SASDA55: Nucleoplasmin (NP)

Basic information

• Entry: Database: SASBDB / ID: SASDA55

Sample

Nucleoplasmin

• Nucleoplasmin (protein), NP, Escherichia coli

• Biological species: Escherichia coli (E. coli)
• Citation: Journal: J Mol Biol / Year: 2009; Title: A mechanism for histone chaperoning activity of nucleoplasmin: thermodynamic and structural models.; Authors: Stefka G Taneva / Sonia Bañuelos / Jorge Falces / Igor Arregi / Arturo Muga / Petr V Konarev / Dmitri I Svergun / Adrián Velázquez-Campoy / María A Urbaneja / ; Abstract: Nucleoplasmin (NP), a histone chaperone, acts as a reservoir for histones H2A-H2B in Xenopus laevis eggs and can displace sperm nuclear basic proteins and linker histones from the chromatin fiber of sperm and quiescent somatic nuclei. NP has been proposed to mediate the dynamic exchange of histones during the expression of certain genes and assists the assembly of nucleosomes by modulating the interaction between histones and DNA. Here, solution structural models of full-length NP and NP complexes with the functionally distinct nucleosomal core and linker histones are presented for the first time, providing a picture of the physical interactions between the nucleosomal and linker histones with NP core and tail domains. Small-angle X-ray scattering and isothermal titration calorimetry reveal that NP pentamer can accommodate five histones, either H2A-H2B dimers or H5, and that NP core and tail domains are intimately involved in the association with histones. The analysis of the binding events, employing a site-specific cooperative model, reveals a negative cooperativity-based regulatory mechanism for the linker histone/nucleosomal histone exchange. The two histone types bind with drastically different intrinsic affinity, and the strongest affinity is observed for the NP variant that mimicks the hyperphosphorylated active protein. The different "affinity windows" for H5 and H2A-H2B might allow NP to fulfill its histone chaperone role, simultaneously acting as a reservoir for the core histones and a chromatin decondensing factor. Our data are compatible with the previously proposed model where NP facilitates nucleosome assembly by removing the linker histones and depositing H2A-H2B dimers onto DNA.

Contact author

• Petr Konarev (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #94: ; Type: mix / Software: BUNCH / Radius of dummy atoms: 1.90 A / Symmetry: P5 / Chi-square value: 0.9216; Search similar-shape structures of this assembly by Omokage search (details)
• Model #95: ; Type: dummy / Software: Dammin / Radius of dummy atoms: 1.90 A / Symmetry: P5 / Chi-square value: 1.557504; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Nucleoplasmin / Sample MW: 110 kDa / Specimen concentration: 1.00-10.00
• Buffer: Name: 20 mM Pipes buffer / pH: 7.5 / Composition: NaCl 150.000 mM

Entity #78

Name: NP / Type: protein / Description: Nucleoplasmin / Formula weight: 22 / Num. of mol.: 5 / Source: Escherichia coli
Sequence:

MASTVSNTSK LEKPVVSLIW GCELNEQNKT FEFKVEDDEE KCEHQLALRT VCLGDKAKDE FHIVEIVTQE EGAEKSVPIA TLKPSILPMA TMVGIELTPP VTFRLKAGSG PLYISGQHVA MEEDYSWAEE EDEGEAEGEE EEEEEEDQES PPKAVKRPAA TKKAGQAKKK KLDKEDESSE EDSPTKKGKG AGRGRKPAAK K

Experimental information

• Beam: Instrument name: DORIS III X33 / City: Hamburg / 国: Germany / Shape: 0.6 / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.15 Å / Dist. spec. to detc.: 2.7 mm
• Detector: Name: Pilatus 1M-W / Pixsize x: 0.172 mm

Scan

Title: Nucleoplasmin / Measurement date: Dec 3, 2007 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 15 sec. / Number of frames: 4 / Unit: 1/nm /

	Min	Max
Q	0.1254	5.1708

Distance distribution function P(R)

Sofotware P(R): GNOM 4.5a / Number of points: 422 /

	Min	Max
Q	0.1268	5.171
P(R) point	1	422
R	0	12

Result

D max: 12.6 / Type of curve: merged /

	Experimental	Porod
MW	130 kDa	-
Volume	-	210 nm3

	Guinier	P(R)
Forward scattering, I0	0.501	-
Radius of gyration, Rg	3.99 nm	4.02 nm