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- PDB-8ux1: Cryo-EM structure of Ran bound to RCC1 and the nucleosome core pa... -
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Basic information
Entry | Database: PDB / ID: 8ux1 | |||||||||
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Title | Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle | |||||||||
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![]() | NUCLEAR PROTEIN / GTPase / Guanine nucleotide exchange factor / chromatin-binding | |||||||||
Function / homology | ![]() HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression ...HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RNA Polymerase I Promoter Escape / polytene chromosome band / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / UCH proteinases / polytene chromosome / mitotic nuclear membrane reassembly / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / sulfate binding / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / regulation of mitotic nuclear division / DNA metabolic process / dynein intermediate chain binding / nuclear chromosome / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / spindle assembly / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / nuclear pore / heterochromatin organization / nucleosome binding / nucleosomal DNA binding / centriole / protein export from nucleus / viral process / guanyl-nucleotide exchange factor activity / mitotic spindle organization / G protein activity / condensed nuclear chromosome / male germ cell nucleus / chromosome segregation / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / G1/S transition of mitotic cell cycle / structural constituent of chromatin / protein import into nucleus / GDP binding / nucleosome / nucleosome assembly / melanosome / positive regulation of protein binding / chromatin organization / nuclear envelope / chromosome / mitotic cell cycle / midbody / histone binding / actin cytoskeleton organization / nucleic acid binding / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / protein-containing complex binding / chromatin / nucleolus Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
![]() | Huang, S.K. / Rubinstein, J.L. / Kay, L.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle Authors: Huang, S.K. / Rubinstein, J.L. / Kay, L.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 422.3 KB | Display | ![]() |
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PDB format | ![]() | 325.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 863.7 KB | Display | ![]() |
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Full document | ![]() | 877.1 KB | Display | |
Data in XML | ![]() | 45.5 KB | Display | |
Data in CIF | ![]() | 73.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 42685MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 6 types, 10 molecules AEBFCGDHKL
#1: Protein | Mass: 15405.036 Da / Num. of mol.: 2 / Mutation: C110S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11521.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: An extra isoleucine was inserted at the N-terminus following the first residue methionine Source: (gene. exp.) ![]() ![]() Gene: His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, ...Gene: His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, His4:CG33881, CG33881, His4:CG33883, CG33883, His4:CG33885, CG33885, His4:CG33887, CG33887, His4:CG33889, CG33889, His4:CG33891, CG33891, His4:CG33893, CG33893, His4:CG33895, CG33895, His4:CG33897, CG33897, His4:CG33899, CG33899, His4:CG33901, CG33901, His4:CG33903, CG33903, His4:CG33905, CG33905, His4:CG33907, CG33907, His4:CG33909, CG33909 Production host: ![]() ![]() #3: Protein | Mass: 13388.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A: ...Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865 Production host: ![]() ![]() #4: Protein | Mass: 13897.275 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: An extra glycine was left at the N-terminus as a result of TEV cleavage. An extra isoleucine (residue 3) was inserted after the initiation methionine. Source: (gene. exp.) ![]() ![]() ![]() ![]() #7: Protein | | Mass: 24456.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #8: Protein | | Mass: 44893.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-153-bp Widom 601 DNA ... , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 47457.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 46998.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-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: Ran-RCC1-NCP complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
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: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 401603 Details: The composite map of the Ran-RCC1-NCP complex are made from stitching together two distinct portions from two separate maps. The Ran-RCC1 portion comes from a locally refined map of the Ran- ...Details: The composite map of the Ran-RCC1-NCP complex are made from stitching together two distinct portions from two separate maps. The Ran-RCC1 portion comes from a locally refined map of the Ran-RCC1 region on NCP, which used 401,603 particles and refined to 2.5 angstrom resolution. The NCP portion comes from a map of a 1-side bound Ran-RCC1-NCP complex, which used 199,434 particles and refined to 2.4 angstrom resolution. Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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