6DZK
Cryo-em structure of mycobacterium smegmatis c(minus) 30s ribosomal subunit with mpy
PDB DOI: 10.2210/pdb6dzk/pdb
Classification: RIBOSOME Organism(s): Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum
Deposited: 2018-07-05 Deposition Author(s): Agrawal, R.K. , Derbyshire, K.M. , Gray, A.G. , Kaushal, P.S. , Korripella, R. , Li, Y. , Lin, Q. , Ojha, A. , Sharma, M.R. , Wade, J.T. , Yang, Y.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.6 Å
Cryo-em structure of mycobacterium smegmatis c(minus) 30s ribosomal subunit with mpy
Agrawal, R.K. , Derbyshire, K.M. , Gray, A.G. , Kaushal, P.S. , Korripella, R. , Li, Y. , Lin, Q. , Ojha, A. , Sharma, M.R. , Wade, J.T. , Yang, Y.
Primary Citation of Related Structures: 6DZK
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S rRNA | a | 1511 | NA | UUUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGAAAGGCCCUUUCGGGGGUACUCGAGUGGCGAACGGGUGAGUAACACGUGGGUGAUCUGCCCUGCACUUUGGGAUAAGCCUGGGAAACUGGGUCUAAUACCGAAUACACCCUGCUGGUCGCAUGGCCUGGUAGGGGAAAGCUUUUGCGGUGUGGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUGAUGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGUGACCGGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCACAGACGAAGCGCAAGUGACGGUAUGUGCAGAAGAAGGACCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUCCGAGCGUUGUCCGGAAUUACUGGGCGUAAAGAGCUCGUAGGUGGUUUGUCGCGUUGUUCGUGAAAACUCACAGCUUAACUGUGGGCGUGCGGGCGAUACGGGCAGACUAGAGUACUGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGGAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGGUCUCUGGGCAGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGUACUAGGUGUGGGUUUCCUUCCUUGGGAUCCGUGCCGUAGCUAACGCAUUAAGUACCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGUUUGACAUGCACAGGACGCCGGCAGAGAUGUCGGUUCCCUUGUGGCCUGUGUGCAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUCAUGUUGCCAGCACGUUAUGGUGGGGACUCGUGAGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACACAUGCUACAAUGGCCGGUACAAAGGGCUGCGAUGCCGUGAGGUGGAGCGAAUCCUUUCAAAGCCGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGUCGGUAACACCCGAAGCCGGUGGCCUAACCCUUGUGGAGGGAGCCGUCGAAGGUGGGAUCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUC |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S10 | J | 101 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MAGQKIRIRLKAYDHEAIDASARKIVETVTRTGASVVGPVPLPTEKNVYCVIRSPHKYKDSREHFEMRTHKRLIDILDPTPKTVDALMRIDLPASVDVNIQ |
| 30S ribosomal protein S11 | K | 138 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MAQAKKGGTAAKKGQKTRRREKKNVPHGAAHIKSTFNNTIVSITDPQGNVIAWASSGHVGFKGSRKSTPFAAQLAAENAARKAQEHGVKKVDVFVKGPGSGRETAIRSLQAAGLEVGTISDVTPQPHNGCRPPKRRRV |
| 30S ribosomal protein S12 | L | 124 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MPTIQQLVRKGRRDKIAKVKTAALKGSPQRRGVCTRVYTTTPKKPNSALRKVARVKLTSQVEVTAYIPGEGHNLQEHSMVLVRGGRVKDLPGVRYKIIRGSLDTQGVKNRKQARSRYGAKKEKS |
| 30S ribosomal protein S13 | M | 124 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MARLVGVDLPRDKRMEIALTYIYGIGRTRSNEILAATGIDKNMRTKDLTDDQVTVLRDYIEGNLKVEGDLRREVQADIRRKIEIGCYQGLRHRRGLPVRGQRTKTNARTRKGPKRTIAGKKKAR |
| 30S ribosomal protein S15 | O | 88 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | ALTAEQKKEILGQYGLHDTDTGSPEAQVALLTKRIQDLTEHLKVHKHDHHSRRGLLLLVGRRRRLLKYVAQVDVARYRSLIERLGLRR |
| 30S ribosomal protein S16 | P | 156 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MAVKIKLTRLGKIRNPQYRIIVADARTRRDGRAIEVIGRYHPKEEPSLIQIDSERAQYWLGVGAQPTEPVLALLKITGDWQKFKGLPGAEGTLKVKEPKPSKLDLFNAALAEAESGTTAAATTPKKKKAPKKDEAAEAPAEAAEAPAEAADAASES |
| 30S ribosomal protein S17 | Q | 98 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MADQKGPKYTPAAEKPRGRRKTAIGYVVSDKMQKTIVVELEDRKSHPLYGKIIRTTKKVKAHDENGEAGIGDRVSLMETRPLSATKRWRLVEILEKAK |
| 30S ribosomal protein S19 | S | 93 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MPRSLKKGPFVDDHLLKKVDVQNEKNTKQVIKTWSRRSTIIPDFIGHTFAVHDGRKHVPVFVTEAMVGHKLGEFAPTRTFKGHIKDDRKSKRR |
| 30S ribosomal protein S20 | T | 86 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MANIKSQIKRIRTNERRRLRNQSVKSSLRTAIRGFREAVDAGDKDKASELLHATSRKLDKAASKGVIHPNQAANKKSALALALNKL |
| 30S ribosomal protein S2 | V | 277 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MAVVTMKQLLDSGAHFGHQTRRWNPKMKRFIFTDRNGIYIIDLQQTLTYIDKAYEFVKETVAHGGTVLFVGTKKQAQESIAEEATRVGMPYVNQRWLGGMLTNFSTVHKRLQRLKELEAMEQTGGFEGRTKKEILMLTREKNKLERSLGGIRDMQKVPSAVWVVDTNKEHIAVGEARKLGIPVIAILDTNCDPDVVDYPIPGNDDAIRSAALLTKVIASAVAEGLQARAGQGSGEKPAEGAEPLAEWEQELLAGATAGAADASAEGAAAPESSTDAS |
| Conserved domain protein | B | 32 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | GSVIKKRRKRMSKKKHRKLLRRTRVQRRKLGK |
| 30S ribosomal protein S18 1 | R | 85 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MMAVKKSRKRTAATELKKPRRNQLEALGVTTIDYKDVAVLRTFLSERGKIRSRHVTGLTPQQQRQVATAIKNAREMALLPMAGPR |
| Ribosome hibernation promoting factor | Y | 230 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MSSHSMDSSRTMVVEDDRESTAGTTPERPHAEVVVKGRNVEVPDHFRTYVSEKLSRLERFDKTIYLFDVELDHERNRRQRKNCQHVEITARGRGPVVRGEACADSFYTAFESAVQKLEGRLRRAKDRRKIHYGDKTPVSLAEATAKDPLAGLDVSREDGEARYNDGVAEHEPGRIVRIKDHPATPMTVDDALYEMELVGHDFFLFHDKETDRPSVVYRRHAFDYGLIRLA |
| 30S ribosomal protein S14 | N | 100 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | AKKSKIVKNEQRRELVQRYAERRAELKRTIRDPASSPERRAAAVSALQRLPRDSSPVRLRNRDVVDGRPRGHLRKFGLSRVRVREMAHRGELPGVRKASW |
| 30S ribosomal protein S7 | G | 156 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MPRKGPAPKRPLVNDPVYGSQLVTQLVNKVLLEGKKSLAERIVYGALEQAREKTGTDPVVTLKRALDNVKPALEVRSRRVGGATYQVPVEVRPDRSTTLALRWLVNFSRQRREKTMVERLANEILDASNGLGASVKRREDTHKMAEANRAFAHYRW |
| 30S ribosomal protein S3 | C | 275 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MGQKINPHGFRLGITTEWKSRWYADKQYKDYVKEDVAIRKLLATGLERAGIADVEIERTRDRVRVDIHTARPGIVIGRRGTEADRIRADLEKLTGKQVQLNILEVKNPESQAQLVAQGVAEQLSNRVAFRRAMRKAIQSAMRQPNVKGIRVQCSGRLGGAEMSRSEFYREGRVPLHTLRADIDYGLYEAKTTFGRIGVKVWIYKGDIVGGKRELAAAAPASDRPRRERPSGTRPRRSGSAGTTATSTEAGRAATSDAPAAGTAAAAEAPAESTES |
| 30S ribosomal protein S4 | D | 201 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MARYTGPATRKSRRLGVDLVGGDQSFEKRPYPPGQHGRARIKESEYRQQLQEKQKARFSYGVMEKQFRRYYEEANRQPGKTGDNLLRILESRLDNVVYRAGLARTRRMARQLVSHGHFLVNGVKVDIPSYRVSQYDIIDVKEKSLNTLPFQIARETAGERPIPSWLQVVGERQRILVHQLPERAQIDVPLTEQLIVELYSK |
| 30S ribosomal protein S5 | E | 213 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | AEQAGAGSAQDNRGGRGRRDDRGGRGRDGGDKSNYIERVVSINRVSKVVKGGRRFSFTALVIVGDGKGMVGVGYGKAKEVPAAIAKGVEEARKNFFRVPLIGSTITHPVQGEAAAGVVMLRPASPGTGVIAGGAARAVLECAGVHDILAKSLGSDNAINVVHATVAALKLLQRPEEVAARRGLPIEDVAPAGMLKARRESEALAAAAAREGSA |
| 30S ribosomal protein S6 | F | 96 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MRPYEIMVILDPTLDERTVAPSLETFLNVIRKDGGTVDKVDIWGRRRLAYEIAKHAEGIYAVIDVKAEPATVSELDRQLNLNESVLRTKVLRTDKH |
| 30S ribosomal protein S8 | H | 131 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | TMTDPIADFLTRLRNANSAYHDEVTLPHSKLKANIAEILKREGYISDYRTEDARVGKSLVVQLKYGPSRERSIAGLRRVSKPGLRVYAKSTNLPRVLGGLGVAIISTSSGLLTDRQAARQGVGGEVLAYVW |
| 30S ribosomal protein S9 | I | 150 | Bovine Enterovirus (Strain Vg-5-27) , Leptospira Kmetyi Serovar Malaysia Str. Bejo-Iso9 , Trichoderma Harzianum | MTDVTETEVVTESAEPREPVIIDRPIQTVGRRKEAVVRVRLVPGTGQFNLDGRTLENYFPNKVHQQLIKAPLVTVDRVDQFDIYAHLDGGGPSGQAGALRLAIARALILVQPEDRPALKKAGFLTRDPRAIERKKYGLKKARKAPQYSKR |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2018-07-05 Deposition Author(s): Agrawal, R.K. , Derbyshire, K.M. , Gray, A.G. , Kaushal, P.S. , Korripella, R. , Li, Y. , Lin, Q. , Ojha, A. , Sharma, M.R. , Wade, J.T. , Yang, Y.