9606, Homo sapiens, Plasmid
Alt source flag: sample
Beg seq num: 1
End seq num: 3066
Seq type: Biological sequence
Plasmid name: pDEST12.2-OriP
LinksUniProt: Q13315, Sequence view
Sample
Entity assembly
Detailshomodimer
Entity id list1
NameDimeric human ATM (Ataxia telangiectasia mutated) kinase
SourceRECOMBINANT
TypeORGANELLE OR CELLULAR COMPONENT
Buffer
Specimen id1
PH8
Experiment
Aggregation statePARTICLE
Reconstruction methodSINGLE PARTICLE
Sample support
Specimen id1
Grid materialGOLD
Grid mesh size300
Grid typeQuantifoil R1.2/1.3
Sample support
Specimen id1
Grid materialGOLD
Grid mesh size300
Grid typeQuantifoil UltrAuFoil R1.2/1.3
Vitrification
Specimen id1
Chamber temperature277.15
Cryogen nameETHANE
Details3 uL of sample/grid blotted for 12 s
Humidity100
InstrumentHOMEMADE PLUNGER
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TITAN KRIOS
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 35714 X, Nominal: 97902 X
CsNominal: 2.7 mm
Nominal defocusMax: 4000 nm, Min: 2500 nm
Specimen holder
Specimen holderModel: FEI TITAN KRIOS AUTOGRID HOLDER
Recording temperatureMinimum: 80.15
Image scans
Image recording id1
Frames per image20
Used frames per image1-20
Processing
Single particle entity
Image processing id1
Point symmetryC1
3D reconstruction
Image processing id1
Num class averages1
Number of particles25315
Resolution5.7 A
Resolution methodFSC 0.143 CUT-OFF
Symmetry typePOINT
3D fitting
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
Detailsbuilding de novo the structure of ATM N-solenoid and modelling of the ATM FATKIN (using mTOR FATKIN PDB:4JSP)
PDB entry ID4JSP
Refine
Refine idELECTRON MICROSCOPY
Software
Ordinal1
Classificationrefinement
NamePHENIX
Version1.10.1_2155:
Download
PDB format
Allpdb5np0.ent.gz
pdb5np0.ent (uncompressed file)
Header onlypdb5np0.ent.gz
mmCIF format
mmCIF5np0.cif.gz
XML format
All5np0.xml.gz
No-atom5np0-noatom.xml.gz
Ext-atom5np0-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 5.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 7.1 MB