Fig. 1. DNA binding is conserved between archaeal and eukaryotic
histones. (A) The structure of three (HMfB)2 dimers bound to a 90-bp SELEX
DNA is highly similar to the (B) nucleosome hexasome, shown by removing one
H2A-H2B heterodimer and the histone tails from the published nucleosome
structure (1AOI). The axes of symmetry in both protein assemblies are
indicated (F). SELEX, systematic evolution of ligands by exponential enrichment. (C) HFs of an (HMfB)2 dimer and (D) (H3-H4) heterodimer shown in
the same orientation with associated DNA. E, glutamic acid. (E) The L1L2
interface of an (HMfB)2 dimer and (F) an (H3-H4) dimer is shown with conserved interactions with DNA. (G) The a1a1 interface in an (HMfB)2 dimer and
(H) in an (H3-H4) dimer. Further comparisons of the structures formed
by HMfB and eukaryotic histones with DNA are shown in fig. S2. In all figures,
although identical, the two HMfB monomers in an (HMfB)2 dimer are
colored in cyan and magenta; H3 is blue; H4 is green; H2A is yellow; H2B is red.
Regions of core histones that are not part of the histone fold are shown
in white. DNA organized by HMfB is pale yellow; nucleosomal DNA is gray.
Fig. 2. Archaeal histones form a continuous superhelical ramp.
(A) Archaeal (HMfB)2 dimers and eukaryotic core-histone heterodimers
polymerize through the assembly of 4HBs involving the C termini of a2 and
a3 of the HF. Although the symmetric (HMfB)2 dimers can continue to
polymerize, forming a protein fiber with consecutive, identical 4HB bundles
(oval and inset), the asymmetry of eukaryotic core-histone dimers prevents
continued polymerization at the site marked by the red X. (B) Nine (HMfB)2
dimers are shown forming a continuous protein superhelix via 4HB interactions,
with groups of three consecutive dimers shown in pink, teal, and tan. Modeling
confirmed that the superhelix can also be formed by (HMfA)2 homodimers and
by HMfA-HMfB heterodimers. The arrow shows the location of the G16-G16
interaction (L1L1). (C) An octamer of archaeal HFs superimposes closely with the
eukaryotic histone octamer (tan) in the nucleosome. Helices are shown as tubes
with the archaeal histones colored magenta and cyan. (D) Archaeal HMfB
octamer (top panel) and eukaryotic histone octamer (bottom panel) differ in
their charge distribution, with a more positively charged helical ramp on the
surface of the histone core (the basic histone tails are excluded for clarity).
Electrostatic surfaces are calculated in the CCP4mg program and displayed
from –0.5 V (red) to 0.5 V (blue). The DNA backbone is shown as a line.
(E) DNA (shown in space-filling mode) wrapped around the HMfB superhelix
shown in the same orientation as in (B). Inset shows a close-up view of the
annealed 2-nt 5′ extensions. One supergroove is indicated by two arrows.
(F) Superposition of 120 bp of DNA organized by four (HMfB)2 HFDs with
146-bp nucleosomal DNA, shown in three orthogonal orientations; the top two
orientations are identical to the orientations shown in (C). Two supergrooves
(minor and major) are indicated by arrows.