Roots, as the core of Proto-Indo-European (PIE) words, are the forms to which suffixes (optionally) and inflectional endings are added. PIE roots encode basic lexical meanings such as 'foot' or 'to bear, carry', while suffixes and endings add grammatical meaning. A PIE root typically had the form CVC-. That is, it began with a consonant (C), had a medial vowel (V), and ended with a consonant -- drawing these from members of the PIE phoneme inventory.
The oldest PIE roots were athematic: they had no suffixes, and added only endings depending on word class. Verbs, for example, added one of three types of person/number endings. Later in the proto-language, root forms might be enlarged (or suffixed) to create "stems." So the form *ker- with basic meaning 'top' is suffixed with -d to form *ker-d- 'heart', and *wer- 'to bend, turn' is suffixed with -t to form *wer-t- 'to turn, wind', both with CVC-C- structure. Stem vowels might also be suffixed to roots to create new noun or adjective stems; for example, the noun stem *peku- 'cattle' is formed by suffixing the stem vowel -u to *pek- 'to fleece'.
Vowel alternation (ablaut) not only varied the root vowel (e.g. between [e] and [o]) but might also produce a root or suffixed form without a vowel (CC-C-) or, with a -VC- suffix, CC-VC-. Zero-grade roots are particularly frequent when one of the consonants is a resonant, a sound that can have either consonantal or vocalic function in a root. Frequent consonant clusters with resonants include Cr and Cl combinations, as in the root for 'three' with CVC- and Cr-VC- variants *ter-, *tr-ey-. In root forms for 'three', the consonant of the suffixed -VC- is also a resonant (glide) with consonantal [y] or vocalic [i] value. Using R for Resonant, these root structures may be described more specifically as CeR- and CR-eR-. The reconstructions *tr-ey- and *tr-ei- are thus variants, one stressing the consonantal and the other the vocalic value of the resonant *Y.
Vowel-initial roots (e.g. *(H)es- 'to be') are often reconstructed with an initial laryngeal consonant (e.g. *H1) that disappeared from PIE after Proto-Anatolian had become a distinct dialect.