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Yorodumi- SASDBY4: Pentameric Nucleoplasmin-histone H2A/H2B complex (Nucleoplasmin c... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDBY4 |
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Sample | Pentameric Nucleoplasmin-histone H2A/H2B complex
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Function / homology | Function and homology information structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function |
Biological species | Xenopus laevis (African clawed frog) |
Citation | Date: 2017 Dec Title: Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release Authors: Warren C / Matsui T / Karp J / Onikubo T / Cahill S / Brenowitz M / Cowburn D / Girvin M |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDBY4 |
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-Related structure data
Similar structure data |
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-External links
Related items in Molecule of the Month |
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-Models
Model #546 | Type: dummy / Software: (r6345) / Radius of dummy atoms: 5.75 A / Symmetry: P5 / Chi-square value: 1.580 Search similar-shape structures of this assembly by Omokage search (details) |
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Model #1701 | Type: mix / Radius of dummy atoms: 1.90 A / Symmetry: P5 / Chi-square value: 1.43 Search similar-shape structures of this assembly by Omokage search (details) |
Model #1702 | Type: mix / Radius of dummy atoms: 1.90 A / Symmetry: P5 / Chi-square value: 1.26 / P-value: 0.000139 Search similar-shape structures of this assembly by Omokage search (details) |
-Sample
Sample | Name: Pentameric Nucleoplasmin-histone H2A/H2B complex / Entity id: 348 / 349 / 350 |
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Buffer | Name: 20 mM Tris 150mM NaCl 1mM EDTA 5mM DTT / Concentration: 20.00 mM / pH: 8 / Composition: 150mM NaCl, 1mM EDTA, 5mM DTT |
Entity #348 | Name: Npm core / Type: protein / Description: Nucleoplasmin core + A2 / Formula weight: 16.165 / Num. of mol.: 5 / Source: Xenopus laevis / References: UniProt: Q6NUC7 Sequence: ASTASNTSKV EKPVSLIWGC ELNEQNKTFA FKIEDEEEKC EHQLALRTVC LGDKAKDEFH IVEIVTQEEG KEKPVPIASL KPSILPMATM VGIELTPPVT FRLKAGSGPV YISGQHVAME EDYSWAEEED EGEEEEEEEE DPESP |
Entity #349 | Name: 2HA / Type: protein / Description: Histone H2A (ΔAla127) / Formula weight: 13.879 / Num. of mol.: 5 / Source: Xenopus laevis / References: UniProt: Q6AZJ8 Sequence: SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLPN IQSVLLPKKT ESSKSKSK |
Entity #350 | Name: H2B / Type: protein / Description: Histone H2B 1.1 (Ser33Thr) / Formula weight: 13.494 / Num. of mol.: 5 / Source: Xenopus laevis / References: UniProt: P02281 Sequence: AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSRE IQTAVRLLLP GELAKHAVSE GTKAVTKYTS AK |
-Experimental information
Beam | Instrument name: Stanford Synchrotron Radiation Lightsource (SSRL) BL4-2 City: Stanford, CA / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1127 Å / Dist. spec. to detc.: 1.7 mm | ||||||||||||||||||||||||||||||||||||
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Detector | Name: Rayonix MX225-HE | ||||||||||||||||||||||||||||||||||||
Scan | Title: Pentameric Nucleoplasmin-histone H2A/H2B complex / Measurement date: Jan 7, 2016 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 55 / Unit: 1/nm /
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Distance distribution function P(R) | Sofotware P(R): GNOM 4.6 / Number of points: 172 /
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Result | Type of curve: merged Comments: The models displayed for this entry are: Top: ab initio bead model representation (derived from individual reconstructions (example fit shown), aligned, spatially averaged and volume- ...Comments: The models displayed for this entry are: Top: ab initio bead model representation (derived from individual reconstructions (example fit shown), aligned, spatially averaged and volume-occupancy corrected): Middle: The best CORAL model using the major A2 site (site #1) of A2:H2A/H2B complex as a starting structure (See Figure 5D in the primary citation). Lacking fragments reconstructed by the program CORAL are shown as spheres. Bottom: The best CORAL model using the minor A2 site (site #2) of A2:H2A/H2B complex as a starting structure (See Figure 5D in the primary citation). Lacking fragments reconstructed by the program CORAL are shown as spheres.
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