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- EMDB-25141: Human ATM Dimer Bound to Nbs1 -

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Basic information

Entry
Database: EMDB / ID: EMD-25141
TitleHuman ATM Dimer Bound to Nbs1
Map dataNc28 consensus dimer
Sample
  • Complex: Human ATM Dimer Bound to Nbs1
    • Protein or peptide: Serine-protein kinase ATM
    • Protein or peptide: Nibrin
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsKinase / SIGNALING PROTEIN
Function / homology
Function and homology information


blastocyst growth / chromosomal region / telomeric 3' overhang formation / telomere maintenance via telomere trimming / Mre11 complex / cellular response to nitrosative stress / negative regulation of telomere capping / BRCA1-C complex / peptidyl-serine autophosphorylation / establishment of RNA localization to telomere ...blastocyst growth / chromosomal region / telomeric 3' overhang formation / telomere maintenance via telomere trimming / Mre11 complex / cellular response to nitrosative stress / negative regulation of telomere capping / BRCA1-C complex / peptidyl-serine autophosphorylation / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / Sensing of DNA Double Strand Breaks / establishment of protein-containing complex localization to telomere / protection from non-homologous end joining at telomere / positive regulation of telomere maintenance via telomere lengthening / R-loop processing / negative regulation of B cell proliferation / regulation of telomere maintenance via telomerase / extrinsic component of synaptic vesicle membrane / phosphorylation-dependent protein binding / DNA-dependent protein kinase activity / histone mRNA catabolic process / pre-B cell allelic exclusion / DNA strand resection involved in replication fork processing / histone H2AXS139 kinase activity / isotype switching / nuclear inclusion body / DNA double-strand break processing / cellular response to X-ray / t-circle formation / homologous recombination / regulation of autophagosome assembly / pexophagy / positive regulation of autophagosome assembly / double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / protein localization to site of double-strand break / Impaired BRCA2 binding to PALB2 / DNA repair complex / mitotic G2/M transition checkpoint / reciprocal meiotic recombination / chromatin-protein adaptor activity / cellular response to stress / 1-phosphatidylinositol-3-kinase activity / mitotic spindle assembly checkpoint signaling / TP53 Regulates Transcription of Caspase Activators and Caspases / response to ionizing radiation / response to starvation / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / HDR through Single Strand Annealing (SSA) / mitotic G2 DNA damage checkpoint signaling / Resolution of D-loop Structures through Holliday Junction Intermediates / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / telomere maintenance in response to DNA damage / peroxisomal matrix / positive regulation of double-strand break repair / Impaired BRCA2 binding to RAD51 / positive regulation of telomere maintenance / replicative senescence / positive regulation of DNA damage response, signal transduction by p53 class mediator / Regulation of HSF1-mediated heat shock response / Presynaptic phase of homologous DNA pairing and strand exchange / regulation of DNA-templated DNA replication initiation / cellular response to retinoic acid / protein K63-linked ubiquitination / DNA damage checkpoint signaling / positive regulation of double-strand break repair via homologous recombination / regulation of cellular response to heat / signal transduction in response to DNA damage / positive regulation of telomere maintenance via telomerase / positive regulation of cell adhesion / negative regulation of TORC1 signaling / protein serine/threonine kinase activator activity / telomere maintenance / replication fork / regulation of signal transduction by p53 class mediator / Pexophagy / DNA damage response, signal transduction by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage / TP53 Regulates Transcription of DNA Repair Genes / cellular response to reactive oxygen species / Nonhomologous End-Joining (NHEJ) / Stabilization of p53 / double-strand break repair via homologous recombination / cellular response to gamma radiation / regulation of autophagy / Autodegradation of the E3 ubiquitin ligase COP1 / PML body / double-strand break repair via nonhomologous end joining / G2/M DNA damage checkpoint / Regulation of TP53 Activity through Methylation / cellular senescence / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / spindle / HDR through Homologous Recombination (HRR)
Similarity search - Function
Nibrin, C-terminal / Nibrin / DNA damage repair protein Nbs1 / DNA damage repair protein Nbs1 / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / Nibrin-related / Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant ...Nibrin, C-terminal / Nibrin / DNA damage repair protein Nbs1 / DNA damage repair protein Nbs1 / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / Nibrin-related / Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / SMAD/FHA domain superfamily / BRCA1 C Terminus (BRCT) domain / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / BRCT domain / BRCT domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Nibrin / Serine-protein kinase ATM
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsWarren C / Pavletich NP
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5F32CA247320 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)CA008748 United States
CitationJournal: Elife / Year: 2022
Title: Structure of the human ATM kinase and mechanism of Nbs1 binding.
Authors: Christopher Warren / Nikola P Pavletich /
Abstract: DNA double-strand breaks (DSBs) can lead to mutations, chromosomal rearrangements, genome instability, and cancer. Central to the sensing of DSBs is the ATM (Ataxia-telangiectasia mutated) kinase, ...DNA double-strand breaks (DSBs) can lead to mutations, chromosomal rearrangements, genome instability, and cancer. Central to the sensing of DSBs is the ATM (Ataxia-telangiectasia mutated) kinase, which belongs to the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family. In response to DSBs, ATM is activated by the MRN (Mre11-Rad50-Nbs1) protein complex through a poorly understood process that also requires double-stranded DNA. Previous studies indicate that the FxF/Y motif of Nbs1 directly binds to ATM, and is required to retain active ATM at sites of DNA damage. Here, we report the 2.5 Å resolution cryo-EM structures of human ATM and its complex with the Nbs1 FxF/Y motif. In keeping with previous structures of ATM and its yeast homolog Tel1, the dimeric human ATM kinase adopts a symmetric, butterfly-shaped structure. The conformation of the ATM kinase domain is most similar to the inactive states of other PIKKs, suggesting that activation may involve an analogous realigning of the N and C lobes along with relieving the blockage of the substrate-binding site. We also show that the Nbs1 FxF/Y motif binds to a conserved hydrophobic cleft within the Spiral domain of ATM, suggesting an allosteric mechanism of activation. We evaluate the importance of these structural findings with mutagenesis and biochemical assays.
History
DepositionOct 13, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-7sid
  • Surface level: 0.02
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25141.png

Downloads & links

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Map

FileDownload / File: emd_25141.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNc28 consensus dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 323.4 Å		1.08 Å/pix.
x 300 pix.
= 323.4 Å		1.08 Å/pix.
x 300 pix.
= 323.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.09154429 - 0.18829167
Average (Standard dev.)0.00031820146 (±0.0046424773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 323.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0781.0781.078
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z323.400323.400323.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0920.1880.000

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Supplemental data

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Additional map: Nc28 symmetry expanded protomer

Fileemd_25141_additional_1.map
AnnotationNc28 symmetry expanded protomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Nc28 symmetry expanded protomer FATKD focused

Fileemd_25141_additional_2.map
AnnotationNc28 symmetry expanded protomer FATKD focused
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Nc28 symmetry expanded protomer HEAT focused

Fileemd_25141_additional_3.map
AnnotationNc28 symmetry expanded protomer HEAT focused
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Nc28 symmetry expanded protomer composite map

Fileemd_25141_additional_4.map
AnnotationNc28 symmetry expanded protomer composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Nc28 dimer composite map

Fileemd_25141_additional_5.map
AnnotationNc28 dimer composite map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human ATM Dimer Bound to Nbs1

EntireName: Human ATM Dimer Bound to Nbs1
Components
  • Complex: Human ATM Dimer Bound to Nbs1
    • Protein or peptide: Serine-protein kinase ATM
    • Protein or peptide: Nibrin
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Human ATM Dimer Bound to Nbs1

SupramoleculeName: Human ATM Dimer Bound to Nbs1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine-protein kinase ATM

MacromoleculeName: Serine-protein kinase ATM / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 351.127688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLVLNDLLI CCRQLEHDRA TERKKEVEKF KRLIRDPETI KHLDRHSDSK QGKYLNWDAV FRFLQKYIQK ETECLRIAKP NVSASTQAS RQKKMQEISS LVKYFIKCAN RRAPRLKCQE LLNYIMDTVK DSSNGAIYGA DCSNILLKDI LSVRKYWCEI S QQQWLELF ...String:
MSLVLNDLLI CCRQLEHDRA TERKKEVEKF KRLIRDPETI KHLDRHSDSK QGKYLNWDAV FRFLQKYIQK ETECLRIAKP NVSASTQAS RQKKMQEISS LVKYFIKCAN RRAPRLKCQE LLNYIMDTVK DSSNGAIYGA DCSNILLKDI LSVRKYWCEI S QQQWLELF SVYFRLYLKP SQDVHRVLVA RIIHAVTKGC CSQTDGLNSK FLDFFSKAIQ CARQEKSSSG LNHILAALTI FL KTLAVNF RIRVCELGDE ILPTLLYIWT QHRLNDSLKE VIIELFQLQI YIHHPKGAKT QEKGAYESTK WRSILYNLYD LLV NEISHI GSRGKYSSGF RNIAVKENLI ELMADICHQV FNEDTRSLEI SQSYTTTQRE SSDYSVPCKR KKIELGWEVI KDHL QKSQN DFDLVPWLQI ATQLISKYPA SLPNCELSPL LMILSQLLPQ QRHGERTPYV LRCLTEVALC QDKRSNLESS QKSDL LKLW NKIWCITFRG ISSEQIQAEN FGLLGAIIQG SLVEVDREFW KLFTGSACRP SCPAVCCLTL ALTTSIVPGT VKMGIE QNM CEVNRSFSLK ESIMKWLLFY QLEGDLENST EVPPILHSNF PHLVLEKILV SLTMKNCKAA MNFFQSVPEC EHHQKDK EE LSFSEVEELF LQTTFDKMDF LTIVRECGIE KHQSSIGFSV HQNLKESLDR CLLGLSEQLL NNYSSEITNS ETLVRCSR L LVGVLGCYCY MGVIAEEEAY KSELFQKAKS LMQCAGESIT LFKNKTNEEF RIGSLRNMMQ LCTRCLSNCT KKSPNKIAS GFFLRLLTSK LMNDIADICK SLASFIKKPF DRGEVESMED DTNGNLMEVE DQSSMNLFND YPDSSVSDAN EPGESQSTIG AINPLAEEY LSKQDLLFLD MLKFLCLCVT TAQTNTVSFR AADIRRKLLM LIDSSTLEPT KSLHLHMYLM LLKELPGEEY P LPMEDVLE LLKPLSNVCS LYRRDQDVCK TILNHVLHVV KNLGQSNMDS ENTRDAQGQF LTVIGAFWHL TKERKYIFSV RM ALVNCLK TLLEADPYSK WAILNVMGKD FPVNEVFTQF LADNHHQVRM LAAESINRLF QDTKGDSSRL LKALPLKLQQ TAF ENAYLK AQEGMREMSH SAENPETLDE IYNRKSVLLT LIAVVLSCSP ICEKQALFAL CKSVKENGLE PHLVKKVLEK VSET FGYRR LEDFMASHLD YLVLEWLNLQ DTEYNLSSFP FILLNYTNIE DFYRSCYKVL IPHLVIRSHF DEVKSIANQI QEDWK SLLT DCFPKILVNI LPYFAYEGTR DSGMAQQRET ATKVYDMLKS ENLLGKQIDH LFISNLPEIV VELLMTLHEP ANSSAS QST DLCDFSGDLD PAPNPPHFPS HVIKATFAYI SNCHKTKLKS ILEILSKSPD SYQKILLAIC EQAAETNNVY KKHRILK IY HLFVSLLLKD IKSGLGGAWA FVLRDVIYTL IHYINQRPSC IMDVSLRSFS LCCDLLSQVC QTAVTYCKDA LENHLHVI V GTLIPLVYEQ VEVQKQVLDL LKYLVIDNKD NENLYITIKL LDPFPDHVVF KDLRITQQKI KYSRGPFSLL EEINHFLSV SVYDALPLTR LEGLKDLRRQ LELHKDQMVD IMRASQDNPQ DGIMVKLVVN LLQLSKMAIN HTGEKEVLEA VGSCLGEVGP IDFSTIAIQ HSKDASYTKA LKLFEDKELQ WTFIMLTYLN NTLVEDCVKV RSAAVTCLKN ILATKTGHSF WEIYKMTTDP M LAYLQPFR TSRKKFLEVP RFDKENPFEG LDDINLWIPL SENHDIWIKT LTCAFLDSGG TKCEILQLLK PMCEVKTDFC QT VLPYLIH DILLQDTNES WRNLLSTHVQ GFFTSCLRHF SQTSRSTTPA NLDSESEHFF RCCLDKKSQR TMLAVVDYMR RQK RPSSGT IFNDAFWLDL NYLEVAKVAQ SCAAHFTALL YAEIYADKKS MDDQEKRSLA FEEGSQSTTI SSLSEKSKEE TGIS LQDLL LEIYRSIGEP DSLYGCGGGK MLQPITRLRT YEHEAMWGKA LVTYDLETAI PSSTRQAGII QALQNLGLCH ILSVY LKGL DYENKDWCPE LEELHYQAAW RNMQWDHCTS VSKEVEGTSY HESLYNALQS LRDREFSTFY ESLKYARVKE VEEMCK RSL ESVYSLYPTL SRLQAIGELE SIGELFSRSV THRQLSEVYI KWQKHSQLLK DSDFSFQEPI MALRTVILEI LMEKEMD NS QRECIKDILT KHLVELSILA RTFKNTQLPE RAIFQIKQYN SVSCGVSEWQ LEEAQVFWAK KEQSLALSIL KQMIKKLD A SCAANNPSLK LTYTECLRVC GNWLAETCLE NPAVIMQTYL EKAVEVAGNY DGESSDELRN GKMKAFLSLA RFSDTQYQR IENYMKSSEF ENKQALLKRA KEEVGLLREH KIQTNRYTVK VQRELELDEL ALRALKEDRK RFLCKAVENY INCLLSGEEH DMWVFRLCS LWLENSGVSE VNGMMKRDGM KIPTYKFLPL MYQLAARMGT KMMGGLGFHE VLNNLISRIS MDHPHHTLFI I LALANANR DEFLTKPEVA RRSRITKNVP KQSSQLDEDR TEAANRIICT IRSRRPQMVR SVEALCDAYI ILANLDATQW KT QRKGINI PADQPITKLK NLEDVVVPTM EIKVDHTGEY GNLVTIQSFK AEFRLAGGVN LPKIIDCVGS DGKERRQLVK GRD DLRQDA VMQQVFQMCN TLLQRNTETR KRKLTICTYK VVPLSQRSGV LEWCTGTVPI GEFLVNNEDG AHKRYRPNDF SAFQ CQKKM MEVQKKSFEE KYEVFMDVCQ NFQPVFRYFC MEKFLDPAIW FEKRLAYTRS VATSSIVGYI LGLGDRHVQN ILINE QSAE LVHIDLGVAF EQGKILPTPE TVPFRLTRDI VDGMGITGVE GVFRRCCEKT MEVMRNSQET LLTIVEVLLY DPLFDW TMN PLKALYLQQR PEDETELHPT LNADDQECKR NLSDIDQSFN KVAERVLMRL QEKLKGVEEG TVLSVGGQVN LLIQQAI DP KNLSRLFPGW KAWV

UniProtKB: Serine-protein kinase ATM

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Macromolecule #2: Nibrin

MacromoleculeName: Nibrin / type: protein_or_peptide / ID: 2 / Details: C-terminal 28aa of Human Nbs1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.514947 KDa
SequenceString:
MEVQNQHAKE ESLADDLFRY NPYLKRRR

UniProtKB: Nibrin

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.42 mg/mL
BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 224367
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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