6EML
Cryo-em structure of a late pre-40s ribosomal subunit from saccharomyces cerevisiae
PDB DOI: 10.2210/pdb6eml/pdb
Classification: RIBOSOME Organism(s): Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C
Deposited: 2017-10-02 Deposition Author(s): Becker, T. , Beckmann, R. , Berninghausen, O. , Heuer, A. , Hurt, E. , Schmidt, C. , Thomson, E.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.6 Å
Cryo-em structure of a late pre-40s ribosomal subunit from saccharomyces cerevisiae
Becker, T. , Beckmann, R. , Berninghausen, O. , Heuer, A. , Hurt, E. , Schmidt, C. , Thomson, E.
Primary Citation of Related Structures: 6EML
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| pre-18S ribosomal RNA | 2 | 1800 | NA | UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCGAUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGUGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 40S ribosomal protein S28-B | L | 67 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MDSKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDILVLMESEREARRLR |
| Ubiquitin-40S ribosomal protein S31 | N | 152 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGKKRKKKVYTTPKKIKHKHKKVKLAVLSYYKVDAEGKVTKLRRECSNPTCGAGVFLANHKDRLYCGKCHSVYKVNA |
| Pre-rRNA-processing protein PNO1 | P | 274 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MVAPTALKKATVTPVSGQDGGSSRIIGINNTESIDEDDDDDVLLDDSDNNTAKEEVEGEEGSRKTHESKTVVVDDQGKPRFTSASKTQGNKIKFESRKIMVPPHRMTPLRNSWTKIYPPLVEHLKLQVRMNLKTKSVELRTNPKFTTDPGALQKGADFIKAFTLGFDLDDSIALLRLDDLYIETFEVKDVKTLTGDHLSRAIGRIAGKDGKTKFAIENATRTRIVLADSKIHILGGFTHIRMARESVVSLILGSPPGKVYGNLRTVASRLKERY |
| 40S ribosomal protein S1-A | Q | 255 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDALKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLIEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTLAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEKGKKVTGFKDEVLETV |
| Serine/threonine-protein kinase RIO2 | R | 425 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MKLDTSHMRYLTTDDFRVLQAVEQGSRSHEVVPTPLIHQISGMRSQSGTNRAISDLAKLSLISKMRNVKYDGYRLTYNGIDYLALKTMLNRDTVYSVGNTIGVGKESDIYKVSDKNGNPRVMKIHRLGRTSFHSVRNNRDYLKKSNQGANWMHLSRLAANKEYQFMSMLYSKGFKVPEPFDNSRHIVVMELIEGYPMRRLRKHKNIPKLYSDLMCFIVDLANSGLIHCDFNEFNIMIKDKLEDENDCGFVVIDFPQCISIQHQDADYYFQRDVDCIRRFFKKKLKYEPKPDSSMLDTEGFGDGYKYAYPDFKRDVKRTDNLDELVQASGFSKKHPGDRGLETAVESMRNAVYNSDDDMSNDEAEEENGEGDYSEEDEYYDSELDNESSEDDSEDAQEEENERIIEALSSGVENLKMDKLGNYILE |
| 40S ribosomal protein S4-A | S | 261 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASYKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLVYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKGKGIKLSIAEERDRRRAQQGL |
| Ribosome biogenesis protein TSR1 | T | 788 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MAGHSHRSSLKNGHKSYKSKHASKGALKRLYKGKVEKEPVGTGKPDKQVSKLQRKNKAKQLRAQRILDSIENRKLFEGKNGAAKIITIVPLVNDLDPLDILYKLLKCADDEGIMVQEVDSKRIFNVHIKKFKSNLKIIIPDMTNFLNILDCAKVADFVVFGLSGVQEVDEEFGEQIIRALELQGIASYIGVISNLSAVHEKEKFQLDVKQSLESYFKHFFPSEERVYNLEKNSDALNVLRTLCQRLPRSINWRDNRGYVVADFVDFVETSPDSGDLVIEGTVRGIGFNANRLVHIPDFGDFQLNKIEKISESSQKRKIIKEKATDSLSLELDLQTVFESNMNRDTLDEYAPEGTEDWSDYDEDFEYDGLTTARYDDHGFLPGREQTSKKAAVPKGTSDYQAKWYLDDVIDANEEEEAEQTNGKDETMMEIDDEMMVEQDNEEVAGDEEYDIEDNEGFEELSPEEEERQLREFRDMEKEDREFPDEIELEPSESAIERLKRYRGLKNLYNCDWQVDEKDPSSPAEWKRLLRIGNYKNTKNRIIKETKNEAQAIAGDRIRMFIRFPKFLLEKIQDPKQLLFAVYGLLLHEHKNAVVNFSLQRWEQYDKPVPSQEPIVVQYGVRRYTIQPLFSQGSNSPNNVHKYERFLHPDTVSVATCIAPVDFTQSPAIFFKPSPTDAKNIELIGHGTFLNADHSRILAKRAILTGHPFRFHKTVVTVRYMFFRPEDVEWFKSIPLFTKSGRSGFIKESLGTHGYFKATFDGKLSAQDVVAMSLYKRMWPMPSLPWNGM |
| 40S ribosomal protein S7-A | U | 190 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVFEIPSETH |
| 40S ribosomal protein S8-A | V | 200 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRIETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQTLGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCDGYILEGEELAFYLRRLTAKK |
| 40S ribosomal protein S9-A | W | 197 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLTRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKAEASGEAADEADEADEE |
| 40S ribosomal protein S24-A | D | 135 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MSDAVTIRTRKVISNPLLARKQFVVDVLHPNRANVSKDELREKLAEVYKAEKDAVSVFGFRTQFGGGKSVGFGLVYNSVAEAKKFEPTYRLVRYGLAEKVEKASRQQRKQKKNRDKKIFGTGKRLAKKVARRNAD |
| 40S ribosomal protein S11-A | X | 156 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MSTELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPFTGLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQCRPISKTVRFNVVKVSAAAGKANKQFAKF |
| 40S ribosomal protein S13 | Y | 151 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN |
| 40S ribosomal protein S14-A | Z | 137 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MSNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAMLAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTPVPSDSTRKKGGRRGRRL |
| 40S ribosomal protein S21-A | A | 87 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MENDKGQLVELYVPRKCSATNRIIKADDHASVQINVAKVDEEGRAIPGEYVTYALSGYVRSRGESDDSLNRLAQNDGLLKNVWSYSR |
| 40S ribosomal protein S5 | B | 225 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR |
| 40S ribosomal protein S17-A | C | 136 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MGRVRTKTVKRASKALIERYYPKLTLDFQTNKRLCDEIATIQSKRLRNKIAGYTTHLMKRIQKGPVRGISFKLQEEERERKDQYVPEVSALDLSRSNGVLNVDNQTSDLVKSLGLKLPLSVINVSAQRDRRYRKRV |
| 40S ribosomal protein S16-A | F | 143 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MSAVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKFSNIDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELKKAFTSYDRTLLIADSRRPEPKKFGGKGARSRFQKSYR |
| 40S ribosomal protein S30-A | G | 63 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MAKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVNGKRRMNPGPSVQ |
| 40S ribosomal protein S15 | E | 142 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MSQAVNAKKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHGRAGATTSRFIPLK |
| 40S ribosomal protein S18-A | H | 146 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MSLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRVRGQHTKTTGRRRA |
| 40S ribosomal protein S19-A | I | 144 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MPGVSVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARHIYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRISENGQRDLDRIAAQTLEEDE |
| 40S ribosomal protein S25-A | K | 108 | Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) , Saccharomyces Cerevisiae S288C | MPPKQQLSKAAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYTRATASE |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2017-10-02 Deposition Author(s): Becker, T. , Beckmann, R. , Berninghausen, O. , Heuer, A. , Hurt, E. , Schmidt, C. , Thomson, E.