It was an atom, that contained in the form of pure energy, the fundamental components of entire universe. If it might help, read it the way stated above. It actually means that, atom is a thing that contained fundamental components of entire universe in the form of pure energy.

I would divide the sentence in the same way Nabeel did. Literal translation: 「宇宙全体を構成している基本要素を純粋なエネルギーという形で包含しているのは原子である。」

A Wikipedia Essay on the subject of Mass/Energy Equivalence is informative: . . ================================================ "E=MC2" redirects here. For other uses, see E=MC2 (disambiguation). 4-meter-tall sculpture of Einstein's 1905 E = mc2 formula at the 2006 Walk of Ideas, Berlin, GermanyIn physics, mass-energy equivalence is the concept that the mass of a body is a measure of its energy content. In this concept, mass is a property of all energy, and energy is a property of all mass, and the two properties are connected by a constant. This means (for example) that the total internal energy E of a body at rest is equal to the product of its rest mass m and a suitable conversion factor to transform from units of mass to units of energy. Albert Einstein proposed mass-energy equivalence in 1905 in one of his Annus Mirabilis papers entitled "Does the inertia of a body depend upon its energy-content?"[1] The equivalence is described by the famous equation: E = MC(squared) where E is energy, m is mass, and c is the speed of light in a vacuum. The formula is dimensionally consistent and does not depend on any specific system of measurement units. The equation E = mc2 indicates that energy always exhibits relativistic mass in whatever form the energy takes."----from the website @ http://en.wikipedia.org/wiki/Mass%E2%80%93energy_equivalence ==============================================

Hi HCast Because the sentence refers to a SINGLE ATOM with the fundamental components of the entire Universe in it, I believe you are reading about the moment of Singularity, commonly referred as the Theory of the Big Bang, when all Space, Time, Energy and Matter were created. ================================= "About 15 billion years ago a tremendous explosion started the expansion of the universe. This explosion is known as the Big Bang. At the point of this event ALL OF THE MATTER AND ENERGY OF SPACE was contained at one point."-------sentences 1, 2, & 3 of paragraph 5, from the online essay entitled "THE BIG BANG" by Chris LaRocco and Blair Rothstein of the University of Michigan Department of Education @ http://www.umich.edu/~gs265/bigbang.htm ================ Your other question was: "The universe is made up of pure energy that are atoms." ??? Energy and Matter (atoms) are complementary of each other. It would not be appropriate however to say that the Universe is made up of "pure energy" because to say that would mean there was no Energy which was congealed as Matter. (continued... .