6Q8Y
Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | 2 | 18S ribosomal RNA | polymer | 1797 | 578836.4 | 1 | GenBank (1329886537) | Saccharomyces cerevisiae | |
| 2 | AA | 60S ribosomal protein L8-A | polymer | 233 | 25815.0 | 1 | UniProt (P17076) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5 |
| 3 | AB | 60S ribosomal protein L23-A | polymer | 136 | 14362.8 | 1 | UniProt (P0CX41) Pfam (PF00238) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L17a,Large ribosomal subunit protein uL14-A,YL32 |
| 4 | AC | 60S ribosomal protein L36-A | polymer | 100 | 11151.3 | 1 | UniProt (P05745) Pfam (PF01158) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L39,Large ribosomal subunit protein eL36-A,YL39 |
| 5 | AD | 60S ribosomal protein L9-A | polymer | 191 | 21605.1 | 1 | UniProt (P05738) Pfam (PF00347) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L8,Large ribosomal subunit protein uL6-A,RP24,YL11 |
| 6 | AE | 60S ribosomal protein L24-A | polymer | 67 | 7843.2 | 1 | UniProt (P04449) Pfam (PF01246) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L30,Large ribosomal subunit protein eL24-A,RP29,YL21 |
| 7 | AF | 60S ribosomal protein L37-A | polymer | 87 | 9746.2 | 1 | UniProt (P49166) Pfam (PF01907) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L43,Large ribosomal subunit protein eL37-A,YL35,YP55 |
| 8 | AG | 60S ribosomal protein L11-B | polymer | 169 | 19266.1 | 1 | UniProt (Q3E757) Pfam (PF00281) Pfam (PF00673) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L16,Large ribosomal subunit protein uL5-B,RP39,YL22 |
| 9 | AH | 60S ribosomal protein L25 | polymer | 121 | 13771.2 | 1 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein uL23,RP16L,YL25,YP42' |
| 10 | AI | 60S ribosomal protein L38 | polymer | 77 | 8714.4 | 1 | UniProt (P49167) Pfam (PF01781) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL38 |
| 11 | AJ | 60S ribosomal protein L13-A | polymer | 193 | 21885.2 | 1 | UniProt (Q12690) Pfam (PF01294) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL13-A |
| 12 | AK | 60S ribosomal protein L26-A | polymer | 126 | 14134.6 | 1 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L33,Large ribosomal subunit protein uL24-A,YL33 |
| 13 | AL | 60S ribosomal protein L39 | polymer | 50 | 6227.4 | 1 | UniProt (P04650) Pfam (PF00832) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L46,Large ribosomal subunit protein eL39,YL40 |
| 14 | AM | 60S ribosomal protein L14-A | polymer | 136 | 14976.8 | 1 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL14-A |
| 15 | AN | 60S ribosomal protein L27-A | polymer | 135 | 15437.2 | 1 | UniProt (P0C2H6) Pfam (PF01777) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL27-A |
| 16 | AO | Ubiquitin-60S ribosomal protein L40 | polymer | 52 | 6032.3 | 1 | UniProt (P0CH08) Pfam (PF01020) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 17 | AP | 60S ribosomal protein L42-A | polymer | 105 | 12115.5 | 1 | UniProt (P0CX27) Pfam (PF00935) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L41,Large ribosomal subunit protein eL42-A,YL27,YP44 |
| 18 | AQ | 60S ribosomal protein L15-A | polymer | 203 | 24351.2 | 1 | UniProt (P05748) Pfam (PF00827) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18 |
| 19 | AR | 60S ribosomal protein L28 | polymer | 148 | 16630.5 | 1 | UniProt (P02406) Pfam (PF00828) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L27a,L29,Large ribosomal subunit protein uL15,RP44,RP62,YL24 |
| 20 | AS | 60S ribosomal protein L41-B | polymer | 25 | 3354.2 | 1 | UniProt (P0CX87) Pfam (PF05162) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L47,Large ribosomal subunit protein eL41-B,YL41 |
| 21 | AT | 60S ribosomal protein L43-A | polymer | 91 | 9981.8 | 1 | UniProt (P0CX25) Pfam (PF01780) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L37a,Large ribosomal subunit protein eL43-A,YL35 |
| 22 | AU | 60S ribosomal protein L16-A | polymer | 197 | 22029.0 | 1 | UniProt (P26784) Pfam (PF00572) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15 |
| 23 | AV | 60S ribosomal protein L29 | polymer | 58 | 6560.7 | 1 | UniProt (P05747) Pfam (PF01779) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL29,YL43 |
| 24 | AW | 60S ribosomal protein L2-A | polymer | 252 | 27217.3 | 1 | UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L5,Large ribosomal subunit protein uL2-A,RP8,YL6 |
| 25 | AX | 60S ribosomal protein L17-A | polymer | 183 | 20458.3 | 1 | UniProt (P05740) Pfam (PF00237) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L20A,Large ribosomal subunit protein uL22-A,YL17 |
| 26 | a | 40S ribosomal protein S21-A | polymer | 87 | 9758.8 | 1 | UniProt (P0C0V8) Pfam (PF01249) In PDB | Saccharomyces cerevisiae (Baker's yeast) | S26,Small ribosomal subunit protein eS21-A,YS25 |
| 27 | b | 40S ribosomal protein S22-A | polymer | 129 | 14518.9 | 1 | UniProt (P0C0W1) Pfam (PF00410) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP50,S24,Small ribosomal subunit protein uS8-A,YP58,YS22 |
| 28 | c | 40S ribosomal protein S23-A | polymer | 144 | 15942.7 | 1 | UniProt (P0CX29) Pfam (PF00164) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP37,S28,Small ribosomal subunit protein uS12-A,YS14 |
| 29 | d | 40S ribosomal protein S24-A | polymer | 132 | 15045.5 | 1 | UniProt (P0CX31) Pfam (PF01282) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP50,Small ribosomal subunit protein eS24-A |
| 30 | e | 40S ribosomal protein S26-B | polymer | 97 | 11023.0 | 1 | UniProt (P39939) Pfam (PF01283) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Small ribosomal subunit protein eS26-B |
| 31 | f | 40S ribosomal protein S27-A | polymer | 81 | 8762.2 | 1 | UniProt (P35997) Pfam (PF01667) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP61,Small ribosomal subunit protein eS27-A,YS20 |
| 32 | g | 40S ribosomal protein S30-A | polymer | 60 | 6779.1 | 1 | UniProt (P0CX33) Pfam (PF04758) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Small ribosomal subunit protein eS30-A |
| 33 | z | 5'-3' exoribonuclease 1 | polymer | 916 | 107653.7 | 1 | UniProt (P22147) Pfam (PF03159) Pfam (PF17846) Pfam (PF18332) In PDB | Saccharomyces cerevisiae (Baker's yeast) | DNA strand transfer protein beta,STP-beta,KAR(-)-enhancing mutation protein,Strand exchange protein 1,p175 |
| 34 | l | mRNA | polymer | 17 | 5490.4 | 1 | Saccharomyces cerevisiae | ||
| 35 | n | P-site tRNA | polymer | 76 | 24468.6 | 1 | GenBank (1329886529) | Saccharomyces cerevisiae | |
| 36 | m | E-site tRNA | polymer | 75 | 24004.3 | 1 | GenBank (176418) | Saccharomyces cerevisiae | |
| 37 | AY | 60S ribosomal protein L30 | polymer | 97 | 10558.3 | 1 | UniProt (P14120) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L32,Large ribosomal subunit protein eL30,RP73,YL38 |
| 38 | BA | 60S ribosomal protein L3 | polymer | 386 | 43719.6 | 1 | UniProt (P14126) Pfam (PF00297) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
| 39 | BB | 60S ribosomal protein L18-A | polymer | 185 | 20478.1 | 1 | UniProt (P0CX49) Pfam (PF17135) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL18-A,RP28 |
| 40 | BC | 60S ribosomal protein L31-A | polymer | 109 | 12649.8 | 1 | UniProt (P0C2H8) Pfam (PF01198) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L34,Large ribosomal subunit protein eL31-A,YL28 |
| 41 | BD | 60S ribosomal protein L10 | polymer | 220 | 25279.3 | 1 | UniProt (P41805) Pfam (PF00252) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L9,Large ribosomal subunit protein uL16,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein |
| 42 | BE | 60S ribosomal protein L4-A | polymer | 361 | 39027.9 | 1 | UniProt (P10664) Pfam (PF00573) Pfam (PF14374) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L2,Large ribosomal subunit protein uL4-A,RP2,YL2 |
| 43 | BF | 60S ribosomal protein L19-A | polymer | 188 | 21631.1 | 1 | UniProt (P0CX82) Pfam (PF01280) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14 |
| 44 | BG | 60S ribosomal protein L32 | polymer | 127 | 14478.1 | 1 | UniProt (P38061) Pfam (PF01655) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL32 |
| 45 | BH | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 1 | UniProt (P0CX23) Pfam (PF01775) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L18a,Large ribosomal subunit protein eL20-A |
| 46 | BI | 60S ribosomal protein L5 | polymer | 296 | 33633.6 | 1 | UniProt (P26321) Pfam (PF17144) Pfam (PF14204) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L1,L1a,Large ribosomal subunit protein uL18,Ribosomal 5S RNA-binding protein,YL3 |
| 47 | BJ | 60S ribosomal protein L21-A | polymer | 159 | 18148.1 | 1 | UniProt (Q02753) Pfam (PF01157) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL21-A |
| 48 | BK | 60S ribosomal protein L33-A | polymer | 106 | 12045.9 | 1 | UniProt (P05744) Pfam (PF01247) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L37,Large ribosomal subunit protein eL33-A,RP47,YL37 |
| 49 | BL | 60S ribosomal protein L22-A | polymer | 100 | 11263.9 | 1 | UniProt (P05749) Pfam (PF01776) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L1c,Large ribosomal subunit protein eL22-A,RP4,YL31 |
| 50 | BM | 60S ribosomal protein L6-A | polymer | 175 | 19869.4 | 1 | UniProt (Q02326) Pfam (PF01159) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L17,Large ribosomal subunit protein eL6-A,RP18,YL16 |
| 51 | BN | 60S ribosomal protein L34-A | polymer | 112 | 12608.8 | 1 | UniProt (P87262) Pfam (PF01199) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL34-A |
| 52 | BO | 60S ribosomal protein L7-A | polymer | 222 | 25240.4 | 1 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L6,Large ribosomal subunit protein uL30-A,RP11,YL8 |
| 53 | BP | 60S ribosomal protein L35-A | polymer | 119 | 13811.4 | 1 | UniProt (P0CX84) Pfam (PF00831) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein uL29-A |
| 54 | BQ | 25S ribosomal RNA | polymer | 3396 | 1097493.9 | 1 | GenBank (834774822) | Saccharomyces cerevisiae | |
| 55 | BR | 5S ribosomal RNA | polymer | 121 | 38951.1 | 1 | GenBank (1329886537) | Saccharomyces cerevisiae | |
| 56 | BS | 5.8S ribosomal RNA | polymer | 158 | 50682.9 | 1 | GenBank (1331532632) | Saccharomyces cerevisiae | |
| 57 | A | 40S ribosomal protein S3 | polymer | 223 | 24702.8 | 1 | UniProt (P05750) Pfam (PF07650) Pfam (PF00189) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP13,Small ribosomal subunit protein uS3,YS3 |
| 58 | B | Rps5p | polymer | 206 | 22908.3 | 1 | UniProt (A0A1L4AA68) Pfam (PF00177) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 59 | C | 40S ribosomal protein S10-A | polymer | 96 | 11571.1 | 1 | UniProt (Q08745) Pfam (PF03501) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Small ribosomal subunit protein eS10-A |
| 60 | D | 40S ribosomal protein S12 | polymer | 121 | 13028.0 | 1 | UniProt (P48589) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Small ribosomal subunit protein eS12 |
| 61 | E | 40S ribosomal protein S15 | polymer | 121 | 13870.4 | 1 | UniProt (Q01855) Pfam (PF00203) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RIG protein,RP52,S21,Small ribosomal subunit protein uS19,YS21 |
| 62 | F | 40S ribosomal protein S16-A | polymer | 141 | 15659.2 | 1 | UniProt (P0CX51) Pfam (PF00380) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP61R,Small ribosomal subunit protein uS9-A |
| 63 | G | 40S ribosomal protein S17-A | polymer | 125 | 14268.5 | 1 | UniProt (P02407) Pfam (PF00833) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP51A,Small ribosomal subunit protein eS17-A |
| 64 | H | 40S ribosomal protein S18-A | polymer | 139 | 16239.6 | 1 | UniProt (P0CX55) Pfam (PF00416) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Small ribosomal subunit protein uS13-A |
| 65 | J | 40S ribosomal protein S20 | polymer | 107 | 12190.2 | 1 | UniProt (P38701) Pfam (PF00338) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Small ribosomal subunit protein uS10 |
| 66 | K | 40S ribosomal protein S25-A | polymer | 70 | 8001.4 | 1 | UniProt (Q3E792) Pfam (PF03297) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP45,S31,Small ribosomal subunit protein eS25-A,YS23 |
| 67 | L | 40S ribosomal protein S28-A | polymer | 63 | 7116.3 | 1 | UniProt (Q3E7X9) Pfam (PF01200) In PDB | Saccharomyces cerevisiae (Baker's yeast) | S33,Small ribosomal subunit protein eS28-A,YS27 |
| 68 | M | 40S ribosomal protein S29-A | polymer | 53 | 6335.3 | 1 | UniProt (P41057) Pfam (PF00253) In PDB | Saccharomyces cerevisiae (Baker's yeast) | S36,Small ribosomal subunit protein uS14-A,YS29 |
| 69 | N | Ubiquitin-40S ribosomal protein S31 | polymer | 51 | 5704.6 | 1 | UniProt (P05759) Pfam (PF01599) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 70 | O | Guanine nucleotide-binding protein subunit beta-like protein | polymer | 318 | 34710.0 | 1 | UniProt (P38011) Pfam (PF00400) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1,Small ribosomal subunit protein RACK1 |
| 71 | P | 40S ribosomal protein S0-A | polymer | 219 | 24255.5 | 1 | UniProt (P32905) Pfam (PF00318) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Nucleic acid-binding protein NAB1A,Small ribosomal subunit protein uS2-A |
| 72 | Q | 40S ribosomal protein S1-A | polymer | 214 | 24312.2 | 1 | UniProt (P33442) Pfam (PF01015) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP10A,Small ribosomal subunit protein eS1-A |
| 73 | R | 40S ribosomal protein S2 | polymer | 220 | 23718.7 | 1 | UniProt (P25443) Pfam (PF00333) Pfam (PF03719) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Omnipotent suppressor protein SUP44,RP12,S4,Small ribosomal subunit protein uS5,YS5 |
| 74 | S | 40S ribosomal protein S4-A | polymer | 260 | 29338.1 | 1 | UniProt (P0CX35) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP5,S7,Small ribosomal subunit protein eS4-A,YS6 |
| 75 | T | 40S ribosomal protein S6-A | polymer | 226 | 25895.1 | 1 | UniProt (P0CX37) Pfam (PF01092) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP9,S10,Small ribosomal subunit protein eS6-A,YS4 |
| 76 | U | 40S ribosomal protein S7-A | polymer | 184 | 21000.5 | 1 | UniProt (P26786) Pfam (PF01251) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP30,RP40,Small ribosomal subunit protein eS7-A |
| 77 | V | 40S ribosomal protein S8-A | polymer | 199 | 22406.6 | 1 | UniProt (P0CX39) Pfam (PF01201) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP19,S14,Small ribosomal subunit protein eS8-A,YS9 |
| 78 | W | 40S ribosomal protein S9-A | polymer | 178 | 20366.7 | 1 | UniProt (O13516) Pfam (PF00163) Pfam (PF01479) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP21,S13,Small ribosomal subunit protein uS4-A,YP28,YS11 |
| 79 | X | 40S ribosomal protein S11-A | polymer | 155 | 17654.7 | 1 | UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP41,S18,Small ribosomal subunit protein uS17-A,YS12 |
| 80 | Y | 40S ribosomal protein S13 | polymer | 150 | 16928.7 | 1 | UniProt (P05756) Pfam (PF08069) Pfam (PF00312) In PDB | Saccharomyces cerevisiae (Baker's yeast) | S27a,Small ribosomal subunit protein uS15,YS15 |
| 81 | Z | 40S ribosomal protein S14-B | polymer | 127 | 13446.4 | 1 | UniProt (P39516) Pfam (PF00411) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP59B,Small ribosomal subunit protein uS11-B |
| 82 | I | 40S ribosomal protein S19-A | polymer | 143 | 15810.9 | 1 | UniProt (P07280) Pfam (PF01090) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP55A,S16a,Small ribosomal subunit protein eS19-A,YP45,YS16A |
| 83 | AF, AO, AP, AT, e... | ZINC ION | non-polymer | 65.4 | 8 | Chemie (ZN) | |||
| 84 | z, l | MAGNESIUM ION | non-polymer | 24.3 | 2 | Chemie (MG) |
Sequence modifications
2: 1 - 1798 (GenBank: 1329886537)
n: 1 - 73 (GenBank: 1329886529)
m: 1 - 75 (GenBank: 176418)
| PDB | External Database | Details |
|---|---|---|
| G 1570 | A 468586 | conflict |
| PDB | External Database | Details |
|---|---|---|
| C 74 | - | insertion |
| C 75 | - | insertion |
| A 76 | - | insertion |
| PDB | External Database | Details |
|---|---|---|
| C 11 | U 11 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 82 |
| Total formula weight | 3179440.8 | |
| Non-Polymers* | Number of molecules | 10 |
| Total formula weight | 571.9 | |
| All* | Total formula weight | 3180012.7 |
