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Yorodumi- PDB-5ujm: Structure of the active form of human Origin Recognition Complex ... -
+Open data
-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 | ||||||
Components | (Origin recognition complex subunit ...) x 5 | ||||||
Keywords | REPLICATION / ORC / ATPase | ||||||
Function / homology | Function and homology information 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 / Activation of the pre-replicative complex / 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 / Activation of the pre-replicative complex / mitotic DNA replication checkpoint signaling / neural precursor cell proliferation / Activation of ATR in response to replication stress / G1/S-Specific Transcription / regulation of DNA replication / DNA replication origin binding / protein polymerization / DNA replication initiation / glial cell proliferation / heterochromatin / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / chromosome, telomeric region / DNA replication / nuclear body / chromatin binding / centrosome / nucleotide 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 | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 18 Å | ||||||
Authors | Tocilj, A. / On, K. / Yuan, Z. / Sun, J. / Elkayam, E. / Li, H. / Stillman, B. / Joshua-Tor, L. | ||||||
Citation | Journal: Elife / Year: 2017 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ujm.cif.gz | 367.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ujm.ent.gz | 274.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ujm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ujm_validation.pdf.gz | 1007.6 KB | Display | wwPDB validaton report |
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Full document | 5ujm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5ujm_validation.xml.gz | 62.2 KB | Display | |
Data in CIF | 5ujm_validation.cif.gz | 93.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/5ujm ftp://data.pdbj.org/pub/pdb/validation_reports/uj/5ujm | HTTPS FTP |
-Related structure data
Related structure data | 8541MC 8523C 5uj7C 5uj8C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: ORC1, ORC1L, PARC1 Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) 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.) Homo sapiens (human) / Gene: ORC2, ORC2L Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: Q13416 |
#3: Protein | Mass: 82436.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ORC3, LATHEO, ORC3L Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: Q9UBD5 |
#4: Protein | Mass: 50443.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ORC4, ORC4L Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: O43929 |
#5: Protein | Mass: 50349.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ORC5, ORC5L Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: O43913 |
-Non-polymers , 2 types, 5 molecules
#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 |
-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: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) 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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-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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