[English] 日本語
Yorodumi
- PDB-5x6o: Intact ATR/Mec1-ATRIP/Ddc2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x6o
TitleIntact ATR/Mec1-ATRIP/Ddc2 complex
Components
  • DNA damage checkpoint protein LCD1
  • Serine/threonine-protein kinase MEC1
KeywordsTRANSFERASE/DNA BINDING PROTEIN / ATR/Mec1 / Kinase / Dimeric / TRANSFERASE / TRANSFERASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


ATR-ATRIP complex / positive regulation of DNA-templated DNA replication / telomere maintenance via recombination / regulation of double-strand break repair / nucleobase-containing compound metabolic process / reciprocal meiotic recombination / nuclear chromosome / signal transduction in response to DNA damage / telomere maintenance via telomerase / telomere maintenance ...ATR-ATRIP complex / positive regulation of DNA-templated DNA replication / telomere maintenance via recombination / regulation of double-strand break repair / nucleobase-containing compound metabolic process / reciprocal meiotic recombination / nuclear chromosome / signal transduction in response to DNA damage / telomere maintenance via telomerase / telomere maintenance / DNA damage checkpoint signaling / establishment of protein localization / chromosome / chromatin organization / DNA recombination / damaged DNA binding / DNA replication / protein kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
MEC1-like, HEAT repeats / DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein / : / Serine/threonine-protein kinase ATR, M-HEAT region / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Serine/threonine-protein kinase ATR-like, HEAT repeats / : ...MEC1-like, HEAT repeats / DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein / : / Serine/threonine-protein kinase ATR, M-HEAT region / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Serine/threonine-protein kinase ATR-like, HEAT repeats / : / 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 / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase MEC1 / DNA damage checkpoint protein LCD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.9 Å
AuthorsWang, X. / Ran, T. / Cai, G.
Funding support China, 3items
OrganizationGrant numberCountry
National Basic Research Program2014CB910700 China
National Basic Research Program2013CB910200 China
National Natural Science Foundation of China31222017 China
CitationJournal: Science / Year: 2017
Title: 3.9 Å structure of the yeast Mec1-Ddc2 complex, a homolog of human ATR-ATRIP.
Authors: Xuejuan Wang / Tingting Ran / Xuan Zhang / Jiyu Xin / Zhihui Zhang / Tengwei Wu / Weiwu Wang / Gang Cai /
Abstract: The ataxia telangiectasia-mutated and Rad3-related (ATR) kinase is a master regulator of DNA damage response and replication stress in humans, but the mechanism of its activation remains unclear. ATR ...The ataxia telangiectasia-mutated and Rad3-related (ATR) kinase is a master regulator of DNA damage response and replication stress in humans, but the mechanism of its activation remains unclear. ATR acts together with its partner ATRIP. Using cryo-electron microscopy, we determined the structure of intact Mec1-Ddc2 (the yeast homolog of ATR-ATRIP), which is poised for catalysis, at a resolution of 3.9 angstroms. Mec1-Ddc2 forms a dimer of heterodimers through the PRD and FAT domains of Mec1 and the coiled-coil domain of Ddc2. The PRD and Bridge domains in Mec1 constitute critical regulatory sites. The activation loop of Mec1 is inhibited by the PRD, revealing an allosteric mechanism of kinase activation. Our study clarifies the architecture of ATR-ATRIP and provides a structural framework for the understanding of ATR regulation.
History
DepositionFeb 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.3Jun 25, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-6708
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6708
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Serine/threonine-protein kinase MEC1
G: DNA damage checkpoint protein LCD1


Theoretical massNumber of molelcules
Total (without water)360,2142
Polymers360,2142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8670 Å2
ΔGint-45 kcal/mol
Surface area137250 Å2

-
Components

#1: Protein Serine/threonine-protein kinase MEC1 / ATR homolog / DNA-damage checkpoint kinase MEC1 / Mitosis entry checkpoint protein 1


Mass: 273680.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P38111, non-specific serine/threonine protein kinase
#2: Protein DNA damage checkpoint protein LCD1 / DNA damage checkpoint protein 2 / Lethal / checkpoint-defective / DNA damage-sensitive protein 1


Mass: 86533.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04377
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: ATR/Mec1-ATRIP/Ddc2 / Type: COMPLEX / Details: ATR/Mec1 "butterfly" / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES / Details: ATR/Mec1 "butterfly"
EM stainingType: NONE / Material: Uranyl Formate
VitrificationCryogen name: ETHANE

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: dev_2247: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63132 / Symmetry type: POINT
RefinementHighest resolution: 3.9 Å
Refinement stepCycle: 1 / Total: 20282
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00719569
ELECTRON MICROSCOPYf_angle_d1.00526595
ELECTRON MICROSCOPYf_dihedral_angle_d11.84411819
ELECTRON MICROSCOPYf_chiral_restr0.0593218
ELECTRON MICROSCOPYf_plane_restr0.0053431
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.535 8779 -
Rfree-0 -
obs--100 %

+
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