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- PDB-7wzw: Cryo-EM structure of MEC1-DDC2-MMS -

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Basic information

Entry
Database: PDB / ID: 7wzw
TitleCryo-EM structure of MEC1-DDC2-MMS
Components
  • DNA damage checkpoint protein LCD1
  • Serine/threonine-protein kinase MEC1
KeywordsHYDROLASE / SERINE/THREONINE PROTEIN KINASE / COMPLEX / DNA DAMAGE RESPONSE / CHECKPOINT CONTROL
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 / reciprocal meiotic recombination / nucleobase-containing compound metabolic process / 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 / reciprocal meiotic recombination / nucleobase-containing compound metabolic process / nuclear chromosome / signal transduction in response to DNA damage / telomere maintenance via telomerase / telomere maintenance / DNA damage checkpoint signaling / establishment of protein localization / chromatin organization / chromosome / DNA recombination / damaged DNA binding / eukaryotic translation initiation factor 2alpha kinase activity / 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 / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Serine/threonine-protein kinase ATR-like, HEAT repeats / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / : / FATC domain ...DNA damage checkpoint protein, Lcd1 / DNA damage checkpoint protein / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / Serine/threonine-protein kinase ATR-like, HEAT repeats / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / : / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase MEC1 / DNA damage checkpoint protein LCD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsZhang, Q. / Zhang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2022
Title: Structures of Mec1/ATR kinase endogenously stimulated by different genotoxins.
Authors: Qingjun Zhang / Po Wang / Tengwei Wu / Yueyue Zhang / Zexuan Zheng / Shangzhi Zhou / Dong Qian / Xuejuan Wang / Gang Cai /
History
DepositionFeb 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jun 26, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / refine
Item: _em_admin.last_update / _refine.ls_d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Serine/threonine-protein kinase MEC1
C: DNA damage checkpoint protein LCD1
D: DNA damage checkpoint protein LCD1
E: Serine/threonine-protein kinase MEC1


Theoretical massNumber of molelcules
Total (without water)720,4294
Polymers720,4294
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 273680.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: MEC1 / Production host: Saccharomyces cerevisiae (brewer's yeast)
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: LCD1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04377

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: MEC1-DDC2 / Type: COMPLEX
Details: MEC1-DDC2 EXPRESSED AND PURIFIED FROM YEAST INDUCED BY MMS
Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 20185

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
Image processing
IDImage recording-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22NONE
33PHASE FLIPPING AND AMPLITUDE CORRECTION
44PHASE FLIPPING ONLY
55PHASE FLIPPING AND AMPLITUDE CORRECTION
66PHASE FLIPPING AND AMPLITUDE CORRECTION
77NONE
88NONE
99NONE
1010NONE
1111PHASE FLIPPING AND AMPLITUDE CORRECTION
1212NONE
1313PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
14FSC 0.143 CUT-OFF1200017WZWPOINT
24FSC 0.143 CUT-OFF1200027WZWPOINT
34FSC 0.143 CUT-OFF1200037WZWPOINT
44FSC 0.143 CUT-OFF1200047WZWPOINT
54FSC 0.143 CUT-OFF1200057WZWPOINT
64FSC 0.143 CUT-OFF1200067WZWPOINT
74FSC 0.143 CUT-OFF1200077WZWPOINT
84FSC 0.143 CUT-OFF1200087WZWPOINT
94FSC 0.143 CUT-OFF1200097WZWPOINT
104FSC 0.143 CUT-OFF12000107WZWPOINT
114FSC 0.143 CUT-OFF12000117WZWPOINT
124FSC 0.143 CUT-OFF12000127WZWPOINT
134FSC 0.143 CUT-OFF12000137WZWPOINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 4 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00845999
ELECTRON MICROSCOPYf_angle_d1.18662247
ELECTRON MICROSCOPYf_dihedral_angle_d23.2086018
ELECTRON MICROSCOPYf_chiral_restr0.0637190
ELECTRON MICROSCOPYf_plane_restr0.0077814

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