Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.

Warren C, Matsui T, Karp JM, Onikubo T, Cahill S, Brenowitz M, Cowburn D, Girvin M, Shechter D, Nat Commun 8(1):2215 (2017) Europe PMC

SASDBY4 – Pentameric Nucleoplasmin-histone H2A/H2B complex

Nucleoplasmin core + A2
Histone H2A (ΔAla127)
Histone H2B 1.1 (Ser33Thr)

MW^experimental	251	kDa
MW^expected	218	kDa
V^Porod	402	nm³

log I(s) 2.87×10³ 2.87×10² 2.87×10¹ 2.87×10⁰

Nucleoplasmin core + A2 Histone H2A (ΔAla127) Histone H2B 1.1 (Ser33Thr) small angle scattering data

s, nm^-1

Log plot Log-Log plot

ln I(s)

Nucleoplasmin core + A2 Histone H2A (ΔAla127) Histone H2B 1.1 (Ser33Thr) Guinier plot

ln 2.88×10³ R_g: 4.4 nm 0 (4.4 nm)^-2 s²

(sR_g)²I(s)/I(0)

Nucleoplasmin core + A2 Histone H2A (ΔAla127) Histone H2B 1.1 (Ser33Thr) Kratky plot

1.104 0 √3 sR_g

p(r)	R_g: 4.3 nm 0 D_max: 14 nm

Data validation

Experimental data range

p(r) fit to data

Metric

Value

s_min D_max / π

0.7

N_Shannon

Worse

Better

Metric

Value

p_cormap

χ²

0.002
0.613

Worse

Better

Fits and models

log I(s)	s, nm^-1
+3 Δ/σ -3	s, nm^-1

Nucleoplasmin core + A2 Histone H2A (ΔAla127) Histone H2B 1.1 (Ser33Thr) DAMFILT model

log I(s)	s, nm^-1
+3 Δ/σ -3	s, nm^-1

Nucleoplasmin core + A2 Histone H2A (ΔAla127) Histone H2B 1.1 (Ser33Thr) CORAL model

log I(s)	s, nm^-1
+3 Δ/σ -3	s, nm^-1

Synchrotron SAXS data measured from solutions of the pentameric nucleoplasmin-histone H2A/H2B complex in 20 mM Tris 150mM NaCl, 1mM EDTA, 5mM DTT, pH 8.0, were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (Stanford, USA) using a Rayonix MX225-HE detector (I(s) vs s; s = 4π sin θ/λ, where 2θ is the scattering angle and λ=0.1127 nm). Fifty five successive 1 s data frames were collected immediately after the protein complex eluted from a size-exclusion chromatography (SEC) column. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank (derived from the SEC running solvent) was subtracted and the individual solvent-corrected SAXS profiles were scaled and averaged to produce the final merged SAXS data profile.

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.

Nucleoplasmin core + A2 (Npm core)
Mol. type		Protein
Organism		Xenopus laevis
Olig. state		Pentamer
Mon. MW		16.2 kDa

UniProt		Q6NUC7 (2-145)
Sequence		FASTA

Histone H2A (ΔAla127) (2HA)
Mol. type		Protein
Organism		Xenopus laevis
Olig. state		Pentamer
Mon. MW		13.9 kDa

UniProt		Q6AZJ8 (2-130)
Sequence		FASTA

Histone H2B 1.1 (Ser33Thr) (H2B)
Mol. type		Protein
Organism		Xenopus laevis
Olig. state		Pentamer
Mon. MW		13.5 kDa

UniProt		P02281 (5-126)
Sequence		FASTA