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- PDB-5ujm: Structure of the active form of human Origin Recognition Complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ujm | ||||||
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Title | Structure of the active form of human Origin Recognition Complex and its ATPase motor module | ||||||
![]() | (Origin recognition complex subunit ...) x 5 | ||||||
![]() | REPLICATION / ORC / ATPase | ||||||
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 / nuclear origin of replication recognition complex / nuclear pre-replicative complex / inner kinetochore / DNA replication preinitiation complex / neural precursor cell proliferation / mitotic DNA replication checkpoint signaling ...polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / nuclear pre-replicative complex / inner kinetochore / DNA replication preinitiation complex / neural precursor cell proliferation / mitotic DNA replication checkpoint signaling / 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 / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / DNA replication / chromosome, telomeric region / nuclear body / nucleotide binding / centrosome / chromatin binding / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 18 Å | ||||||
![]() | Tocilj, A. / On, K. / Yuan, Z. / Sun, J. / Elkayam, E. / Li, H. / Stillman, B. / Joshua-Tor, L. | ||||||
![]() | ![]() Title: Structure of the active form of human origin recognition complex and its ATPase motor module. Authors: Ante Tocilj / Kin Fan On / Zuanning Yuan / Jingchuan Sun / Elad Elkayam / Huilin Li / Bruce Stillman / Leemor Joshua-Tor / ![]() Abstract: Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of ...Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of the active form of human ORC determined by X-ray crystallography and cryo-electron microscopy. The complex is composed of an ORC1/4/5 motor module lobe in an organization reminiscent of the DNA polymerase clamp loader complexes. A second lobe contains the ORC2/3 subunits. The complex is organized as a double-layered shallow corkscrew, with the AAA+ and AAA+-like domains forming one layer, and the winged-helix domains (WHDs) forming a top layer. CDC6 fits easily between ORC1 and ORC2, completing the ring and the DNA-binding channel, forming an additional ATP hydrolysis site. Analysis of the ATPase activity of the complex provides a basis for understanding ORC activity as well as molecular defects observed in Meier-Gorlin Syndrome mutations. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 367.1 KB | Display | ![]() |
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PDB format | ![]() | 274.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1007.6 KB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 62.2 KB | Display | |
Data in CIF | ![]() | 93.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8541MC ![]() 8523C ![]() 5uj7C ![]() 5uj8C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Origin recognition complex subunit ... , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 58729.707 Da / Num. of mol.: 1 / Fragment: UNP residues 471-861 Source method: isolated from a genetically manipulated source Details: Strep-strep-SUMO-tagged / Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: Q13415 |
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#2: Protein | Mass: 40309.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: Q13416 |
#3: Protein | Mass: 82436.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: Q9UBD5 |
#4: Protein | Mass: 50443.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: O43929 |
#5: Protein | Mass: 50349.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: O43913 |
-Non-polymers , 2 types, 5 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#6: Chemical | #7: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human ORC / Type: COMPLEX / Details: Human Origin Recognition Complex / Entity ID: #1-#5 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() Plasmid: PFl, PSPL, PUCDM |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10980 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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