6GSM
Structure of a partial yeast 48s preinitiation complex in open conformation.
PDB DOI: 10.2210/pdb6gsm/pdb
Classification: RIBOSOME Organism(s): Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct
Deposited: 2018-06-14 Deposition Author(s): Gordiyenko, Y. , Hussain, T. , Llacer, J.L. , Ramakrishnan, V.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 5.15 Å
Structure of a partial yeast 48s preinitiation complex in open conformation.
Gordiyenko, Y. , Hussain, T. , Llacer, J.L. , Ramakrishnan, V.
Primary Citation of Related Structures: 6GSM
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Met-tRNAi | 1 | 76 | NA | AGCGCCGUGGCGCAGUGGAAGCGCGCAGGGCUCAUAACCCUGAUGUCCUCGGAUCGAAACCGAGCGGCGCUACCAX |
| 18S ribosomal RNA | 2 | 1798 | NA | UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUUCCUUUACUACAUGGAUAUCUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCCUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGUCUGGUUGUCCGGUCCGACUUUAUGUCGCGCACUGGUUUUCAACCGGAUCUUUCCUUCUGGCUAACCUGUACUCCUUGUGGGUGCAGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGAAAGCUCGAAUAUAUUAGCAUGGAAUAAUGGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUCUUAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGGGUUGCUGGCACUUGCCGGUUGACUCUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUACAACCUUGGCCGAGAGGUCUGGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUUUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGAAGAAUCUGGUCAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA |
| mRNA (5'-R(P*AP*AP*U)-3') | 3 | 3 | NA | AAU |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| KLLA0E12277p | G | 324 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | SSNIMLVLRGTLEGHNGWVTSLSTSAAQPNLLVSGSRDKTLISWRLTENEQQFGVPVRSYKGHSHIVQDVVVSADGNYAVSASWDKTLRLWNLATGNSEARFVGHTGDVLSVAIDANSSKIISASRDKTIRVWNTVGDCAYVLLGHTDWVTKVRVAPKNLEDGEVDDGRITFVSAGMDKIVRSWSLNEDSYRIEADFIGHNNYINVVQPSPDGSLAASAGKDGQIYVWNLKHKSAFMNFDAKDEVFALAFSPSRFWLTAATASGIKIYDLENEVLIDELKPEFAGYTKAQDPHAVSLAWSADGQTLFAGYTDNVIRVWQVMTAN |
| 60S ribosomal protein L41-A | H | 25 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | MRAKWRKKRTRRLKRKRRKVRARSK |
| Eukaryotic translation initiation factor 1A | I | 95 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | GPKRELIYKEEGQEYAQITKMLGNGRVEASCFDGNKRMAHIRGKLRKKVWMGQGDIILVSLRDFQDDQCDVVHKYNLDEARTLKNQGELPENAKI |
| Eukaryotic translation initiation factor 2 subunit alpha | J | 263 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | TSHCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSIIDETVWEGIEPPSKDVLDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDALKSAEDMSTEQMQVKVKLVAAPLYVLTTQALDKQKGIEQLESAIEKITEVITKYGGVCNIT |
| Eukaryotic translation initiation factor 2 subunit gamma | K | 430 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | LSAEIINRQATINIGTIGHVAHGKSTVVRAISGVQTVRFKDELERNITIKLGYANAKIYKCQEPTCPEPDCYRSFKSDKEISPKCQRPGCPGRYKLVRHVSFVDCPGHDILMSTMLSGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHVIILQNKVDLMREESALEHQKSILKFIRGTIADGAPIVPISAQLKYNIDAVNEFIVKTIPVPPRDFMISPRLIVIRSFDVNKPGAEIEDLKGGVAGGSILNGVFKLGDEIEIRPGIVTKDDKGKIQCKPIFSNIVSLFAEQNDLKFAVPGGLIGVGTKVDPTLCRADRLVGQVVGAKGHLPNIYTDIEINYFLLRRLLGVKTDGQKQAKVRKLEPNEVLMVNIGSTATGARVVAVKADMARLQLTSPACTEINEKIALSRRIEKHWRLIGWATIKK |
| Eukaryotic translation initiation factor 2 subunit beta | L | 144 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | VGLPYSELLSRFFNILRTNNPELAGDRSGPKFRIPPPVCLRDGKKTIFSNIQDIAEKLHRSPEHLIQYLFAELGTSGSVDGQKRLVIKGKFQSKQMENVLRRYILEYVTCKTCKSINTELKREQSNRLFFMVCKSCGSTRSVSS |
| Eukaryotic translation initiation factor eIF-1 | M | 96 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | ADTGDDETATSNYIHIRIQQRNGRKTLTTVQGVPEEYDLKRILKVLKKDFACNGNIVKDPEMGEIIQLQGDQRAKVCEFMISQLGLQKKNIKIHGF |
| KLLA0F18040p | N | 150 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | GRMHSKGKGMSSSAIPYSRNAPAWFKGSSDGVVEQIIKYARKGLTPSQIGVLLRDAHGVTQAKVITGNKILRILKSNGLAPEIPEDLYFLIKKAVSVRKHLERNRKDKDAKFRLILIESRIHRLARYYRTVSVLPPNWKYESATASALVN |
| Eukaryotic translation initiation factor 3 subunit A,Eukaryotic translation initiation factor 3 subunit A,eIF3a | O | 567 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | PFRPENAIKRADELISVGEKQAALQSLHDFITARRIRWATPSTVEPVVFKFLEIGVELKKGKLLKDGLHQYKKLIQGSTEGLVSVGAVARKFIDLVESKIASEQTRADELQKQEIDDDLEGGVTPENLLISVYESDQSVAGFNDEAITSWLRFTWESYRAVLDLLRNNALLEITYSGVVKKTMHFCLKYQRKNEFKRLAEMLRQHLDAANYQQSKSGNNLVDLSDADTLQRYLDQRFQQVDVSVKLELWHEAYRSIEDVFHLMKISKRAPKPSTLANYYENLVKVFFVSGDPLLHTTAWKKFYKLYSTNPRATEEEFKTYSSTIFLSAISTQLDEIPSIGYDPHLRMYRLLNLDAKPTRKEMLQSIIEDESIYGKVDEELKELYDIIEVNFDVDTVKQQLENLLVKLSSKTYFSQYIAPLRDVIMRRVFVAASQKFTTVSQSELYKLATLPAPLDLSAWDIEKSLLQAAVEDYVSITIDHESAKVTFAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
| Eukaryotic translation initiation factor 3 subunit B | P | 651 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | QYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVERYNSDDFDTEFREPDMPTFVPSSSLKSWLMDDKVRDQFVLQDDVKTSVFWNSMFNEEDSLVESRENWSTNYVRFSPKGTYLFSYHQQGVTAWGGPNFDRLRRFYHPDVRNSSVSPNEKYLVTFSTEPIIVEEDNEFSPFTKKNEGHQLCIWDIASGLLMATFPVIKSPYLKWPLVRWSYNDKYCARMVGDSLIVHDATKNFMPLEAKALKPSGIRDFSFAPEGVKLQPFRNGDEPSVLLAYWTPETNNSACTATIAEVPRGRVLKTVNLVQVSNVTLHWQNQAEFLCFNVERHTKSGKTQFSNLQICRLTERDIPVEKVELKDSVFEFGWEPHGNRFVTISVHEVADMNYAIPANTIRFYAPETKEKTDVIKRWSLVKEIPKTFANTVSWSPAGRFVVVGALVGPNMRRSDLQFYDMDYPGEKNINDNNDVSASLKDVAHPTYSAATNITWDPSGRYVTAWSSSLKHKVEHGYKIFNIAGNLVKEDIIAGFKNFAWRPRPLSNAERKKVRKNLREWSEEQDAMEADTAMRHQRELLKQWTEYREKIGQEMEKSMNFKIFDVQP |
| Eukaryotic translation initiation factor 3 subunit C | Q | 665 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | YDSSDEESDEEDGKKVVKSAKEKLLDEMQDVYNKISQAENSDWLTISNEFDLISRLLVRAQQQNWGTPNIFIKVVAQVEDAVNNTQQADLKAVARAYNTTKQRVKKVSRENEDSMAKFRNDQEDFFTRLQTIIDSRGKKTVNQQSLISTLEELLTVAEKPYEFIMAYLTLIPSRFDASANLSYQPIDQWKSSFNDISKLLSILDQTIDTYQVNEFADPIDFIEDEPKEDSDGVKRILGSIFSFVERLDDEFMKSLLNIDPHSSDYLIRLRDEQSIYNLILRTQLYFEATLKDEHDLERALTRPFVKRLDHIYYKSENLIKIMETAAWNIIPAQFKSKFTSKDQLDSADYVDNLIDGLSTILSKQNNIAVQKRAILYNIYYTALNKDFQTAKDMLLTSQVQTNINQFDSSLQILFNRVVVQLGLSAFKLCLIEECHQILNDLLSSSHLREILGQQSLHRISLNSSNNASADERARQCLPYHQHINLDLIDVVFLTCSLLIEIPRMTAFYSGIKVKRIPYSPKSIRRSLEHYDKLSFQGPPETLRDYVLFAAKSMQKGNWRDSVKYLREIKSWALLPNMETVLNSLTERVQVESLKTYFFSFKRFYSSFSVAKLAELFDLPENKVVEVLQSVIAELEIPAKLNDEKTIFVVEKGDEITKLEEAMVKL |
| Eukaryotic translation initiation factor 3 subunit G | R | 49 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | SVAERKNWHKYGSEKGSPAGPSAVTARLGEEVELRLSRNWKQAEEERIQ |
| Eukaryotic translation initiation factor 3 subunit I | S | 342 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | MKAIKLTGHERPLTQVKYNKEGDLLFSCSKDSSASVWYSLNGERLGTLDGHTGTIWSIDVDCFTKYCVTGSADYSIKLWDVSNGQCVATWKSPVPVKRVEFSPCGNYFLAILDNVMKNPGSINIYEIERDSATHELTKVSEEPIHKIITHEGLDAATVAGWSTKGKYIIAGHKDGKISKYDVSNNYEYVDSIDLHEKSISDMQFSPDLTYFITSSRDTNSFLVDVSTLQVLKKYETDCPLNTAVITPLKEFIILGGGQEAKDVTTTSANEGKFEARFYHKIFEEEIGRVQGHFGPLNTVAISPQGTSYASGGEDGFIRLHHFEKSYFDFKYDVEKAAEAKEH |
| KLLA0A07194p | T | 143 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | PGVSVRDVPAQDFINNYASFLQRQGKLEVPGYVDIVKTSAGNELPPQDSEGWFYKRAASVARHIYLRKQVGVGKLNKLYGGAKNRGVRPHKHVDASGSINRKVLQSLEKLGVVEISPKGGRRISDNGLRDLDRIAAATLEDEE |
| KLLA0F25542p | U | 106 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | QEVVIHKIRINLTSTKVKQLENVSANIIKNAETFKLVKKGPVRLPTKVLKISTRKTPNGEGSKTWDTYEMRIHKRYIDLEAPAHIVKRITQITIEPGVDVEVIIAA |
| 40S ribosomal protein S21 | V | 87 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | MENDKGQLVELYVPRKCSATNRIIKAKDHSSVQINIAQVDEEGRAIPGEYVTYALSGYIRARGEADDSLNRLAQQDGLLKNVWSYSR |
| 40S ribosomal protein S22 | W | 129 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | TRTSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRSGKIVVQLNGRLNKCGVISPRFNVKIADVEKWTANLLPARQFGYVILTTSAGIMDHEEAHRKHVSGKILGFVY |
| KLLA0B11231p | X | 144 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | GKGKPRGLNSARKLRVHRRNNRWAETTYKKRLLGTAFKSSPFGGSSHAKGIVLEKIGIESKQPNSAIRKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFKVVKVSGVSLLALWKEKKEKPRS |
| 40S ribosomal protein S24 | Y | 134 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | SDAITIRTRKVISNPLLARKQFVVDVLHPNRANVSKDELREKLAEAYKAEKDAVSVFGFRTQYGGGKSTGFGLVYNSVADAKKFEPAYRLVRYGLAEKVEKASRQQRKQRKNRGKKIFGTGKSIAKKAARRNAD |
| KLLA0B06182p | Z | 70 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | AKHAVVLDQDKFDRIMKEAPTYRYVSVSVLVDRFKLGGSLARVALRHLENEGIIKPVSKHSKQAIYTRAT |
| 40S ribosomal protein S26 | A | 98 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | PKKRASNGRNKKGRGHVKPVRCVNCSRSVPKDKAIKRMAIRNIVEAAAIRDLSEASVYAEYALPKTYNKLHYCISCAIHARIVRVRSRTDRRIRAPPQ |
| 40S ribosomal protein S1 | B | 231 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | VGKNKRLSKGKKGLKKRVVDPFTRKEWYDIKAPSTFENRNVGKTLVNKSVGLKNASDSLKGRVVEVCLADLQGSEDHSFRKVKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLIEANVTVKTSDDYVLRIFAIAFTRKQANQVKRTSYAQSSHIRQIRKVISEILTREVQNSTLAQLTSKLIPEVINKEIENATKDIFPLQNVHIRKVKLLKQPKFDLGSLLSLHG |
| KLLA0F09812p | C | 217 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | GWVPVTKLGRLVKAGKISSIEEIFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTSGKCGSVSVRLIPAPRGSGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKAAFVAIGNTYGFLTPNLWEVQALTPSPMDVYADYATAS |
| KLLA0D08305p | D | 223 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | AIISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEIIIRATKVQDVVGENGRRINELTLLIEKRFKYKRGTIALYAERVHDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMESGAKGCEVVISGKLRAARAKSMKFADGFLIHSGQPVNDFIETATRHVLLRQGVLGIKVKIMKDPSRNTSGPKALPDAVTIIEPKEEEPVLEPSVKDY |
| 40S ribosomal protein S4 | E | 260 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | ARGPKKHLKRLAAPHHWMLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTFPAGFMDVITLEATNENFRLVYDVKGRFAVHRITDEEASYKLAKVKKVQLGKKGIPYVVTHDGRTIRYPDPNIKVNDTVKVDLATGTITDFIKFDTGKLVYVTGGRNLGRVGTIVHRERHEGGFDLVHIKDSLENTFVTRLNNVFVIGEPGRPWISLPKGKGIKLTISEERDRRRAQHGL |
| KLLA0D10659p | F | 206 | Kluyveromyces Lactis Nrrl Y-1140 , Saccharomyces Cerevisiae S288C , Synthetic Construct | FVPVELATTIPVEIQQAQQEIKLFNKWSFEDVEVKDASLVDYIQISKPIYVAHTAGRYANKRFRKAQCPIVERLTNSLMMNGRNNGKKLKAVRIVKHTLEIINVLTDQNPLQVVVDAIINSGPREDTTRVGGGGAARRQAVDVSPLRRVNQSIALLTIGAREAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2018-06-14 Deposition Author(s): Gordiyenko, Y. , Hussain, T. , Llacer, J.L. , Ramakrishnan, V.