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Open data
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Basic information
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Title | H. sapiens MCM bound to double stranded DNA and ORC1-6 | |||||||||||||||
![]() | Composite map of the H. sapiens MCM-ORC complex bound to DNA | |||||||||||||||
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![]() | AAA+ ATPase / DNA helicase / REPLICATION | |||||||||||||||
Function / homology | ![]() polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / alpha DNA polymerase:primase complex / mitotic DNA replication ...polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / alpha DNA polymerase:primase complex / mitotic DNA replication / CMG complex / inner kinetochore / regulation of phosphorylation / nuclear pre-replicative complex / DNA replication preinitiation complex / MCM complex / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / mitotic DNA replication initiation / neural precursor cell proliferation / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / cochlea development / G1/S-Specific Transcription / regulation of DNA replication / DNA replication origin binding / protein polymerization / Activation of the pre-replicative complex / DNA replication initiation / glial cell proliferation / heterochromatin / Activation of ATR in response to replication stress / cellular response to epidermal growth factor stimulus / Assembly of the ORC complex at the origin of replication / cellular response to interleukin-4 / Assembly of the pre-replicative complex / fibrillar center / Orc1 removal from chromatin / cellular response to xenobiotic stimulus / nucleosome assembly / single-stranded DNA binding / DNA helicase / histone binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / cell population proliferation / DNA replication / nuclear body / cilium / nucleotide binding / intracellular membrane-bounded organelle / apoptotic process / centrosome / DNA damage response / chromatin binding / chromatin / nucleolus / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | synthetic construct (others) / ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
![]() | Greiwe JF / Weissmann F / Diffley JFX / Costa A | |||||||||||||||
Funding support | ![]()
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![]() | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() ![]() ![]() Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. #1: ![]() Title: MCM Double Hexamer Loading Visualised with Human Proteins Authors: Weissmann F / Greiwe JF / Puhringer T / Miller TCR / Diffley JFX / Costa A | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 211.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 44.7 KB 44.7 KB | Display Display | ![]() |
Images | ![]() | 119.4 KB | ||
Filedesc metadata | ![]() | 13.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8s0dMC ![]() 8s09C ![]() 8s0aC ![]() 8s0bC ![]() 8s0cC ![]() 8s0eC ![]() 8s0fC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of the H. sapiens MCM-ORC complex bound to DNA | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : H. sapiens MCM bound to double stranded DNA and ORC1-6
+Supramolecule #1: H. sapiens MCM bound to double stranded DNA and ORC1-6
+Supramolecule #2: Double stranded DNA
+Supramolecule #3: H. sapiens MCM
+Supramolecule #4: H. sapiens ORC1-5
+Supramolecule #5: H. sapiens ORC6
+Macromolecule #1: Origin recognition complex subunit 6
+Macromolecule #2: DNA replication licensing factor MCM2
+Macromolecule #3: DNA replication licensing factor MCM3
+Macromolecule #4: DNA replication licensing factor MCM4
+Macromolecule #5: DNA replication licensing factor MCM5
+Macromolecule #6: DNA replication licensing factor MCM6
+Macromolecule #7: DNA replication licensing factor MCM7
+Macromolecule #10: Origin recognition complex subunit 1
+Macromolecule #11: Origin recognition complex subunit 2
+Macromolecule #12: Isoform 2 of Origin recognition complex subunit 3
+Macromolecule #13: Origin recognition complex subunit 4
+Macromolecule #14: Origin recognition complex subunit 5
+Macromolecule #8: DNA (58-mer)
+Macromolecule #9: DNA (58-mer)
+Macromolecule #15: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
+Macromolecule #16: MAGNESIUM ION
+Macromolecule #17: ZINC ION
+Macromolecule #18: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
Details | The MCM recruitment reaction was reconstituted in vitro using purified H. sapiens proteins, a short DNA template and ATPgammaS. Four microlitres of the entire reaction was applied on a grid and incubated for 1 min at room temperature before blotting with filter paper for 5 s and plunge-freezing in liquid ethane. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 31569 / Average exposure time: 9.4 sec. / Average electron dose: 49.28 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) Details: The here represented map is a composite map of the consensus refinement and the locally refined map encompassing the ORC1-5 complex. Number images used: 182341 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2) |
-Atomic model buiding 1
Details | The models of MCM2-7-ORC6 and ORC1-5 that were refined against the consensus refinement of the MCM-ORC complex and the locally refined ORC1-5, respectively, were fitted into the composite map using rigid body docking. |
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Output model | ![]() PDB-8s0d: |