Table 2. Assessment of possible hypernucleosome formation by archaeal histones.
| Dimer–dimer interfacea | Stacking interfaceb | Potential stacking interactionsc |
Hypernucleosome formation | Histone features |
||
|---|---|---|---|---|---|---|
| Heimdall | LC_3 HA | ± | + | 3 (E14-R48, K26-E57, R41-E45) | ± | N-terminal tail |
| Heimdall | LC_3 HB | + | + | 5 (E30-K61, Q14-R48, R13-Q18, K27-E57, K37-E45) | + | |
| Heimdall | LC_3 HC | ± | + | 3 (N34-R65, T15-K41, Y14-Q53) | ± | |
| Loki | GC14_75 (HLkE) | − | + | 2 (D14-R48, K34-E45) | − | Truncated C-term |
| Loki | CR_4 | + | + | 2 (Q14-D48, Q41-Q41) | + | |
| Odin | LCB_4 | + | − | 3 (K30-Q61, K14-E18, E38-R41) | ± | |
| Thor | SMTZ1-45 | + | + | 5 (Q30-D61, E34-K65, K14-E48, E37-R41, E26-K58) | + | |
| Woese | CG1_02_33_12 | + | + | 4 (R14-T48, R34-E61, E26-K57, E37-R41) | + | |
| Pace | CG1_02_31_27 | + | + | 4 (S30-K61, E34-K65, K14-T48, E37-K45) | + | |
| Huber | CG_4_9_14_3_um_filter_31_125 (HA) | ± | + | 2 (E14-K48, E14-K18) | ± | |
| Huber | CG_4_9_14_3_um_filter_31_125 (HB) | + | + | 2 (N30-R61, K34-E65) | + | N-terminal tail |
| Diaphero | CG_4_10_14_0_2_um_filter_31_5 | ± | ± | 4 (E33-R48, E37-R41, E37-R48, E27-K61) | ± | |
| Aenigm | CG1_02_38_14 | + | + | 5 (E30-K61, D34-R65, E14-H48, A15-K41, E37-K41) | + | |
| Micr | M. acidiphilum ARMAN-2 | + | + | 3 (E30-K61, K34-Q65, Y2-K48) | + | |
| Nanohalo | Haloredivivus sp. G17 | ± | − | 2 (E27-R61, Q37-E45) | − | Truncated N-term |
| Nanohalo | Nanosalina sp. J07AB43 (HA) | + | + | 5 (Q30-K61, D34-R65, K14-E48, K14-E18, Q37-Q45) | + | |
| Nanohalo | Nanosalina sp. J07AB43 (HB) | − | ± | 2 (Q30-R61, D14-K18) | − | |
| Nano | N. equitans Kin4-M | + | + | 4 (E30-R61, Q14-K48, Q14(bb)-R41, K37-E45) | + | |
| Kor |
ARK-16 (HA) |
± | ± | 7 (R30-E61, Q14-K48, K15-E41, E26-R58, E27-R57, E33-K48, R38-E41) | ± | |
| Kor | ARK-16 (HB) | + | + | 3 (Y30-E61, D14-K48, R27-E61) | + | |
| Thaum | N. gargensis Ga9.2 | + | + | 4 (E34-K65, K14-E18, E27-R61, E37-K41) | + | |
| Bathy | B23 | ± | ± | 4 (R14-V44, E34-K61, E37-R41, E26-R58) | ± | N-terminal tail |
| Bathy | B24 | + | + | 3 (E34-R65, K14-E18, E27-R61) | + | Truncated N-term |
| Bathy | SMTZ-80 | + | + | 3 (E34-K65, K41-E45, E27-R61) | + | |
| Cren | C. maquilingensis IC-167 | + | + | 4 (D30-K61, N34-R65, K14-E18, Y37-K48) | + | |
| Cren | T. pendens Hrk5 | + | + | 4 (E30-K61, S14-R48, R37-E45, R13-E18) | + | |
| Cren | V. distributa DSM14429 | + | + | 4 (D30-K61, Y34-R65, K14(bb)-R48, K14-E18) | + | |
| Eury | M. wolinii (HA) | ± | + | 4 (N30-E61, E34-K65, E14-K48, K41-E45) | ± | |
| Eury | M. wolinii (HB) | + | + | 5 (E30-K61, E34-K65, N14-R48, N14-Q18, Q41-Q41) | + | |
| Eury | M. jannaschii DSM2661 | + | − | 4 (N30-K61, Q14-R48, K37-Q45, D26-R58) | ± | C-terminal tail |
| Eury | M. methylutens | ± | − | 2 (D30-K61, S14-E18) | − | |
| Eury | T. kodakarensis KOD1 (HTkB) | + | + | 4 (E30-K61, E34-K65, K14-Q48, K26-E58) | + | |
| Eury | M. fervidus DSM2088 (HMfB) | + | + | 3 (K30-E61, E34-R65, D14-R48) | + |
Dimer–dimer interactions in the tetrameric interface are expected to be essential for hypernucleosome formation. Absence of bulky residues in the first loop and a high number of potential hydrogen bonds in the stacking interface will enhance the compactness and stability of the hypernucleosome. Likely, uncertain and unlikely stacking ability is indicated with +, ±, and −, respectively.
a Dimer–dimer interface includes residues at positions 46, 49, 59, and 62.
b Stacking interface includes residues at positions 15–17.
c For all potential stacking interactions, residue numbering of HMfB was used according to the alignment in Fig 3.
Abbreviations: HA, Histone A; HB, Histone B; HLkE, Histone E from Lokiarchaeota; HMfB, Histone B from Methanothermus fervidus; HTkB, Histone B from Thermococcus kodakarensis.