[English] 日本語
Yorodumi
- PDB-6k9l: 4.27 Angstrom resolution cryo-EM structure of human dimeric ATM kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k9l
Title4.27 Angstrom resolution cryo-EM structure of human dimeric ATM kinase
ComponentsSerine-protein kinase ATM
KeywordsCELL CYCLE / DNA damage response / KInase
Function / homology
Function and homology information


establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / cellular response to nitrosative stress / negative regulation of telomere capping / establishment of protein-containing complex localization to telomere / Sensing of DNA Double Strand Breaks / peptidyl-serine autophosphorylation / positive regulation of telomere maintenance via telomere lengthening / meiotic telomere clustering / pre-B cell allelic exclusion ...establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / cellular response to nitrosative stress / negative regulation of telomere capping / establishment of protein-containing complex localization to telomere / Sensing of DNA Double Strand Breaks / peptidyl-serine autophosphorylation / positive regulation of telomere maintenance via telomere lengthening / meiotic telomere clustering / pre-B cell allelic exclusion / DNA-dependent protein kinase activity / extrinsic component of synaptic vesicle membrane / male meiotic nuclear division / histone H2AXS139 kinase activity / histone mRNA catabolic process / regulation of telomere maintenance via telomerase / female meiotic nuclear division / lipoprotein catabolic process / DNA double-strand break processing / regulation of autophagosome assembly / cellular response to X-ray / V(D)J recombination / oocyte development / pexophagy / Impaired BRCA2 binding to PALB2 / DNA repair complex / reciprocal meiotic recombination / positive regulation of DNA damage response, signal transduction by p53 class mediator / 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) / 1-phosphatidylinositol-3-kinase activity / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / response to ionizing radiation / negative regulation of B cell proliferation / cellular response to stress / TP53 Regulates Transcription of Caspase Activators and Caspases / mitotic spindle assembly checkpoint signaling / positive regulation of double-strand break repair / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / peroxisomal matrix / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / signal transduction in response to DNA damage / Regulation of HSF1-mediated heat shock response / somitogenesis / ovarian follicle development / regulation of cellular response to heat / cellular response to retinoic acid / positive regulation of telomere maintenance via telomerase / negative regulation of TORC1 signaling / positive regulation of cell adhesion / telomere maintenance / Pexophagy / DNA damage checkpoint signaling / thymus development / regulation of signal transduction by p53 class mediator / determination of adult lifespan / post-embryonic development / cellular response to reactive oxygen species / TP53 Regulates Transcription of DNA Repair Genes / DNA damage response, signal transduction by p53 class mediator / Nonhomologous End-Joining (NHEJ) / Stabilization of p53 / Autodegradation of the E3 ubiquitin ligase COP1 / cellular response to gamma radiation / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / brain development / Regulation of TP53 Activity through Methylation / double-strand break repair via nonhomologous end joining / DNA Damage/Telomere Stress Induced Senescence / HDR through Homologous Recombination (HRR) / Meiotic recombination / multicellular organism growth / spindle / intrinsic apoptotic signaling pathway in response to DNA damage / cellular senescence / Regulation of TP53 Degradation / double-strand break repair / positive regulation of neuron apoptotic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / heart development / chromosome / protein autophosphorylation / Processing of DNA double-strand break ends / neuron apoptotic process / regulation of apoptotic process / Regulation of TP53 Activity through Phosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / regulation of autophagy / positive regulation of cell migration
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 / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine-protein kinase ATM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.27 Å
AuthorsXiao, J. / Liu, M. / Qi, Y. / Chaban, Y. / Gao, C. / Tian, Y. / Yu, Z. / Li, J. / Zhang, P. / Xu, Y.
CitationJournal: Cell Res / Year: 2019
Title: Structural insights into the activation of ATM kinase.
Authors: Jianxiong Xiao / Mengjie Liu / Yilun Qi / Yuriy Chaban / Chao Gao / Beiqing Pan / Yuan Tian / Zishuo Yu / Jie Li / Peijun Zhang / Yanhui Xu /
History
DepositionJun 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9950
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine-protein kinase ATM
B: Serine-protein kinase ATM


Theoretical massNumber of molelcules
Total (without water)702,2552
Polymers702,2552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, equilibrium centrifugation, microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5740 Å2
ΔGint-30 kcal/mol
Surface area272800 Å2

-
Components

#1: Protein Serine-protein kinase ATM / Ataxia telangiectasia mutated / A-T mutated


Mass: 351127.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATM / Cell line (production host): 293F / Production host: Homo sapiens (human)
References: UniProt: Q13315, non-specific serine/threonine protein kinase

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: 293F
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 282 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1132FEI FALCON III (4k x 4k)
2138GATAN K2 SUMMIT (4k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.15.2_3472refinement
PHENIX1.15.2_3472refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232416 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001130759
ELECTRON MICROSCOPYf_angle_d0.397942149
ELECTRON MICROSCOPYf_chiral_restr0.03685405
ELECTRON MICROSCOPYf_plane_restr0.00175733
ELECTRON MICROSCOPYf_dihedral_angle_d9.664918503

+
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