4D61
Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (1) | 18S RRNA | polymer | 1869 | 602776.9 | 1 | ORYCTOLAGUS CUNICULUS (RABBIT) | ||
| 2 | B (A) | 40S RIBOSOMAL PROTEIN SA | polymer | 295 | 32883.9 | 1 | Pfam (PF00318) Pfam (PF16122) UniProt (by SIFTS) (G1TLT8) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US2,37 KDA LAMININ RECEPTOR PRECURSOR, 37LRP, 37/67 KDA LAMININ RECEPTOR, LRP/LR, 67 KDA LAMININ RECEPTOR, 67LR, COLON CARCINOMA LAMININ-BINDING PROTEIN, LAMININ RECEPTOR 1, LAMR, LAMININ-BINDING PROTEIN PRECURSOR P40, LBP/P40, MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN MGR1-AG, NEM/1CHD4 |
| 3 | C (B) | 40S RIBOSOMAL PROTEIN S3A | polymer | 264 | 30002.1 | 1 | Pfam (PF01015) UniProt (by SIFTS) (G1SS70) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES1, V-FOS TRANSFORMATION EFFECTOR PROTEIN, FTE-1 |
| 4 | D (C) | 40S RIBOSOMAL PROTEIN S2 | polymer | 293 | 31376.5 | 1 | Pfam (PF00333) Pfam (PF03719) UniProt (by SIFTS) (G1SWM1) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US5, PROTEIN LLREP3 |
| 5 | E (D) | 40S RIBOSOMAL PROTEIN S3 | polymer | 243 | 26729.4 | 1 | Pfam (PF07650) Pfam (PF00189) UniProt (by SIFTS) (G1TNM3) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US3 |
| 6 | F (E) | 40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1 | polymer | 263 | 29512.8 | 1 | Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) Pfam (PF08071) UniProt (by SIFTS) (G1TK17) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES4 |
| 7 | G (F) | 40S RIBOSOMAL PROTEIN S5 | polymer | 204 | 22913.5 | 1 | Pfam (PF00177) UniProt (by SIFTS) (G1TFM5) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US7 |
| 8 | H (G) | 40S RIBOSOMAL PROTEIN S6 | polymer | 249 | 28751.9 | 1 | Pfam (PF01092) UniProt (by SIFTS) (G1TM55) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES6, PHOSPHOPROTEIN NP33 |
| 9 | I (H) | 40S RIBOSOMAL PROTEIN S7 | polymer | 194 | 22168.9 | 1 | UniProt (by SIFTS) (G1SVB0) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES7 |
| 10 | J (I) | 40S RIBOSOMAL PROTEIN S8 | polymer | 208 | 24263.4 | 1 | Pfam (PF01201) UniProt (by SIFTS) (G1TJW1) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES8 |
| 11 | K (J) | 40S RIBOSOMAL PROTEIN S9 | polymer | 194 | 22641.6 | 1 | Pfam (PF00163) Pfam (PF01479) UniProt (by SIFTS) (B7NZS8) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US4 |
| 12 | L (K) | 40S RIBOSOMAL PROTEIN S10 | polymer | 165 | 18933.8 | 1 | Pfam (PF03501) UniProt (by SIFTS) (G1T168) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES10 |
| 13 | M (L) | 40S RIBOSOMAL PROTEIN S11 | polymer | 158 | 18468.8 | 1 | Pfam (PF16205) Pfam (PF00366) UniProt (by SIFTS) (G1TRM4) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US17 |
| 14 | N (M) | 40S RIBOSOMAL PROTEIN S12 | polymer | 132 | 14539.0 | 1 | Pfam (PF01248) UniProt (by SIFTS) (G1SFR8) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES12 |
| 15 | O (N) | 40S RIBOSOMAL PROTEIN S13 | polymer | 151 | 17259.4 | 1 | Pfam (PF08069) Pfam (PF00312) UniProt (by SIFTS) (G1SP51) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US15 |
| 16 | P (O) | 40S RIBOSOMAL PROTEIN S14 | polymer | 151 | 16302.8 | 1 | Pfam (PF00411) UniProt (by SIFTS) (G1T1F0) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US11 |
| 17 | Q (P) | 40S RIBOSOMAL PROTEIN S15 | polymer | 145 | 17076.2 | 1 | Pfam (PF00203) UniProt (by SIFTS) (G1U0Q2) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US19, RIG PROTEIN |
| 18 | R (Q) | 40S RIBOSOMAL PROTEIN S16 | polymer | 146 | 16477.4 | 1 | Pfam (PF00380) UniProt (by SIFTS) (G1SGX4) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US9 |
| 19 | S (R) | 40S RIBOSOMAL PROTEIN S17 | polymer | 135 | 15578.2 | 1 | Pfam (PF00833) UniProt (by SIFTS) (G1TU13) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES17 |
| 20 | T (S) | 40S RIBOSOMAL PROTEIN S18 | polymer | 152 | 17759.8 | 1 | Pfam (PF00416) UniProt (by SIFTS) (G1TPG3) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US13, KE-3, KE3 |
| 21 | U (T) | 40S RIBOSOMAL PROTEIN S19 | polymer | 145 | 16091.6 | 1 | Pfam (PF01090) UniProt (by SIFTS) (G1TN62) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES19 |
| 22 | V (U) | 40S RIBOSOMAL PROTEIN S20 | polymer | 119 | 13398.8 | 1 | Pfam (PF00338) UniProt (by SIFTS) (G1SIZ2) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US10 |
| 23 | W (V) | 40S RIBOSOMAL PROTEIN S21 | polymer | 83 | 9124.4 | 1 | Pfam (PF01249) UniProt (by SIFTS) (G1TM82) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES21 |
| 24 | X (W) | 40S RIBOSOMAL PROTEIN S15A | polymer | 130 | 14865.6 | 1 | Pfam (PF00410) UniProt (by SIFTS) (G1TG89) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US8 |
| 25 | Y (X) | 40S RIBOSOMAL PROTEIN S23 | polymer | 143 | 15844.7 | 1 | Pfam (PF00164) UniProt (by SIFTS) (G1SZ47) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US12 |
| 26 | Z (Y) | 40S RIBOSOMAL PROTEIN S24 | polymer | 133 | 15463.3 | 1 | Pfam (PF01282) UniProt (by SIFTS) (G1TS40) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES24 |
| 27 | AA (Z) | 40S RIBOSOMAL PROTEIN S25 | polymer | 125 | 13776.2 | 1 | Pfam (PF03297) UniProt (by SIFTS) (G1TDB3) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES25 |
| 28 | BA (a) | 40S RIBOSOMAL PROTEIN S26 | polymer | 115 | 13047.5 | 1 | Pfam (PF01283) UniProt (by SIFTS) (G1TFE8) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES26 |
| 29 | CA (b) | 40S RIBOSOMAL PROTEIN S27 | polymer | 84 | 9480.2 | 1 | Pfam (PF01667) UniProt (by SIFTS) (G1TZ76) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES27, METALLOPAN-STIMULIN 1, MPS-1 |
| 30 | DA (c) | 40S RIBOSOMAL PROTEIN S28 | polymer | 69 | 7855.1 | 1 | Pfam (PF01200) UniProt (by SIFTS) (G1TIB4) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES28 |
| 31 | EA (d) | 40S RIBOSOMAL PROTEIN S29 | polymer | 56 | 6690.8 | 1 | Pfam (PF00253) UniProt (by SIFTS) (G1U7M4) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN US14 |
| 32 | FA (e) | 40S RIBOSOMAL PROTEIN S30 | polymer | 59 | 6668.9 | 1 | Pfam (PF04758) UniProt (by SIFTS) (G1T8A2) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES30 |
| 33 | GA (f) | UBIQUITIN-40S RIBOSOMAL PROTEIN S27A | polymer | 156 | 18004.0 | 1 | Pfam (PF00240) Pfam (PF01599) UniProt (by SIFTS) (G1SK22) | ORYCTOLAGUS CUNICULUS (RABBIT) | 40S RIBOSOMAL PROTEIN ES31, UBIQUITIN CARBOXYL EXTENSION PROTEIN 80 |
| 34 | HA (g) | GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 | polymer | 317 | 35115.7 | 1 | Pfam (PF00400) UniProt (by SIFTS) (G1SJB4) | ORYCTOLAGUS CUNICULUS (RABBIT) | CELL PROLIFERATION-INDUCING GENE 21 PROTEIN, GUANINE NUCLEO TIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN 12.3, HUMAN LUNG CA NCER ONCOGENE 7 PROTEIN, HLC-7, RECEPTOR FOR ACTIVATED C KINASE, R ECEPTOR OF ACTIVATED PROTEIN KINASE C 1, RACK1 |
| 35 | IA (h) | EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 | polymer | 436 | 49040.7 | 1 | UniProt (P62495) Pfam (PF03463) Pfam (PF03464) Pfam (PF03465) | HOMO SAPIENS (HUMAN) | EUKARYOTIC RELEASE FACTOR 1, ERF1, PROTEIN CL1, TB3-1, |
| 36 | JA (i) | EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A | polymer | 426 | 47888.2 | 1 | UniProt (P15170) Pfam (PF00009) Pfam (PF03144) Pfam (PF22594) | HOMO SAPIENS (HUMAN) | EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 3A, ERF3A, G1 TO S PHASE TRANSITION PROTEIN 1 HOMOLOG |
| 37 | KA (j) | CRICKET PARALYSIS VIRUS IRES RNA | polymer | 201 | 64363.9 | 1 | GenBank (AF218039) | CRICKET PARALYSIS VIRUS |
Sequence modifications
h: 5 - 437 (UniProt: P62495)
j: 6030 - 6216 (GenBank: AF218039)
j: 6217 - 6230 (PDB: 4D61)
| PDB | External Database | Details |
|---|---|---|
| Leu 438 | - | expression tag |
| Glu 439 | - | expression tag |
| His 440 | - | expression tag |
j: 6217 - 6230 (PDB: 4D61)
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 37 |
| Total formula weight | 1383135.7 | |
| All* | Total formula weight | 1383135.7 |
