[English] 日本語
Yorodumi
- EMDB-61006: ATM/Tel1 bound to CHK2 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61006
TitleATM/Tel1 bound to CHK2 peptide
Map data
Sample
  • Cell: ATM/Tel1 bound to CHK2 peptide
    • Protein or peptide: VAL-SER-THR-GLN-GLU-LEU-TYR-SER
    • Protein or peptide: Serine/threonine-protein kinase tel1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsATM / Tel1 / activation / AMPPNP / MMS-induced / DNA / STRUCTURAL PROTEIN
Function / homology
Function and homology information


spatial regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / positive regulation of initiation of premeiotic DNA replication / Regulation of TP53 Activity through Phosphorylation / Pexophagy / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA damage checkpoint signaling / telomere maintenance ...spatial regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / positive regulation of initiation of premeiotic DNA replication / Regulation of TP53 Activity through Phosphorylation / Pexophagy / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA damage checkpoint signaling / telomere maintenance / DNA damage checkpoint signaling / double-strand break repair / chromosome / eukaryotic translation initiation factor 2alpha kinase activity / chromosome, telomeric region / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytosol
Similarity search - Function
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 / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain ...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 / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase tel1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast) / Homo sapiens (human) / Schizosaccharomyces pombe 972h- (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsWang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Mechanisms of ATM/Tel1 kinase Activation
Authors: Wang P
History
DepositionJul 31, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61006.png

Downloads & links

-
Map

FileDownload / File: emd_61006.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 288 pix.
= 308.16 Å		1.07 Å/pix.
x 288 pix.
= 308.16 Å		1.07 Å/pix.
x 288 pix.
= 308.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-1.2934091 - 2.4942145
Average (Standard dev.)0.0040121255 (±0.065281734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 308.16 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61006_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61006_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ATM/Tel1 bound to CHK2 peptide

EntireName: ATM/Tel1 bound to CHK2 peptide
Components
  • Cell: ATM/Tel1 bound to CHK2 peptide
    • Protein or peptide: VAL-SER-THR-GLN-GLU-LEU-TYR-SER
    • Protein or peptide: Serine/threonine-protein kinase tel1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

-
Supramolecule #1: ATM/Tel1 bound to CHK2 peptide

SupramoleculeName: ATM/Tel1 bound to CHK2 peptide / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

-
Macromolecule #1: VAL-SER-THR-GLN-GLU-LEU-TYR-SER

MacromoleculeName: VAL-SER-THR-GLN-GLU-LEU-TYR-SER / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 925.98 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VSTQELYS

-
Macromolecule #2: Serine/threonine-protein kinase tel1

MacromoleculeName: Serine/threonine-protein kinase tel1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast)
Molecular weightTheoretical: 327.514094 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)
SequenceString: MTSLNDIVNK LSSSKIKTRS DALQNLRSYI IYSRNGNSLN QEDALIIEKA IKRAFELEWQ ISANHGKRQI SKASQEQKLQ DISYLLRTC VESYILLFRE PHILALLDII LRHTFTANGS ICEVVCLNFS KALRLLLSHS PHLHHLRFSD WQSLVSYCCQ A IEKLSIAE ...String:
MTSLNDIVNK LSSSKIKTRS DALQNLRSYI IYSRNGNSLN QEDALIIEKA IKRAFELEWQ ISANHGKRQI SKASQEQKLQ DISYLLRTC VESYILLFRE PHILALLDII LRHTFTANGS ICEVVCLNFS KALRLLLSHS PHLHHLRFSD WQSLVSYCCQ A IEKLSIAE ETYVSDSEEE PISQKNYQEI SIWKSHDVIR VKQEVVELIY VMRSLVQWYA APINFVSEQL LKFFEFFFYA YT EETDAHL PALQCLFQLC AYAIPNCNDY SASVVLLVFK ILINSDKWKR LDLRLQLIQC LAISYPLWSN SETWDPHRSI RSF NLDLLN SSFFSLKNFL NFFGKRSSLS LANFRFHTVE PKNNIAKLYD PRLHLFFSLR HNSFFESYFI YFFLAKLILL KKTV LSLAS TEQANKKQKT CSQIEELLLQ AELANISASS FSLQLMVIIT AISDNLTNDD LLSIQKMSLN FTEKKNELQS WSFFI LFNI CYNKAYSSML TTSCKKEILA AASRGLLNSV TSPVCYQILT YFNMYRPLCF ASIFPFIKQQ FILFNDYSPM LSYEAI DYW KSLYILLNEN LFVGQSSFKS VFLKWLKWHL YHLFSKEGEL PFFSFTDSSI IIFDLLMMIF YRPLSLSYIT TEIRSPF ER NLFHLKEAWS PVTLRFPYTT DEICKQSTEG CYPFNSNHTI DCDSLQNVIK MLESSIDEIS SASYDKDELD KETPSFEA V MIFSQISFLC GFLNCFIQKK GIHNVTPNNL VIFKNLFPEV LSFVKSNHSY DPIINCISTN LQFTISDEPK HLRYEIGSD LIRSTHFRDS NPLKTLVLYI MDMASKNVFI KPQEFDHDEY FSQEEEDIYR PENLIRNHQI LGLMEGSLEQ IRNTDLFILQ KYIDYFSSH PHDSLINILH LYPIETFCFG MSAIGAYFLD VARTSEPIFY KCLEILAQKI LMNYDYERDE VYLMIFIKIF Q KCVHSKLQ FTDATLKLIV KITKFIEKVF IETKFSSLSG RQTFLKFIFQ LSPTSHVYSK FDYQKLISLT LKDSDVCVIY NF VDDLVIF LKKCDKTLIE GFVLPILSIK IEKSLYKGFC YLYLTLKVFL SISSNRSALL YQLLKLANSY ETSTIFEPLL RKL HIQSAN IKQLFRIYRL EIFWSFVSKD LSNTTNDFLE FPYKPIYFSL SDFLKENSDE IILVLILTKN ITLAKLITSR MSVD FSEKY TQLIPVITTY THLSEVENKK YSLRFNSIDE ALDVELLNRS KAFLFCLEML KEVKELGSTF KSISSTSFKV YSQLT IFAN RVSFNNSTAI PFFSTKSVLW YCNRLFQELE GFSSIPSVID LVLRRLAIQL HFATDEELQV TISFRLCAFL CFSDPF ITS NYLVMIVLRI ARQLLSIPCT QSLGLGIARF HLKKFKPTDF DYFFQLAEFC MDFLGFCYNT IGTKMEAIQD FYTWFDG YV TALLNFEYEG YGFLRCQINF VRSVMTTKNE WIEVSNKLFE RGHFLKRIAM NNYLCLYFWQ VLDACPRNVL HSLSLEIW K CYKAYDITEF PDSLKLFFSD IMGWNFFKSP EIADLNHYIP KTDPRLCDTK TYEESKLIIW KLICQKACSL LFKYDILLD SFIEDCIRMF FENGNHQELR KFLNFPKDSI IYDSDFKTLV SEEGSFQWVK LQPTNFDSLS NWTKEETLKL LNMMGKSSTT HSLKLLSTY MVGFSTSIIQ YIIHLILLEF DFNGNNKKQK EYVTQLILSG LLNKNTNSIR KTCMNILLYL RRQLGHHALN P FEANYWVP INYSVAASTA YDCHLYEQSL LFLTIHNTKT DELDITLLSD ILSQLPCPDA YYGIKRETSF KNILLKAVHE KR SPLAISY LDAANMYRSN EDEGTKMMFS NTLNNAGFFS LNEFYIDSLK ANDAIDECSN EVYASAWRMQ KWDIPPLSLD NKT TKDCLV FEVLHAVHNY AIYGNYLHLE EYINKKLLLI NPNEEPDSLL FYALAYDLKF LIRCNQSQFN CDILQLLKEN KQMS SQLHE CFQLLLEIRN VLLSLLQSHK QLDLSDDLAS FRKYYILELL KISESFLIVD NLQNAFSVAM LSDALYRKFD LADEN LKHD IDFLSSKILW QRDEKIDAIG MLSESLSKTN SSIFPSISYA YLGNWLYTTK SEKTELVSKN YFEKSLSHMS HLNAKE KAK IYCMFAQFCD NNYSSPDLTE DFKRMEKLYF EKKNDIQQLE RSIVNASNMK EEKMLKNHHS REMSSFIIDE REYLRMS TF RSKMLTQSIT HYLKCLSESD ENDVLISRCC TMWLSNSHLD ELNNSLQHYL QNLPCKKFIP VFYQLAARLM NENSKFQQ S LTSICYNVGR NHPYHSLHVL FSLVSNVPEI ENLDAGSRYR AVKKILDLLK VNQGLSNLVT KLLCSFENYV SLAEWNPRS KVDSTSFSRF PGYKWFLKDA ANYGLPPITM NVKVNDTGDY SNIPTVSSFD DTIHFASGIN APKVITCLGS NGHTYKQLVK GGNDDLRQD AVMEQVFEQV NGFLRSYRKT SQRNLSMRTY KVIPLALKTG VIEWVQDTIP LGEYLDSAHK VYHPKEWSLS T CRKLIAEK QMEDLETRLK VYDLVCRHYR PVFRHFFLES YADPVQWFTT QTNYARSTAV ASVLGHVLGL GDRHGQNILI DK TSGEVIH IDLGIAFEQG KKLPVPECVP FRLTRDVVDG MGITGVEGVF RRCMEFTLET LRREEDSLLS VLEVLRYDPL FSW LISPLR RMKKQKMQLE NFNQPESGNI TTDASRDPKI QRNNVSGESE AERAILKVRQ KLSSTLSVEA SVGELIRIAQ DPSY LALMF CGWSAFQ

UniProtKB: Serine/threonine-protein kinase tel1

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64713
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more