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Structure of the Nuclear Chaperone Nucleoplamsin.
by single particle reconstruction, at 21 A resolution
#1: Surface view with section colored by density value, Surface level: 0.0225, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 0.0225, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1778 |
|---|---|
| Title | Structure of the Nuclear Chaperone Nucleoplamsin. |
| Map | This a map of the nuclear chaperone nucleoplasmin. |
| Sample | Nucleoplasmin chaperone |
| Keywords |  Nucleoplasmin, Histone H2A, Histone H2B, Chaperone, Chromatin, Nuclear-chaperone, Histone-chaperone |
| Authors | Ramos I, Martin-Benito J, Finn R, Bretana L, Aloria K, Arizmendi JM, Ausio J, Muga A, Valpuesta JM, Prado A |
| Date | Deposition: 2010-08-31, Header release: 2010-10-26, Map release: 2010-10-26, Last update: 2010-10-26 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.0225, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.0225, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Biol. Chem., Vol. 285, Issue 44, Page 33771-8, Year 2010 |
|---|---|
| Title | Nucleoplasmin binds histone H2A-H2B dimers through its distal face. |
| Authors | Isbaal Ramos, Jaime Martín-Benito, Ron Finn, Laura Bretaña, Kerman Aloria, Jesús M Arizmendi, Juan Ausió, Arturo Muga, José M Valpuesta, Adelina Prado Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, 48080 Bilbao, Spain. |
| Keywords | Animals, Dimerization, Histones (chemistry), Mass Spectrometry (methods), Microscopy, Electron (methods), Nucleoplasmins (chemistry), Phosphorylation, Protein Folding, Protein Interaction Mapping, Protein Structure, Tertiary, Xenopus laevis (metabolism) |
| Links | DOI: 10.1074/jbc.M110.150664, PubMed: 20696766, PMC: PMC2962476 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1778.map ( map file in CCP4 format, 2050 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||
| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A= B= C: 184 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.3 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This a map of the nuclear chaperone nucleoplasmin. | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Nucleoplasmin chaperone |
|---|---|
| Number of Components | 1 |
| Oligomeric State | Pentameric |
| Theoretical Mass | 0.11MDa |
| Experimental Mass | 0.11MDa |
| Component #1: protein - Nucleoplasmin | |
| Scientific name | Nucleoplasmin |
| Theoretical Mass | 0.11 MDa |
| Experimental Mass | 0.11 MDa |
| Oligomeric Details | Pentamer |
| Number of Copies | 5 |
| Scientific Name of Species | Xenopus laevis
|
| Common Name of Species | African clawed frog |
| NCBI taxonomy | 8355 |
| Recombinant expression | No |
| Natural Source | Cell: Oocyte Organ Or Tissue: Egg Organelle: Nucleus |
| Links | Inter Pro: IPR:004301 |
 Experiment | |
| Sample Preparation | |
| Staining | Grids were stained with 2% w/v Uranyl Acetate solution for 1 minute. |
|---|---|
| Specimen Support Details | 200 mesh CuRh grid |
| Specimen State | particle |
| Buffer | Details: 2mM MgCl2, 240mM NaCl, 25 mM Tris-HCl pH: 7.5 |
| Vitrification | |
| Cryogen Name | NONE |
| Instrument | NONE |
| Imaging | |
| Microscope | JEOL 1200EXII |
| Electron Gun | |
| Electron Source | TUNGSTEN HAIRPIN |
| Accelerating Voltage | 100 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 60000 |
| Astigmatism | Objective lens astigmatism was corrected at 200,000 times magnification |
| Nominal Cs | 5.6 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1000 nm - 2500 nm |
| Specimen Holder | |
| Holder | Eucentric |
| Model | JEOL |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 10 |
| Sampling Size | 2.3 |
| Quant Bit Number | 8 |
| Details | downsampling factor of 2 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Projection matching |
| Software | EMAN, XMIPP, SPIDER |
| CTF Correction | Each plate |
| Resolution By Author | 21 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 9862 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1778.xml (7.2 KB) | ||
|---|---|---|---|
| Map data | emd_1778.map.gz (1.8 MB) | ||
| Images | image_EMD1778.tif (756.1 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1778 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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