6GSM
Structure of a partial yeast 48S preinitiation complex in open conformation.
This is a non-PDB format compatible entry.
Replaces: 3JAQEntity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (1) | Met-tRNAi | polymer | 76 | 24799.1 | 1 | Saccharomyces cerevisiae S288C | ||
| 2 | B (2) | 18S ribosomal RNA | polymer | 1798 | 579239.6 | 1 | Kluyveromyces lactis NRRL Y-1140 | ||
| 3 | C (A) | 40S ribosomal protein S0 | polymer | 208 | 23140.4 | 1 | UniProt (Q6CN12) Pfam (PF00318) | Kluyveromyces lactis NRRL Y-1140 | |
| 4 | D (3) | mRNA (5'-R(P*AP*AP*U)-3') | polymer | 3 | 919.6 | 1 | Kluyveromyces lactis | ||
| 5 | E (B) | 40S ribosomal protein S1 | polymer | 231 | 26404.7 | 1 | UniProt (Q6CWD0) Pfam (PF01015) | Kluyveromyces lactis NRRL Y-1140 | |
| 6 | F (C) | KLLA0F09812p | polymer | 217 | 23162.9 | 1 | UniProt (Q6CKL3) Pfam (PF00333) Pfam (PF03719) | Kluyveromyces lactis NRRL Y-1140 | |
| 7 | G (D) | KLLA0D08305p | polymer | 223 | 24830.9 | 1 | UniProt (Q6CRK7) Pfam (PF07650) Pfam (PF00189) | Kluyveromyces lactis NRRL Y-1140 | |
| 8 | H (E) | 40S ribosomal protein S4 | polymer | 260 | 29486.3 | 1 | UniProt (Q6CWJ2) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) Pfam (PF08071) Pfam (PF01479) | Kluyveromyces lactis NRRL Y-1140 | |
| 9 | I (F) | KLLA0D10659p | polymer | 206 | 22912.4 | 1 | UniProt (Q6CRA3) Pfam (PF00177) | Kluyveromyces lactis NRRL Y-1140 | |
| 10 | J (G) | 40S ribosomal protein S6 | polymer | 226 | 25811.0 | 1 | UniProt (Q6CM04) Pfam (PF01092) | Kluyveromyces lactis NRRL Y-1140 | |
| 11 | K (H) | 40S ribosomal protein S7 | polymer | 184 | 21033.6 | 1 | UniProt (Q6CTD6) Pfam (PF01251) | Kluyveromyces lactis NRRL Y-1140 | |
| 12 | L (I) | 40S ribosomal protein S8 | polymer | 200 | 22511.5 | 1 | UniProt (Q6CMG3) Pfam (PF01201) | Kluyveromyces lactis NRRL Y-1140 | |
| 13 | M (J) | KLLA0E23673p | polymer | 182 | 20882.3 | 1 | UniProt (Q6CM18) Pfam (PF00163) Pfam (PF01479) | Kluyveromyces lactis NRRL Y-1140 | |
| 14 | N (K) | KLLA0B08173p | polymer | 96 | 11423.1 | 1 | UniProt (Q6CVZ5) Pfam (PF03501) | Kluyveromyces lactis NRRL Y-1140 | |
| 15 | O (L) | KLLA0A10483p | polymer | 155 | 17712.7 | 1 | UniProt (Q6CX80) Pfam (PF16205) Pfam (PF00366) | Kluyveromyces lactis NRRL Y-1140 | |
| 16 | P (M) | 40S ribosomal protein S12 | polymer | 118 | 12710.5 | 1 | UniProt (Q6CLU4) Pfam (PF01248) | Kluyveromyces lactis NRRL Y-1140 | |
| 17 | Q (N) | KLLA0F18040p | polymer | 150 | 16858.7 | 1 | UniProt (Q6CJK0) Pfam (PF08069) Pfam (PF00312) | Kluyveromyces lactis NRRL Y-1140 | |
| 18 | R (O) | 40S ribosomal protein S14 | polymer | 127 | 13458.4 | 1 | UniProt (P27069) Pfam (PF00411) | Kluyveromyces lactis NRRL Y-1140 | RP59 |
| 19 | S (P) | KLLA0F07843p | polymer | 119 | 13448.8 | 1 | UniProt (Q6CKV4) Pfam (PF00203) | Kluyveromyces lactis NRRL Y-1140 | |
| 20 | T (Q) | 40S ribosomal protein S16 | polymer | 141 | 15656.3 | 1 | UniProt (Q875N2) Pfam (PF00380) | Kluyveromyces lactis NRRL Y-1140 | |
| 21 | U (R) | KLLA0B01474p | polymer | 125 | 14200.4 | 1 | UniProt (Q6CWU3) Pfam (PF00833) | Kluyveromyces lactis NRRL Y-1140 | |
| 22 | V (S) | KLLA0B01562p | polymer | 145 | 16953.4 | 1 | UniProt (Q6CWT9) Pfam (PF00416) | Kluyveromyces lactis NRRL Y-1140 | |
| 23 | W (T) | KLLA0A07194p | polymer | 143 | 15747.8 | 1 | UniProt (Q6CXM0) Pfam (PF01090) | Kluyveromyces lactis NRRL Y-1140 | |
| 24 | X (U) | KLLA0F25542p | polymer | 106 | 12032.1 | 1 | UniProt (Q6CIM1) Pfam (PF00338) | Kluyveromyces lactis NRRL Y-1140 | |
| 25 | Y (V) | 40S ribosomal protein S21 | polymer | 87 | 9797.9 | 1 | UniProt (Q6CXT6) Pfam (PF01249) | Kluyveromyces lactis NRRL Y-1140 | |
| 26 | Z (W) | 40S ribosomal protein S22 | polymer | 129 | 14513.8 | 1 | UniProt (Q6CW21) Pfam (PF00410) | Kluyveromyces lactis NRRL Y-1140 | |
| 27 | AA (X) | KLLA0B11231p | polymer | 144 | 15916.7 | 1 | UniProt (F2Z602) Pfam (PF00164) | Kluyveromyces lactis NRRL Y-1140 | |
| 28 | BA (Y) | 40S ribosomal protein S24 | polymer | 134 | 15063.4 | 1 | UniProt (Q6CU44) Pfam (PF01282) | Kluyveromyces lactis NRRL Y-1140 | |
| 29 | CA (Z) | KLLA0B06182p | polymer | 70 | 7939.2 | 1 | UniProt (Q6CW78) Pfam (PF03297) | Kluyveromyces lactis NRRL Y-1140 | |
| 30 | DA (a) | 40S ribosomal protein S26 | polymer | 98 | 11166.2 | 1 | UniProt (Q6CS01) Pfam (PF01283) | Kluyveromyces lactis NRRL Y-1140 | |
| 31 | EA (b) | 40S ribosomal protein S27 | polymer | 81 | 8753.2 | 1 | UniProt (Q6CNL2) Pfam (PF01667) | Kluyveromyces lactis NRRL Y-1140 | |
| 32 | FA (c) | 40S ribosomal protein S28 | polymer | 62 | 6972.2 | 1 | UniProt (P33285) Pfam (PF01200) | Kluyveromyces lactis NRRL Y-1140 | S33 |
| 33 | GA (d) | 40S ribosomal protein S29 | polymer | 53 | 6322.1 | 1 | UniProt (Q6CPG3) Pfam (PF00253) | Kluyveromyces lactis NRRL Y-1140 | |
| 34 | HA (e) | 40S ribosomal protein S30 | polymer | 58 | 6608.8 | 1 | UniProt (Q6CUH5) Pfam (PF04758) | Kluyveromyces lactis NRRL Y-1140 | |
| 35 | IA (f) | Ubiquitin-40S ribosomal protein S27a | polymer | 69 | 7958.4 | 1 | UniProt (P69061) Pfam (PF01599) | Kluyveromyces lactis NRRL Y-1140 | |
| 36 | JA (g) | KLLA0E12277p | polymer | 324 | 35612.7 | 1 | UniProt (Q6CNI7) Pfam (PF00400) | Kluyveromyces lactis NRRL Y-1140 | |
| 37 | KA (h) | 60S ribosomal protein L41-A | polymer | 25 | 3354.2 | 1 | UniProt (P0CX86) Pfam (PF05162) | Kluyveromyces lactis NRRL Y-1140 | L47,Large ribosomal subunit protein eL41-A,YL41 |
| 38 | LA (i) | Eukaryotic translation initiation factor 1A | polymer | 95 | 10953.5 | 1 | UniProt (P38912) Pfam (PF01176) | Saccharomyces cerevisiae S288C | eIF-1A,Eukaryotic translation initiation factor 4C,eIF-4C |
| 39 | MA (j) | Eukaryotic translation initiation factor 2 subunit alpha | polymer | 263 | 30222.0 | 1 | UniProt (P20459) Pfam (PF00575) Pfam (PF07541) | Saccharomyces cerevisiae S288C | eIF-2-alpha |
| 40 | NA (k) | Eukaryotic translation initiation factor 2 subunit gamma | polymer | 430 | 47230.1 | 1 | UniProt (P32481) Pfam (PF00009) Pfam (PF03144) Pfam (PF09173) | Saccharomyces cerevisiae S288C | eIF-2-gamma |
| 41 | OA (l) | Eukaryotic translation initiation factor 2 subunit beta | polymer | 144 | 16458.1 | 1 | UniProt (P09064) Pfam (PF01873) | Saccharomyces cerevisiae S288C | eIF-2-beta |
| 42 | PA (m) | Eukaryotic translation initiation factor eIF-1 | polymer | 96 | 10919.5 | 1 | UniProt (P32911) Pfam (PF01253) | Saccharomyces cerevisiae S288C | Protein translation factor SUI1 |
| 43 | QA (o) | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic translation initiation factor 3 subunit A,eIF3a | polymer | 567 | 62822.8 | 1 | UniProt (P38249) Pfam (PF22591) | Saccharomyces cerevisiae S288C | eIF3a,Eukaryotic translation initiation factor 3 110 kDa subunit homolog,eIF3 p110,Translation initiation factor eIF3,p110 subunit homolog |
| 44 | RA (p) | Eukaryotic translation initiation factor 3 subunit B | polymer | 651 | 75014.0 | 1 | UniProt (P06103) Pfam (PF00076) Pfam (PF08662) | Saccharomyces cerevisiae S288C | eIF3b,Cell cycle regulation and translation initiation protein,Eukaryotic translation initiation factor 3 90 kDa subunit,eIF3 p90,Translation initiation factor eIF3 p90 subunit |
| 45 | SA (q) | Eukaryotic translation initiation factor 3 subunit C | polymer | 665 | 76963.2 | 1 | UniProt (P32497) Pfam (PF05470) Pfam (PF01399) | Saccharomyces cerevisiae S288C | eIF3c,Eukaryotic translation initiation factor 3 93 kDa subunit,eIF3 p93,Nuclear transport protein NIP1,Translation initiation factor eIF3,p93 subunit |
| 46 | TA (s) | Eukaryotic translation initiation factor 3 subunit I | polymer | 342 | 38229.8 | 1 | UniProt (P40217) Pfam (PF00400) | Saccharomyces cerevisiae S288C | eIF3i,Eukaryotic translation initiation factor 3 39 kDa subunit,eIF3 p39 |
| 47 | UA (r) | Eukaryotic translation initiation factor 3 subunit G | polymer | 49 | 5576.2 | 1 | UniProt (Q04067) Pfam (PF12353) | Saccharomyces cerevisiae S288C | eIF3g,Eukaryotic translation initiation factor 3 RNA-binding subunit,eIF-3 RNA-binding subunit,Translation initiation factor eIF3 p33 subunit,eIF3 p33 |
| 48 | VA (1) | [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl] (2~{S})-2-azanyl-4-methylsulfanyl-butanoate | non-polymer | 478.4 | 1 | Chemie (7NO) | |||
| 49 | AB, AC, AD, BB, BC... (2, k, C, O, Q) | MAGNESIUM ION | non-polymer | 24.3 | 82 | Chemie (MG) | |||
| 50 | AE, BE, EE, YD (b, f, l, O) | ZINC ION | non-polymer | 65.4 | 4 | Chemie (ZN) | |||
| 51 | DE (k) | PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER | non-polymer | 521.2 | 1 | Chemie (GCP) |
Sequence modifications
o: 5 - 492 (UniProt: P38249)
o: 693 - 771 (PDB: 6GSM)
p: 77 - 737 (UniProt: P06103)
q: 96 - 794 (UniProt: P32497)
o: 693 - 771 (PDB: 6GSM)
p: 77 - 737 (UniProt: P06103)
| PDB | External Database | Details |
|---|---|---|
| - | Ala 665 | deletion |
| - | Ser 666 | deletion |
| - | Ile 667 | deletion |
| - | Ala 685 | deletion |
| - | Gln 686 | deletion |
| - | Phe 687 | deletion |
| - | Asp 701 | deletion |
| - | Leu 702 | deletion |
| - | Ile 703 | deletion |
| - | Leu 704 | deletion |
| PDB | External Database | Details |
|---|---|---|
| - | Asp 137 | deletion |
| - | Lys 187 | deletion |
| - | Asn 188 | deletion |
| - | Pro 220 | deletion |
| - | Glu 221 | deletion |
| - | Ser 222 | deletion |
| - | Phe 223 | deletion |
| - | Asp 224 | deletion |
| - | Lys 225 | deletion |
| - | Glu 226 | deletion |
| - | Pro 227 | deletion |
| - | Thr 228 | deletion |
| - | Ala 229 | deletion |
| - | Asp 230 | deletion |
| - | Leu 231 | deletion |
| - | Asp 232 | deletion |
| - | Ile 233 | deletion |
| - | Ser 234 | deletion |
| - | Ala 235 | deletion |
| - | Asn 236 | deletion |
| - | Gly 237 | deletion |
| - | Phe 238 | deletion |
| - | Thr 239 | deletion |
| - | Ile 240 | deletion |
| - | Ser 241 | deletion |
| - | Ser 242 | deletion |
| - | Ser 243 | deletion |
| - | Gln 244 | deletion |
| - | Gly 245 | deletion |
| - | Asn 246 | deletion |
| - | Asp 247 | deletion |
| - | Gln 248 | deletion |
| - | Ala 249 | deletion |
| - | Val 250 | deletion |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 47 |
| Total formula weight | 1529704.6 | |
| Non-Polymers* | Number of molecules | 88 |
| Total formula weight | 3254.3 | |
| All* | Total formula weight | 1532958.9 |
