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- PDB-3jc6: Structure of the eukaryotic replicative CMG helicase and pumpjack... -

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Basic information

Entry
Database: PDB / ID: 3jc6
TitleStructure of the eukaryotic replicative CMG helicase and pumpjack motion
Components
  • (DNA replication complex GINS protein ...) x 4
  • (DNA replication licensing factor ...) x 5
  • Cell division control protein 45
  • Minichromosome maintenance protein 5
KeywordsREPLICATION / CMG helicase / Cryo-EM
Function / homologyMCM6 C-terminal winged-helix domain / GINS complex subunit Sld5 / MCM N-terminal domain / P-loop containing nucleoside triphosphate hydrolase / GINS subunit, domain A / Mini-chromosome maintenance, conserved site / Nucleic acid-binding, OB-fold / GINS complex, subunit Psf3 / DNA replication licensing factor Mcm7 / DNA replication complex GINS protein SLD5, C-terminal ...MCM6 C-terminal winged-helix domain / GINS complex subunit Sld5 / MCM N-terminal domain / P-loop containing nucleoside triphosphate hydrolase / GINS subunit, domain A / Mini-chromosome maintenance, conserved site / Nucleic acid-binding, OB-fold / GINS complex, subunit Psf3 / DNA replication licensing factor Mcm7 / DNA replication complex GINS protein SLD5, C-terminal / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm5 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm3 / DNA replication licensing factor Mcm2 / DNA replication complex GINS protein Psf2 / GINS complex, subunit Psf1 / Mini-chromosome maintenance protein / MCM OB domain / MCM domain / MCM OB domain / MCM AAA-lid domain / Switching of origins to a post-replicative state / Activation of the pre-replicative complex / Orc1 removal from chromatin / MCM family domain profile. / MCM family signature. / DNA replication complex GINS protein SLD5 C-terminus / GINS, helical bundle-like domain superfamily / MCM N-terminal domain / Mini-chromosome maintenance protein 2 / GINS complex protein / CDC45-like protein / MCM P-loop domain / GINS complex protein Sld5, alpha-helical domain / GINS complex, subunit Psf3 superfamily / AAA+ ATPase domain / CDC45 family / DNA strand elongation involved in mitotic DNA replication / GINS complex / mitotic DNA replication preinitiation complex assembly / MCM complex binding / MCM core complex / negative regulation of ATP-dependent DNA helicase activity / CMG complex / nuclear DNA replication / regulation of chromatin silencing at telomere / negative regulation of chromatin silencing at telomere / MCM complex / establishment of chromatin silencing / mitotic DNA replication initiation / regulation of DNA-dependent DNA replication initiation / nuclear pre-replicative complex / DNA replication preinitiation complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / 3'-5' DNA helicase activity / single-stranded DNA-dependent ATPase activity / double-strand break repair via break-induced replication / nuclear replication fork / DNA strand elongation involved in DNA replication / replication fork protection complex / chromatin silencing at silent mating-type cassette / DNA duplex unwinding / DNA helicase activity / DNA unwinding involved in DNA replication / positive regulation of G1/S transition of mitotic cell cycle / chromatin silencing at telomere / DNA replication origin binding / DNA replication initiation / DNA helicase / helicase activity / chromosome, telomeric region / single-stranded DNA binding / DNA-dependent DNA replication / nuclear chromosome, telomeric region / cellular response to DNA damage stimulus / chromatin binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / DNA replication licensing factor MCM3 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM7 / DNA replication complex GINS protein PSF2 / DNA replication licensing factor MCM6 / DNA replication complex GINS protein SLD5 / Cell division control protein 45 / DNA replication complex GINS protein PSF3 / DNA replication complex GINS protein PSF1 / DNA replication licensing factor MCM2
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsLi, H. / Bai, L. / Yuan, Z. / Sun, J. / Georgescu, R.E. / Liu, J. / O'Donnell, M.E.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2016
Title: Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation.
Authors: Zuanning Yuan / Lin Bai / Jingchuan Sun / Roxana Georgescu / Jun Liu / Michael E O'Donnell / Huilin Li
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 24, 2015 / Release: Feb 10, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 10, 2016Structure modelrepositoryInitial release
1.1Feb 24, 2016Structure modelDatabase references
1.2Mar 16, 2016Structure modelDatabase references
1.3Jan 24, 2018Structure modelData processing / Structure summaryaudit_author / em_software_audit_author.name / _em_software.name
1.4Jul 18, 2018Structure modelData collectionem_software_em_software.image_processing_id

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-6534
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
2: DNA replication licensing factor MCM2
3: DNA replication licensing factor MCM3
4: DNA replication licensing factor MCM4
5: Minichromosome maintenance protein 5
6: DNA replication licensing factor MCM6
7: DNA replication licensing factor MCM7
E: Cell division control protein 45
D: DNA replication complex GINS protein SLD5
B: DNA replication complex GINS protein PSF2
A: DNA replication complex GINS protein PSF1
C: DNA replication complex GINS protein PSF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)788,76612
Polyers788,70111
Non-polymers651
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA replication licensing factor ... , 5 types, 5 molecules 23467

#1: Protein/peptide DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2


Mass: 98911.539 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: MCM2, YBL023C, YBL0438 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P29469, DNA helicase
#2: Protein/peptide DNA replication licensing factor MCM3 / Minichromosome maintenance protein 3


Mass: 107653.508 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: MCM3, YEL032W, SYGP-ORF23 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P24279, DNA helicase
#3: Protein/peptide DNA replication licensing factor MCM4 / Cell division control protein 54


Mass: 105138.375 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: MCM4, CDC54, HCD21, YPR019W, YP9531.13 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P30665, DNA helicase
#5: Protein/peptide DNA replication licensing factor MCM6 / Minichromosome maintenance protein 6


Mass: 113110.211 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: MCM6, YGL201C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53091, DNA helicase
#6: Protein/peptide DNA replication licensing factor MCM7 / Cell division control protein 47 / Minichromosome maintenance protein 7


Mass: 95049.875 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: MCM7, CDC47, YBR202W, YBR1441 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38132, DNA helicase

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Protein/peptide , 2 types, 2 molecules 5E

#4: Protein/peptide Minichromosome maintenance protein 5 / / Cell division control protein 46


Mass: 86505.734 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: MCM5, CDC46, YLR274W, L9328.1 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P29496, DNA helicase
#7: Protein/peptide Cell division control protein 45


Mass: 77043.539 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: CDC45, SLD4, YLR103C, L8004.11 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q08032

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DNA replication complex GINS protein ... , 4 types, 4 molecules DBAC

#8: Protein/peptide DNA replication complex GINS protein SLD5


Mass: 33983.617 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: SLD5, YDR489W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q03406
#9: Protein/peptide DNA replication complex GINS protein PSF2 / Partner of Sld five 2


Mass: 25096.807 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: PSF2, YJL072C, HRF213, J1086 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40359
#10: Protein/peptide DNA replication complex GINS protein PSF1 / Partner of Sld five 1


Mass: 24230.576 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: PSF1, YDR013W, PZA208, YD8119.18 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12488
#11: Protein/peptide DNA replication complex GINS protein PSF3 / Partner of Sld five 3


Mass: 21977.135 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: PSF3, YOL146W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q12146

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Non-polymers , 1 types, 1 molecules

#12: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Saccharomyces cerevisiae CMG complex / Type: COMPLEX
Molecular weightValue: 0.7 MDa / Experimental value: NO
Buffer solutionName: 20 mM Tris acetate, pH 7.5, 40 mM potassium glutamate, 2 mM DTT, 0.1 mM EDTA
Details: 20 mM Tris acetate, pH 7.5, 40 mM potassium glutamate, 2 mM DTT, 0.1 mM EDTA
pH: 7.5
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh holey carbon C-flat grid, glow-discharged in air
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 %
Details: Blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Method: Blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Aug 1, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 / Calibrated magnification: 49505 / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNumber digital images: 8000

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Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2RELION1.43D reconstruction
CTF correctionDetails: CTFFIND4
SymmetryPoint symmetry: C1
3D reconstructionMethod: Single particle reconstructionSingle particle analysis
Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 469818 / Nominal pixel size: 1.01 / Actual pixel size: 1.01
Details: (Single particle details: All steps, including automatic particle picking, 2D classification, 3D classification, and 3D refinement were performed in Relion 1.4.) (Single particle--Applied symmetry: C1)
Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body / Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 2Q9Q
RefineOverall SU ML: 1.1 / Sigma F: 0 / Overall phase error: 42.73 / Stereochemistry target values: MLHL
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 381.32 Å2 / B iso mean: 144.6555 Å2 / B iso min: 3 Å2
Least-squares processR factor R free: 0.331 / R factor R work: 0.306 / R factor obs: 0.306 / Highest resolution: 3.7 Å / Lowest resolution: 258.56 Å / Number reflection R free: 2026 / Number reflection R work: 712152 / Number reflection obs: 714178 / Percent reflection R free: 0.28 / Percent reflection obs: 99.94
Refine hist #LASTHighest resolution: 3.7 Å / Lowest resolution: 258.56 Å
Number of atoms included #LASTProtein: 23731 / Nucleic acid: 0 / Ligand: 1 / Solvent: 0 / Total: 23732
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00824207
ELECTRON MICROSCOPYf_angle_d1.38032742
ELECTRON MICROSCOPYf_chiral_restr0.0523754
ELECTRON MICROSCOPYf_plane_restr0.0064195
ELECTRON MICROSCOPYf_dihedral_angle_d13.8829118
Refine LS shell

Refine ID: ELECTRON MICROSCOPY / Total number of bins used: 14

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
3.70010.84630.82503.79271445094551089100.0000
3.79270.58370.56493.89521445046850612100.0000
3.89520.49040.46874.00991685108351251100.0000
4.00990.39920.42024.13931445105451198100.0000
4.13930.40830.34734.28731325084250974100.0000
4.28730.28470.30034.45891445129951443100.0000
4.45890.32590.27084.66191565052850684100.0000
4.66190.28420.25034.90771325087151003100.0000
4.90770.29490.25845.21521685078750955100.0000
5.21520.30180.28145.61791445107051214100.0000
5.61790.33300.32606.18331205080050920100.0000
6.18330.36100.33527.07811925072750919100.0000
7.07810.36430.30528.9177965131351409100.0000
8.91770.23920.2308259.1935142503655050799.0000

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