6XIR
Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress
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 | A | 60S ribosomal protein L2-A | polymer | 254 | 27463.6 | 1 | UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L5,Large ribosomal subunit protein uL2-A,RP8,YL6 |
| 2 | B | RPL3 isoform 1 | polymer | 387 | 43850.8 | 1 | UniProt (A0A6A5Q627) Pfam (PF00297) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 3 | C | RPL4A isoform 1 | polymer | 362 | 39159.1 | 1 | UniProt (A0A6A5Q3W0) Pfam (PF00573) Pfam (PF14374) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 4 | D | RPL5 isoform 1 | polymer | 297 | 33764.8 | 1 | UniProt (A0A6A5Q0W8) Pfam (PF17144) Pfam (PF14204) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 5 | E | 60S ribosomal protein L6-A | polymer | 176 | 20000.6 | 1 | UniProt (Q02326) Pfam (PF01159) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L17,Large ribosomal subunit protein eL6-A,RP18,YL16 |
| 6 | F | 60S ribosomal protein L7-A | polymer | 244 | 27686.3 | 1 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L6,Large ribosomal subunit protein uL30-A,RP11,YL8 |
| 7 | G | RPL8A isoform 1 | polymer | 256 | 28175.8 | 1 | UniProt (A0A6A5PWW7) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 8 | H | RPL9A isoform 1 | polymer | 191 | 21605.1 | 1 | UniProt (A0A6A5Q0D0) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 9 | I | RPL10 isoform 1 | polymer | 221 | 25410.5 | 1 | UniProt (A0A6A5PUZ5) Pfam (PF00252) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 10 | J | RPL11B isoform 1 | polymer | 174 | 19785.7 | 1 | UniProt (A0A6A5PYM2) Pfam (PF00281) Pfam (PF00673) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 11 | L | 60S ribosomal protein L13-A | polymer | 199 | 22604.2 | 1 | UniProt (Q12690) Pfam (PF01294) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL13-A |
| 12 | M | 60S ribosomal protein L14-A | polymer | 138 | 15195.1 | 1 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL14-A |
| 13 | N | 60S ribosomal protein L15-A | polymer | 204 | 24482.4 | 1 | UniProt (P05748) Pfam (PF00827) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18 |
| 14 | O | 60S ribosomal protein L16-A | polymer | 199 | 22247.2 | 1 | UniProt (P26784) Pfam (PF00572) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15 |
| 15 | P | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 1 | UniProt (P05740) Pfam (PF00237) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L20A,Large ribosomal subunit protein uL22-A,YL17 |
| 16 | Q | 60S ribosomal protein L18-A | polymer | 186 | 20609.3 | 1 | UniProt (P0CX49) Pfam (PF17135) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL18-A,RP28 |
| 17 | R | 60S ribosomal protein L19-A | polymer | 189 | 21762.3 | 1 | UniProt (P0CX82) Pfam (PF01280) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14 |
| 18 | S | 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 |
| 19 | T | 60S ribosomal protein L21-A | polymer | 160 | 18279.3 | 1 | UniProt (Q02753) Pfam (PF01157) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL21-A |
| 20 | U | 60S ribosomal protein L22-A | polymer | 121 | 13711.4 | 1 | UniProt (P05749) Pfam (PF01776) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L1c,Large ribosomal subunit protein eL22-A,RP4,YL31 |
| 21 | V | 60S ribosomal protein L23-A | polymer | 137 | 14494.0 | 1 | UniProt (P0CX41) Pfam (PF00238) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L17a,Large ribosomal subunit protein uL14-A,YL32 |
| 22 | W | RPL24A isoform 1 | polymer | 155 | 17661.7 | 1 | UniProt (A0A6A5PY83) Pfam (PF01246) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 23 | X | 60S ribosomal protein L25 | polymer | 142 | 15787.6 | 1 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein uL23,RP16L,YL25,YP42' |
| 24 | Y | 60S ribosomal protein L26-A | polymer | 127 | 14265.8 | 1 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L33,Large ribosomal subunit protein uL24-A,YL33 |
| 25 | Z | 60S ribosomal protein L27-A | polymer | 136 | 15568.4 | 1 | UniProt (P0C2H6) Pfam (PF01777) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL27-A |
| 26 | AA | 40S ribosomal protein S10-A | polymer | 105 | 12757.4 | 1 | UniProt (Q08745) Pfam (PF03501) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Small ribosomal subunit protein eS10-A |
| 27 | AB | 40S ribosomal protein S11-A | polymer | 156 | 17785.9 | 1 | UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP41,S18,Small ribosomal subunit protein uS17-A,YS12 |
| 28 | 1 | 35S ribosomal RNA | polymer | 3395 | 1097148.6 | 1 | GenBank (380294104) | Saccharomyces cerevisiae (Baker's yeast) | |
| 29 | 3 | 5S ribosomal RNA | polymer | 121 | 38951.1 | 1 | GenBank (176405) | Saccharomyces cerevisiae (Baker's yeast) | |
| 30 | 4 | 5.8S ribosomal RNA | polymer | 158 | 50682.9 | 1 | GenBank (1267176496) | Saccharomyces cerevisiae (Baker's yeast) | |
| 31 | a | 60S ribosomal protein L28 | polymer | 149 | 16761.7 | 1 | UniProt (P02406) Pfam (PF00828) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L27a,L29,Large ribosomal subunit protein uL15,RP44,RP62,YL24 |
| 32 | b | RPL29 isoform 1 | polymer | 59 | 6691.9 | 1 | UniProt (A0A6A5PWR1) Pfam (PF01779) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 33 | c | 60S ribosomal protein L30 | polymer | 105 | 11430.4 | 1 | UniProt (P14120) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L32,Large ribosomal subunit protein eL30,RP73,YL38 |
| 34 | d | 60S ribosomal protein L31-A | polymer | 113 | 12980.2 | 1 | UniProt (P0C2H8) Pfam (PF01198) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L34,Large ribosomal subunit protein eL31-A,YL28 |
| 35 | e | RPL32 isoform 1 | polymer | 130 | 14809.4 | 1 | UniProt (A0A6A5Q1M9) Pfam (PF01655) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 36 | f | 60S ribosomal protein L33-A | polymer | 107 | 12177.1 | 1 | UniProt (P05744) Pfam (PF01247) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L37,Large ribosomal subunit protein eL33-A,RP47,YL37 |
| 37 | g | 60S ribosomal protein L34-A | polymer | 121 | 13673.2 | 1 | UniProt (P87262) Pfam (PF01199) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL34-A |
| 38 | h | 60S ribosomal protein L35-A | polymer | 120 | 13942.6 | 1 | UniProt (P0CX84) Pfam (PF00831) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein uL29-A |
| 39 | i | 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 |
| 40 | j | 60S ribosomal protein L37-A | polymer | 88 | 9877.4 | 1 | UniProt (P49166) Pfam (PF01907) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L43,Large ribosomal subunit protein eL37-A,YL35,YP55 |
| 41 | k | RPL38 isoform 1 | polymer | 78 | 8845.6 | 1 | UniProt (A0A6A5PUL8) Pfam (PF01781) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 42 | l | 60S ribosomal protein L39 | polymer | 51 | 6358.6 | 1 | UniProt (P04650) Pfam (PF00832) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L46,Large ribosomal subunit protein eL39,YL40 |
| 43 | n | RPL41A isoform 1 | polymer | 25 | 3354.2 | 1 | UniProt (A0A6A5PXU0) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RPL41B isoform 1 |
| 44 | o | 60S ribosomal protein L42-A | polymer | 106 | 12246.7 | 1 | UniProt (P0CX27) Pfam (PF00935) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L41,Large ribosomal subunit protein eL42-A,YL27,YP44 |
| 45 | p | 60S ribosomal protein L43-A | polymer | 92 | 10113.0 | 1 | UniProt (P0CX25) Pfam (PF01780) In PDB | Saccharomyces cerevisiae (Baker's yeast) | L37a,Large ribosomal subunit protein eL43-A,YL35 |
| 46 | 2 | 18S ribosomal RNA | polymer | 1800 | 579761.9 | 1 | GenBank (1262303) | Saccharomyces cerevisiae (Baker's yeast) | |
| 47 | q | 40S ribosomal protein S0-A | polymer | 252 | 28051.3 | 1 | UniProt (P32905) Pfam (PF00318) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Nucleic acid-binding protein NAB1A,Small ribosomal subunit protein uS2-A |
| 48 | r | RPS1A isoform 1 | polymer | 255 | 28798.5 | 1 | UniProt (A0A6A5PRY4) Pfam (PF01015) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 49 | s | RPS2 isoform 1 | polymer | 254 | 27490.8 | 1 | UniProt (A0A6A5PWF7) Pfam (PF00333) Pfam (PF03719) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 50 | t | RPS3 isoform 1 | polymer | 240 | 26542.8 | 1 | UniProt (A0A6A5Q3Q1) Pfam (PF07650) Pfam (PF00189) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 51 | u | 40S ribosomal protein S4-A | polymer | 261 | 29469.3 | 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 |
| 52 | v | Rps5p | polymer | 225 | 25072.6 | 1 | UniProt (A0A1L4AA68) Pfam (PF00177) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 53 | w | 40S ribosomal protein S6-A | polymer | 236 | 27054.5 | 1 | UniProt (P0CX37) Pfam (PF01092) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP9,S10,Small ribosomal subunit protein eS6-A,YS4 |
| 54 | x | 40S ribosomal protein S7-A | polymer | 190 | 21658.2 | 1 | UniProt (P26786) Pfam (PF01251) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP30,RP40,Small ribosomal subunit protein eS7-A |
| 55 | y | RPS8A isoform 1 | polymer | 200 | 22537.8 | 1 | UniProt (A0A6A5Q1H1) Pfam (PF01201) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RPS8B isoform 1 |
| 56 | z | 40S ribosomal protein S9-A | polymer | 197 | 22487.9 | 1 | UniProt (O13516) Pfam (PF00163) Pfam (PF01479) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP21,S13,Small ribosomal subunit protein uS4-A,YP28,YS11 |
| 57 | AD | 40S ribosomal protein S13 | polymer | 151 | 17059.9 | 1 | UniProt (P05756) Pfam (PF08069) Pfam (PF00312) In PDB | Saccharomyces cerevisiae (Baker's yeast) | S27a,Small ribosomal subunit protein uS15,YS15 |
| 58 | AE | 40S ribosomal protein S14-B | polymer | 138 | 14675.8 | 1 | UniProt (P39516) Pfam (PF00411) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP59B,Small ribosomal subunit protein uS11-B |
| 59 | AF | RPS15 isoform 1 | polymer | 142 | 16031.9 | 1 | UniProt (A0A6A5Q6F2) Pfam (PF00203) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 60 | AG | 40S ribosomal protein S16-A | polymer | 143 | 15877.5 | 1 | UniProt (P0CX51) Pfam (PF00380) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP61R,Small ribosomal subunit protein uS9-A |
| 61 | AH | 40S ribosomal protein S17-B | polymer | 136 | 15835.4 | 1 | UniProt (P14127) Pfam (PF00833) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP51B,Small ribosomal subunit protein eS17-B |
| 62 | AI | 40S ribosomal protein S18-A | polymer | 146 | 17071.6 | 1 | UniProt (P0CX55) Pfam (PF00416) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Small ribosomal subunit protein uS13-A |
| 63 | AJ | 40S ribosomal protein S19-A | polymer | 144 | 15942.1 | 1 | UniProt (P07280) Pfam (PF01090) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP55A,S16a,Small ribosomal subunit protein eS19-A,YP45,YS16A |
| 64 | AK | RPS20 isoform 1 | polymer | 121 | 13929.0 | 1 | UniProt (A0A6A5PVE9) Pfam (PF00338) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 65 | AL | 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 |
| 66 | AM | RPS22A isoform 1 | polymer | 130 | 14650.1 | 1 | UniProt (A0A6A5PSE9) Pfam (PF00410) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 67 | AN | 40S ribosomal protein S23-A | polymer | 145 | 16073.9 | 1 | UniProt (P0CX29) Pfam (PF00164) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP37,S28,Small ribosomal subunit protein uS12-A,YS14 |
| 68 | AO | 40S ribosomal protein S24-A | polymer | 135 | 15362.8 | 1 | UniProt (P0CX31) Pfam (PF01282) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP50,Small ribosomal subunit protein eS24-A |
| 69 | AP | RPS25A isoform 1 | polymer | 108 | 12067.3 | 1 | UniProt (A0A6A5PZ18) Pfam (PF03297) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 70 | AQ | RPS26B isoform 1 | polymer | 119 | 13480.9 | 1 | UniProt (A0A6A5Q0E8) Pfam (PF01283) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 71 | AR | 40S ribosomal protein S27-A | polymer | 82 | 8893.4 | 1 | UniProt (P35997) Pfam (PF01667) In PDB | Saccharomyces cerevisiae (Baker's yeast) | RP61,Small ribosomal subunit protein eS27-A,YS20 |
| 72 | AS | RPS28A isoform 1 | polymer | 67 | 7605.8 | 1 | UniProt (A0A6A5Q700) Pfam (PF01200) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 73 | AT | RPS29A isoform 1 | polymer | 56 | 6675.7 | 1 | UniProt (A0A6A5PV92) Pfam (PF00253) In PDB | Saccharomyces cerevisiae (Baker's yeast) | |
| 74 | AV | Guanine nucleotide-binding protein subunit beta-like protein | polymer | 319 | 34841.2 | 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 |
| 75 | AX, AZ | Transfer RNA | polymer | 76 | 24518.6 | 2 | GenBank (176419) | Saccharomyces cerevisiae (Baker's yeast) | |
| 76 | p, AQ, AR, AT, j... | ZINC ION | non-polymer | 65.4 | 6 | Chemie (ZN) |
Sequence modifications
1: 1 - 3396 (GenBank: 380294104)
| PDB | External Database | Details |
|---|---|---|
| - | G 3267 | deletion |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 76 |
| Total formula weight | 3100174.3 | |
| Non-Polymers* | Number of molecules | 6 |
| Total formula weight | 392.5 | |
| All* | Total formula weight | 3100566.8 |
