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- SASDBY4: Pentameric Nucleoplasmin-histone H2A/H2B complex (Nucleoplasmin c... -

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Basic information

Entry
Database: SASBDB / ID: SASDBY4
SamplePentameric Nucleoplasmin-histone H2A/H2B complex
  • Nucleoplasmin core + A2 (protein), Npm core, Xenopus laevis
  • Histone H2A (ΔAla127) (protein), 2HA, Xenopus laevis
  • Histone H2B 1.1 (Ser33Thr) (protein), H2B, Xenopus laevis
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / heterochromatin formation / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A / :
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
CitationDate: 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
Contact author
  • Tsutomu Matsui
  • Christopher Warren
  • Jerome Karp
  • Takashi Onikubo
  • Sean Cahill
  • David Cowburn
  • Michael Brenowitz
  • Mark Girvin
  • David Shechter

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)
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)

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Sample

SampleName: Pentameric Nucleoplasmin-histone H2A/H2B complex / Entity id: 348 / 349 / 350
BufferName: 20 mM Tris 150mM NaCl 1mM EDTA 5mM DTT / Concentration: 20.00 mM / pH: 8 / Composition: 150mM NaCl, 1mM EDTA, 5mM DTT
Entity #348Name: 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 #349Name: 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 #350Name: 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

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Experimental information

BeamInstrument name: Stanford Synchrotron Radiation Lightsource (SSRL) BL4-2
City: Stanford, CA / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.1127 Å / Dist. spec. to detc.: 1.7 mm
DetectorName: 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 /
MinMax
Q0.16 2.9936
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 172 /
MinMax
Q0.02057 0.1769
P(R) point1 172
R0 140
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.
ExperimentalPorod errorPorod
MW251 kDa251 -
Volume--402 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I02822 8 2875.52 14.75
Radius of gyration, Rg4.32 nm0.01 4.39 nm0.03

MinMax
D-14
Guinier point1 16

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