6SW9
IC2A model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (2) | 16S ribosomal RNA | polymer | 1497 | 487700.3 | 1 | Pyrococcus abyssi GE5 | ||
| 2 | B (A) | 30S ribosomal protein S3Ae | polymer | 199 | 22888.1 | 1 | UniProt (Q9V2K7) Pfam (PF01015) | Pyrococcus abyssi (strain GE5 / Orsay) | Ribosomal protein S1e |
| 3 | C (B) | 30S ribosomal protein S2 | polymer | 202 | 23026.9 | 1 | UniProt (Q9V191) Pfam (PF00318) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 4 | D (C) | Zn-ribbon RNA-binding protein involved in translation | polymer | 63 | 7163.4 | 1 | UniProt (G8ZFK7) Pfam (PF07754) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 5 | E (D) | 30S ribosomal protein S4 | polymer | 180 | 21381.9 | 1 | UniProt (P61992) Pfam (PF00163) Pfam (PF01479) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 6 | F (E) | 30S ribosomal protein S4e | polymer | 243 | 28246.1 | 1 | UniProt (Q9V1U8) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 7 | G (F) | 30S ribosomal protein S5 | polymer | 236 | 26523.9 | 1 | UniProt (Q9V1V5) Pfam (PF00333) Pfam (PF03719) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 8 | H (G) | 30S ribosomal protein S6e | polymer | 125 | 14029.5 | 1 | UniProt (Q9UYS3) Pfam (PF01092) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 9 | I (H) | 30S ribosomal protein S7 | polymer | 215 | 24662.8 | 1 | UniProt (Q9V109) Pfam (PF00177) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 10 | J (I) | 30S ribosomal protein S8 | polymer | 130 | 14772.2 | 1 | UniProt (Q9V1V0) Pfam (PF00410) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 11 | K (J) | 30S ribosomal protein S8e | polymer | 127 | 14293.7 | 1 | UniProt (Q9UZL4) Pfam (PF01201) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 12 | L (K) | 30S ribosomal protein S9 | polymer | 135 | 15293.9 | 1 | UniProt (Q9V195) Pfam (PF00380) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 13 | M (L) | 30S ribosomal protein S10 | polymer | 102 | 11795.8 | 1 | UniProt (Q9V0V6) Pfam (PF00338) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 14 | N (M) | 30S ribosomal protein S11 | polymer | 137 | 14773.0 | 1 | UniProt (P62010) Pfam (PF00411) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 15 | O (N) | 30S ribosomal protein S12 | polymer | 147 | 16477.6 | 1 | UniProt (P61994) Pfam (PF00164) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 16 | P (O) | 30S ribosomal protein S13 | polymer | 148 | 16992.9 | 1 | UniProt (Q9V1A0) Pfam (PF00416) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 17 | Q (P) | 30S ribosomal protein S14 type Z | polymer | 56 | 6644.1 | 1 | UniProt (P62012) Pfam (PF00253) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 18 | R (Q) | 30S ribosomal protein S15 | polymer | 158 | 18697.1 | 1 | UniProt (Q9V2K9) Pfam (PF08069) Pfam (PF00312) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 19 | S (R) | 30S ribosomal protein S17 | polymer | 113 | 13364.6 | 1 | UniProt (Q9V1U5) Pfam (PF00366) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 20 | T (S) | 30S ribosomal protein S17e | polymer | 67 | 8059.5 | 1 | UniProt (Q9V0G0) Pfam (PF00833) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 21 | U (T) | 30S ribosomal protein S19 | polymer | 132 | 15307.3 | 1 | UniProt (Q9V1T9) Pfam (PF00203) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 22 | V (U) | 30S ribosomal protein S19e | polymer | 150 | 17422.3 | 1 | UniProt (Q9V0G8) Pfam (PF01090) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 23 | W (V) | 30S ribosomal protein S24e | polymer | 99 | 11798.6 | 1 | UniProt (Q9UY20) Pfam (PF01282) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 24 | X (W) | 30S ribosomal protein S27e | polymer | 65 | 7186.6 | 1 | UniProt (Q9UXZ3) Pfam (PF01667) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 25 | Y (X) | 30S ribosomal protein S28e | polymer | 71 | 8102.3 | 1 | UniProt (P61029) Pfam (PF01200) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 26 | Z (Y) | 30S ribosomal protein S27ae | polymer | 51 | 5992.2 | 1 | UniProt (P61238) Pfam (PF01599) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 27 | AA (Z) | 30S ribosomal protein S3 | polymer | 210 | 23472.3 | 1 | UniProt (Q9V1U1) Pfam (PF07650) Pfam (PF00189) | Pyrococcus abyssi (strain GE5 / Orsay) | |
| 28 | BA (0) | 50S ribosomal protein L41e | polymer | 36 | 4910.2 | 1 | UniProt (by SIFTS) (Q8U232) | Pyrococcus abyssi GE5 | |
| 29 | CA (3) | 50S ribosomal protein L7Ae | polymer | 123 | 13442.7 | 1 | UniProt (P62008) Pfam (PF01248) | Pyrococcus abyssi (strain GE5 / Orsay) | Ribosomal protein L8e |
| 30 | DA (5) | mRNA | polymer | 20 | 6448.9 | 1 | Pyrococcus abyssi GE5 | ||
| 31 | EA (4) | initiator Met-tRNA fMet from E. coli (A1U72 variant) | polymer | 76 | 24504.7 | 1 | Escherichia coli | ||
| 32 | FA (6) | Translation initiation factor 1A | polymer | 113 | 13078.3 | 1 | UniProt (Q9V138) Pfam (PF01176) | Pyrococcus abyssi (strain GE5 / Orsay) | aIF-1A |
| 33 | GA (7) | Translation initiation factor 2 subunit gamma | polymer | 414 | 45718.0 | 1 | UniProt (Q980A5) Pfam (PF00009) Pfam (PF09173) | Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) | aIF2-gamma,eIF-2-gamma |
| 34 | HA (8) | Translation initiation factor 2 subunit beta | polymer | 129 | 14835.5 | 1 | UniProt (Q97W59) Pfam (PF01873) | Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) | aIF2-beta,eIF-2-beta |
| 35 | IA (9) | Translation initiation factor 2 subunit alpha | polymer | 254 | 28946.6 | 1 | UniProt (Q97Z79) Pfam (PF00575) Pfam (PF07541) | Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) | aIF2-alpha,eIF-2-alpha |
| 36 | AB, BB, CB, DB, EB... (2, 5, 4, 7) | MAGNESIUM ION | non-polymer | 24.3 | 34 | Chemie (MG) | |||
| 37 | OB, PB, QB, RB, SB... (C, F, P, R, W) | ZINC ION | non-polymer | 65.4 | 6 | Chemie (ZN) | |||
| 38 | WB (7) | METHIONINE | non-polymer | 149.2 | 1 | Chemie (MET) | |||
| 39 | XB (7) | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | non-polymer | 522.2 | 1 | Chemie (GNP) | |||
| 40 | AC, BC, ZB (K, Q, 2) | water | water | 18.0 | 42 | Chemie (HOH) |
Sequence modifications
8: 3 - 139 (UniProt: Q97W59)
9: 1 - 264 (UniProt: Q97Z79)
| PDB | External Database | Details |
|---|---|---|
| - | Glu 20 | deletion |
| - | Lys 21 | deletion |
| - | Gly 22 | deletion |
| - | Arg 23 | deletion |
| - | Lys 24 | deletion |
| - | Glu 25 | deletion |
| - | Gly 26 | deletion |
| - | Thr 27 | deletion |
| PDB | External Database | Details |
|---|---|---|
| - | Ser 48 | deletion |
| - | Lys 49 | deletion |
| - | Trp 50 | deletion |
| - | Val 51 | deletion |
| - | Lys 52 | deletion |
| - | Lys 170 | deletion |
| - | His 171 | deletion |
| - | Ala 172 | deletion |
| - | Glu 173 | deletion |
| - | Glu 174 | deletion |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 35 |
| Total formula weight | 1047953.7 | |
| Non-Polymers* | Number of molecules | 42 |
| Total formula weight | 1890.2 | |
| All* | Total formula weight | 1049844.0 |
