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- EMDB-3668: Closed dimer (C2) of human ATM (Ataxia telangiectasia mutated) -

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Basic information

Entry
Database: EMDB / ID: EMD-3668
TitleClosed dimer (C2) of human ATM (Ataxia telangiectasia mutated)
Map dataClosed dimer (C2) of human ATM (Ataxia telangiectasia mutated)
Sample
  • Organelle or cellular component: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
    • Protein or peptide: human ATM (Ataxia telangiectasia mutated)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsBaretic D / Johnson CM / Santhanam B / Truman CM / Kouba T / Fersht AR / Phillips C / Williams RL / 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.
History
DepositionApr 13, 2017-
Header (metadata) releaseApr 26, 2017-
Map releaseMay 17, 2017-
UpdateFeb 7, 2018-
Current statusFeb 7, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3668.png

Downloads & links

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Map

FileDownload / File: emd_3668.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClosed dimer (C2) of human ATM (Ataxia telangiectasia mutated)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.05561358 - 0.14483404
Average (Standard dev.)-0.000002798657 (±0.0057593584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 428.99997 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0560.145-0.000

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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
Components
  • Organelle or cellular component: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
    • Protein or peptide: human ATM (Ataxia telangiectasia mutated)

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Supramolecule #1: Dimeric human ATM (Ataxia telangiectasia mutated) kinase

SupramoleculeName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: ATM was produced and imaged with the FLAG tag at the N-terminus. It is a homodimer.
Source (natural)Organism: Homo sapiens (human)
Molecular weightExperimental: 705 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Expi293F

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Macromolecule #1: human ATM (Ataxia telangiectasia mutated)

MacromoleculeName: human ATM (Ataxia telangiectasia mutated) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKH MS LVLNDLL ICCRQLEHDR ATE RKKEVE KFKRLIRDPE TIKH LDRHS DSKQGKYLNW DAVFR FLQK YIQKETECLR IAKPNV SAS TQASRQKKMQ EISSLVK YF IKCANRRAPR LKCQELLN Y IMDTVKDSSN GAIYGADCS NILLKDILSV ...String:
MDYKDDDDKH MS LVLNDLL ICCRQLEHDR ATE RKKEVE KFKRLIRDPE TIKH LDRHS DSKQGKYLNW DAVFR FLQK YIQKETECLR IAKPNV SAS TQASRQKKMQ EISSLVK YF IKCANRRAPR LKCQELLN Y IMDTVKDSSN GAIYGADCS NILLKDILSV RKYWCEISQQ QWLELFSVY FRLYLKPSQD V HRVLVARI IHAVTKGCCS QT DGLNSKF LDFFSKAIQC ARQ EKSSSG LNHILAALTI FLKT LAVNF RIRVCELGDE ILPTL LYIW TQHRLNDSLK EVIIEL FQL QIYIHHPKGA KTQEKGA YE STKWRSILYN LYDLLVNE I SHIGSRGKYS SGFRNIAVK ENLIELMADI CHQVFNEDTR SLEISQSYT TTQRESSDYS V PCKRKKIE LGWEVIKDHL QK SQNDFDL VPWLQIATQL ISK YPASLP NCELSPLLMI LSQL LPQQR HGERTPYVLR CLTEV ALCQ DKRSNLESSQ KSDLLK LWN KIWCITFRGI SSEQIQA EN FGLLGAIIQG SLVEVDRE F WKLFTGSACR PSCPAVCCL TLALTTSIVP GTVKMGIEQN MCEVNRSFS LKESIMKWLL F YQLEGDLE NSTEVPPILH SN FPHLVLE KILVSLTMKN CKA AMNFFQ SVPECEHHQK DKEE LSFSE VEELFLQTTF DKMDF LTIV RECGIEKHQS SIGFSV HQN LKESLDRCLL GLSEQLL NN YSSEITNSET LVRCSRLL V GVLGCYCYMG VIAEEEAYK SELFQKAKSL MQCAGESITL FKNKTNEEF RIGSLRNMMQ L CTRCLSNC TKKSPNKIAS GF FLRLLTS KLMNDIADIC KSL ASFIKK PFDRGEVESM EDDT NGNLM EVEDQSSMNL FNDYP DSSV SDANEPGESQ STIGAI NPL AEEYLSKQDL LFLDMLK FL CLCVTTAQTN TVSFRAAD I RRKLLMLIDS STLEPTKSL HLHMYLMLLK ELPGEEYPLP MEDVLELLK PLSNVCSLYR R DQDVCKTI LNHVLHVVKN LG QSNMDSE NTRDAQGQFL TVI GAFWHL TKERKYIFSV RMAL VNCLK TLLEADPYSK WAILN VMGK DFPVNEVFTQ FLADNH HQV RMLAAESINR LFQDTKG DS SRLLKALPLK LQQTAFEN A YLKAQEGMRE MSHSAENPE TLDEIYNRKS VLLTLIAVVL SCSPICEKQ ALFALCKSVK E NGLEPHLV KKVLEKVSET FG YRRLEDF MASHLDYLVL EWL NLQDTE YNLSSFPFIL LNYT NIEDF YRSCYKVLIP HLVIR SHFD EVKSIANQIQ EDWKSL LTD CFPKILVNIL PYFAYEG TR DSGMAQQRET ATKVYDML K SENLLGKQID HLFISNLPE IVVELLMTLH EPANSSASQS TDLCDFSGD LDPAPNPPHF P SHVIKATF AYISNCHKTK LK SILEILS KSPDSYQKIL LAI CEQAAE TNNVYKKHRI LKIY HLFVS LLLKDIKSGL GGAWA FVLR DVIYTLIHYI NQRPSC IMD VSLRSFSLCC DLLSQVC QT AVTYCKDALE NHLHVIVG T LIPLVYEQVE VQKQVLDLL KYLVIDNKDN ENLYITIKLL DPFPDHVVF KDLRITQQKI K YSRGPFSL LEEINHFLSV SV YDALPLT RLEGLKDLRR QLE LHKDQM VDIMRASQDN PQDG IMVKL VVNLLQLSKM AINHT GEKE VLEAVGSCLG EVGPID FST IAIQHSKDAS YTKALKL FE DKELQWTFIM LTYLNNTL V EDCVKVRSAA VTCLKNILA TKTGHSFWEI YKMTTDPMLA YLQPFRTSR KKFLEVPRFD K ENPFEGLD DINLWIPLSE NH DIWIKTL TCAFLDSGGT KCE ILQLLK PMCEVKTDFC QTVL PYLIH DILLQDTNES WRNLL STHV QGFFTSCLRH FSQTSR STT PANLDSESEH FFRCCLD KK SQRTMLAVVD YMRRQKRP S SGTIFNDAFW LDLNYLEVA KVAQSCAAHF TALLYAEIYA DKKSMDDQE KRSLAFEEGS Q STTISSLS EKSKEETGIS LQ DLLLEIY RSIGEPDSLY GCG GGKMLQ PITRLRTYEH EAMW GKALV TYDLETAIPS STRQA GIIQ ALQNLGLCHI LSVYLK GLD YENKDWCPEL EELHYQA AW RNMQWDHCTS VSKEVEGT S YHESLYNALQ SLRDREFST FYESLKYARV KEVEEMCKRS LESVYSLYP TLSRLQAIGE L ESIGELFS RSVTHRQLSE VY IKWQKHS QLLKDSDFSF QEP IMALRT VILEILMEKE MDNS QRECI KDILTKHLVE LSILA RTFK NTQLPERAIF QIKQYN SVS CGVSEWQLEE AQVFWAK KE QSLALSILKQ MIKKLDAS C AANNPSLKLT YTECLRVCG NWLAETCLEN PAVIMQTYLE KAVEVAGNY DGESSDELRN G KMKAFLSL ARFSDTQYQR IE NYMKSSE FENKQALLKR AKE EVGLLR EHKIQTNRYT VKVQ RELEL DELALRALKE DRKRF LCKA VENYINCLLS GEEHDM WVF RLCSLWLENS GVSEVNG MM KRDGMKIPTY KFLPLMYQ L AARMGTKMMG GLGFHEVLN NLISRISMDH PHHTLFIILA LANANRDEF LTKPEVARRS R ITKNVPKQ SSQLDEDRTE AA NRIICTI RSRRPQMVRS VEA LCDAYI ILANLDATQW KTQR KGINI PADQPITKLK NLEDV VVPT MEIKVDHTGE YGNLVT IQS FKAEFRLAGG VNLPKII DC VGSDGKERRQ LVKGRDDL R QDAVMQQVFQ MCNTLLQRN TETRKRKLTI CTYKVVPLSQ RSGVLEWCT GTVPIGEFLV N NEDGAHKR YRPNDFSAFQ CQ KKMMEVQ KKSFEEKYEV FMD VCQNFQ PVFRYFCMEK FLDP AIWFE KRLAYTRSVA TSSIV GYIL GLGDRHVQNI LINEQS AEL VHIDLGVAFE QGKILPT PE TVPFRLTRDI VDGMGITG V EGVFRRCCEK TMEVMRNSQ ETLLTIVEVL LYDPLFDWTM NPLKALYLQ QRPEDETELH P TLNADDQE CKRNLSDIDQ SF NKVAERV LMRLQEKLKG VEE GTVLSV GGQVNLLIQQ AIDP KNLSR LFPGWKAWV

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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 #1

Preparation ID1
Concentration0.6 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMHEPES pH 7.5
25.0 mMTris pH 8.8
150.0 mMsodium chlorideNaCl
0.01 %Tween 20
2.0 mMTCEP
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER
Details: 3uL of sample/grid blotted for 12 s before plunge-freezing.
DetailsThe sample was purified by anti-FLAG affinity chromatography followed by overnight dialysis and a final size-exclusion chromatography.

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Sample preparation #2

Preparation ID2
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMHEPES pH 7.5
25.0 mMTris pH 8.8
150.0 mMsodium chlorideNaCl
0.01 %Tween 20
2.0 mMTCEP
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER
Details: 3uL of sample/grid blotted for 12 s before plunge-freezing.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.15 K
Specialist opticsEnergy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-20 / Number grids imaged: 4 / Number real images: 2720 / Average exposure time: 0.8 sec. / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 97902
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 371671
CTF correctionSoftware - Name: Gctf (ver. v0.5)
Startup modelType of model: INSILICO MODEL
In silico model: Experimental images were used to generate the initial model in EMAN2.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 25315
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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