4ADX
The cryo-em structure of the archaeal 50s ribosomal subunit in complex with initiation factor 6
PDB DOI: 10.2210/pdb4adx/pdb
Classification: RIBOSOME Organism(s): Methanothermobacter Thermautotrophicus
Deposited: 2012-01-04 Deposition Author(s): Ban, N. , Boehringer, D. , Crnkovic, A. , Godinic-Mikulcic, V. , Greber, B.J. , Ibba, M. , Weygand-Durasevic, I.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 6.6 Å
The cryo-em structure of the archaeal 50s ribosomal subunit in complex with initiation factor 6
Ban, N. , Boehringer, D. , Crnkovic, A. , Godinic-Mikulcic, V. , Greber, B.J. , Ibba, M. , Weygand-Durasevic, I.
Primary Citation of Related Structures: 4ADX
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 23S ribosomal RNA | 0 | 2923 | NA | GUUGGCUACUAUGCCAGCUGGUGGAUUGCUCGGCUCAGGCGCUGAUGAAGGACGUGCCAAGCUGCGAUAAGCUGUGGGGAGCCGCACGGAGGCGAAGAACCACAGAUUUCCGAAUGAGAAUCUCUCUAACAAUUGCUUCGCGCAAUGAGGAACCCCGAGAACUGAAACAUCUCAGUAUCGGGAGGAACAGAAAACGCAACGUGAUGUCGUUAGUAACCGCGAGUGAACGCGAUACAGCCCAAACCGAAGCCCUCACGGGCAAUGUGGUGUCAGGGCUACCUCUCAUCAGCCGACCGUCUUCACGAAGUCUCUUGGAAUAGAGCGUGAUACAGGGUGACAACCCCGUACUGAAGACCAGUACGCUGUGCGGUAGUGCCAGAGUAGCGGGGGUUGGAUAUCCCUCGCGAAUAACGCAGGCAUCGACUGCGAAGGCUAAACACAACCUGAGACCGAUAGUGAACAAGUAGUGUGAACGAACGCUGCAAAGUACCCUCAGAAGGGAGGCGAAAUAGAGCAUGAAAUCAGUUGGCGAUCGAGCGACAGGGCAUACAAGGUCCCUUGACGAAUGACCGAGACGCGAGUCUCCAGUAAGACUCACGGGAAGCCGAUGUUCUGUCGUACGUUUUGAAAAACGAGCCAGGGAGUGUGUCUGUAUGGCAAGUCUAACCGGAGUAUCCGGGGAGGCACAGGGAAACCGACAUGGCCGCAGGGCUUUGCCCGAGGGCCGCCGUCUUCAAGGGCGGGGAGCCAUGUGGACACGACCCGAAUCCGGACGAUCUACGCAUGGACAAGAUGAAGCGUGCCGAAAGGCACGUGGAAGUCUGUUAGAGUUGGUGUCCUACAAUACCCUCUCGUGAUCUAUGUGUAGGGGUGAAAGGCCCAUCGAGUCCGGCAACAGCUGGUUCCAAUCGAAACAUGUCGAAGCAUGACCUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCUGUUUGACGCGGGGAUUCCGGUGCGCGGGGUAAGCCUGUGUACCAGGAGGGGAACAACCCAGAGAUAGGUUAAGGUCCCCAAGUGUGGAUUAAGUGUAAUCCUCUGAAGGUGGUCUCGAGCCCUAGACAGCCGGGAGGUGAGCUUAGAAGCAGCUACCCUCUAAGAAAAGCGUAACAGCUUACCGGCCGAGGUUUGAGGCGCCCAAAAUGAUCGGGACUCAAAUCCACCACCGAGACCUGUCCGUACCACUCAUACUGGUAAUCGAGUAGAUUGGCGCUCUAAUUGGAUGGAAGCAGGGGCGAGAGCUCCUGUGGACCGAUUAGUGACGAAAAUCCUGGCCAUAGUAGCAGCGAUAGUCGGGUGAGAACCCCGACGGCCUAAUGGAUAAGGGUUCCUCAGCACUGCUGAUCAGCUGAGGGUUAGCCGGUCCUAAGUCUCACCGCAACUCGACUGAGACGAAAUGGGAAACAGGUUAAUAUUCCUGUGCCAUCAUGCAGUGAAAGUUGACGCCCUGGGGUCGAUCACGCCGGGCAUUCGCCCGGUCGAACCGUCCAACUCCGUGGAAGCCGUAAUGGCAGGAAGCGGACGAACGGCGGCAUAGGGAAACGUGAUUCAACCUGGGGCCCAUGAAAAGACGAGCAUGAUGUCCGUACCGAGAACCGACACAGGUGUCCAUGGCGGCGAAAGCCAAGGCCUGUCGGGAGCAACCAACGUUAGGGAAUUCGGCAAGUUAGUCCCGUACCUUCGGAAGAAGGGAUGCCUGCUCCGGAACGGAGCAGGUCGCAGUGACUCGGAAGCUCGGACUGUCUAGUAACAACAUAGGUGACCGCAAAUCCGCAAGGACUCGUACGGUCACUGAAUCCUGCCCAGUGCAGGUAUCUGAACACCUCGUACAAGAGGACGAAGGACCUGUCAACGGCGGGGGUAACUAUGACCCUCUUAAGGUAGCGUAGUACCUUGCCGCAUCAGUAGCGGCUUGCAUGAAUGGAUUAACCAGAGCUUCACUGUCCCAACGUUGGGCCCGGUGAACUGUACAUUCCAGUGCGGAGUCUGGAGACACCCAGGGGGAAGCGAAGACCCUAUGGAGCUUUACUGCAGGCUGUCGCUGAGACGUGGUCGCCGAUGUGCAGCAUAGGUAGGAGUCGUUACAGAGGUACCCGCGCUAGCGGGCCACCCAGACAACAGUGAAAUACUACCCGUCGGUGACUGCGACUCUCACUCCGGGAGGAGGACACCGAUAGCCGGGCAGUUUGACUGGGGCGGUACGCGCUCGAAAAGAUAUCGAGCGCGCCCUAUGGUCAUCUCAGCCGGGACAGAGACCCGGCGAAGAGUGCAAGAGCAAAAGAUGACUUGACAGUGUUCUUCCCAACGAGGAACGCUGACGCGAAAGCGUGGUCUAGCGAACCAAUUAGCCUGCUUGAUGCGGGCAAUUGAUGACAGAAAAGCUACCCUAGGGAUAACAGAGUCGUCACUCGCAAGAGCACAUAUCGACCGAGUGGCUUGCUACCUCGAUGUCGGUUCCCUCCAUCCUGCCCGUGCAGAAGCGGGCAAGGGUGAGGUUGUUCGCCUAUUAAAGGAGGUCGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUCGGCUGCUAUCUACUGGGUGUGUAAUGGUGUCUGACAAGAACGACCGUAUAGUACGAGAGGAACUACGGUUGGUGGCCACUGGUGUACCGGUUGUUCGAGAGAGCACGUGCCGGGUAGCCACGCCACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU |
| 5S Ribosomal RNA | 9 | 122 | NA | UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCAGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCACC |
| 23S Ribosomal RNA EXPANSION SEGMENTS | 8 | 133 | NA | GUGGAGGUGUAAAAACCUUCGAAGUGGUCAACACAACAGACGUGGUAUAGAGCGGUAACGCAAAGAAACCCGGAGGCCAGCACCUUUGCUGGCUUCUGGGGGAGACAUAAUUUCACGAGUAGAAUUUCCUACG |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| RPL2 | A | 240 | Methanothermobacter Thermautotrophicus | MGRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVEDGDVIAGTVVDIEHDPARSAPVAAVEFEDGDRRLILAPEGVGVGDELQVGVSAEIAPGNTLPLAEIPEGVPVCNVESSPGDGGKFARASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAVDHPFGGGGRQHPGKPKSISRNAPPGRKVGDIASKRTGRGGNE |
| RPL3 | B | 338 | Methanothermobacter Thermautotrophicus | MPQPSRPRKGSLGFGPRKRSTSETPRFNSWPSDDGQPGVQGFAGYKAGMTHVVLVNDEPNSPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRPLTEVWTDEFHSELDRTLDVPEDHDPDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPKKKPDVMETRVGGGSVSDRLDHALDIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVKRWGVQKRKGKHARQGWRRRIGNLGPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEGDEPTVDGGFVNYGEVDGPYTLVKGSVPGPDKRLVRFRPAVRPNDQPRLDPEVRYVSNESNQG |
| RPL4 | C | 246 | Methanothermobacter Thermautotrophicus | MQATIYDLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRGQAHVPKQDGRARRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATADADLVADRGHEFDRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHADIDRADETKIKAGQGSARGRKYRRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESALAEVAER |
| RPL5 | D | 177 | Methanothermobacter Thermautotrophicus | MSSESESGGDFHEMREPRIEKVVVHMGIGHGGRDLANAEDILGEITGQMPVRTKAKRTVGEFDIREGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGVEEHTEFPSQEYDPSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEVSE |
| RPL6 | E | 178 | Methanothermobacter Thermautotrophicus | MPRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNAKTMSTIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIHGDTDVEIDGEELTVSGPDIEAVGQTAADIEQLTRINDKDVRVFQDGVYITRKPNRGDA |
| RPL7AE | F | 120 | Methanothermobacter Thermautotrophicus | MPVYVDFDVPADLEDDALEALEVARDTGAVKKGTNETTKSIERGSAELVFVAEDVQPEEIVMHIPELADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAVTDAGEADADVEDIADKVEELR |
| RPLX | G | 78 | Methanothermobacter Thermautotrophicus | MKMKTKIFRVKGKFLMGDKLQPFTKELNAIREEEIYERLYSEFGSKHRVPRSKVKIEEIEEISPEEVQDPVVKALVQR |
| RPL10E | H | 177 | Methanothermobacter Thermautotrophicus | MSDKPASMYRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEASRLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKQATGAGADRVSDGMRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVERGEELLIA |
| AIF6 | I | 222 | Methanothermobacter Thermautotrophicus | MIRRINLSGNPNLGVYISVTDSVALIPQNTPEKFEGVLREALEVEVLKVSISGSSLNGALAVGNSNGFVVSNQAMDREIDALAAAGVEAVRIPERFTAVGNLVLANDNGAVASPLLSDDALQVIGDVLEVDVKVSTLAGLNIVGSMGAATNRGALLNPQASSEEIGIIEDTLGVEADVGTVNHGVTLIGACSVANSNGVLVGEETTGPELARIEEALGFLEG |
| RPL37E | 1 | 57 | Methanothermobacter Thermautotrophicus | MTGAGTPSQGKKNTTTHTKCRRCGEKSYHTKKKVCSSCGFGKSAKRRDYEWQSKAGE |
| RPL13 | J | 145 | Methanothermobacter Thermautotrophicus | MSVAEFDADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKYEKRVDIGNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTSLDRLSNIKFVTLGEISETLGANKTW |
| RPL14 | K | 132 | Methanothermobacter Thermautotrophicus | MEALGADVTQGLEKGSLITCADNTGARELKVISVHGYSGTKNRHPKAGLGDKITVSVTKGTPEMRRQVLEAVVVRQRKPIRRPDGTRVKFEDNAAVIVDENEDPRGTELKGPIAREVAQRFGSVASAATMIV |
| RPL15 | L | 165 | Methanothermobacter Thermautotrophicus | MTSKKKRQRGSRTHGGGSHKNRRGAGHRGGRGDAGRDKHEFHNHEPLGKSGFKRPQKVQEEAATIDVREIDENVTLLAADDVAEVEDGGFRVDVRDVVEEADDADYVKVLGAGQVRHELTLIADDFSEGAREKVEGAGGSVELTDLGEERQAEAEETEDADADEE |
| RPL15E | M | 196 | Methanothermobacter Thermautotrophicus | MARSAYSYIRDAWKNPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVARVSVRKGSARKRRHKAGRRSKRQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPAIQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSNGGKGK |
| RPL18 | N | 187 | Methanothermobacter Thermautotrophicus | MATGPRYKVPMRRRREARTDYHQRLRLLKSGKPRLVARKSNKHVRAQLVTLGPNGDDTLASAHSSDLAEYGWEAPTGNMPSAYLTGLLAGLRAQEAGVEEAVLDIGLNSPTPGSKVFAIQEGAIDAGLDIPHNDDVLADWQRTRGAHIAEYDEQLEEPLYSGDFDAADLPEHFDELRETLLDGDIEL |
| RPL18E | O | 116 | Methanothermobacter Thermautotrophicus | MSKTNPRLSSLIADLKSAARSSGGAVWGDVAERLEKPRRTHAEVNLGRIERYAQEDETVVVPGKVLGSGVLQKDVTVAAVDFSGTAETKIDQVGEAVSLEQAIENNPEGSHVRVIR |
| RPL19E | P | 149 | Methanothermobacter Thermautotrophicus | MTDLSAQKRLAADVLDVGKNRVWFNPERQGDIADAITREDVRELVDEGAIQAKDKKGNSRGRARERQKKRAYGHQKGAGSRKGKAGARQNSKEDWESRIRAQRTKLRELRDEGTLSSSQYRDLYDKAGGGEFDSVADLERYIDANHGDA |
| RPL21E | Q | 96 | Methanothermobacter Thermautotrophicus | MPSSNGPLEGTRGKLKNKPRDRGTSPPQRAVEEFDDGEKVHLKIDPSVPNGRFHPRFDGQTGTVEGKQGDAYKVDIVDGGKEKTIIVTAAHLRRQE |
| RPL22 | R | 155 | Methanothermobacter Thermautotrophicus | MGISYSVEADPDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFKQHNSGVGHKSKVDGWDAGRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAHKVGEQQGRKPRAMGRASAWNSPQVDVELILEEPEVED |
| RPL23 | S | 85 | Methanothermobacter Thermautotrophicus | MSWDVIKHPHVTEKAMNDMDFQNKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMDGEKKAVVRLSEDDDAQEVASRIGVF |
| RPL39E | 2 | 50 | Methanothermobacter Thermautotrophicus | MGKKSKATKKRLAKLDNQNSRVPAWVMLKTDREVQRNHKRRHWRRNDTDE |
| RPL24 | T | 120 | Methanothermobacter Thermautotrophicus | MSKQPDKQRKSQRRAPLHERHKQVRATLSADLREEYGQRNVRVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVEDVTLEKTDGEEVPRPLDTSNVRVTDLDLEDEKREARLESEDDSA |
| RPL24E | U | 67 | Methanothermobacter Thermautotrophicus | MPRTRECDYCGTDIEPGTGTMFVHKDGATTHFCSSKCENNADLGREARNLEWTDTARGEAGEAEDEA |
| RPL29 | V | 71 | Methanothermobacter Thermautotrophicus | MTVLHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGEEGDLQENE |
| RPL30 | W | 154 | Methanothermobacter Thermautotrophicus | MHALVQLRGEVNMHTDIQDTLEMLNIHHVNHCTLVPETDAYRGMVAKVNDFVAFGEPSQETLETVLATRAEPLEGDADVDDEWVAEHTDYDDISGLAFALLSEETTLREQGLSPTLRLHPPRGGHDGVKHPVKEGGQLGKHDTEGIDDLLEAMR |
| RPL31E | X | 92 | Methanothermobacter Thermautotrophicus | MSASDFEERVVTIPLRDARAEPNHKRADKAMILIREHLAKHFSVDEDAVRLDPSINEAAWARGRANTPSKIRVRAARFEEEGEAIVEAETAE |
| RPL32E | Y | 241 | Methanothermobacter Thermautotrophicus | MADNEEDVEAEEEYTELTDISGVGPSKAESLREAGFESVEDVRGADQSALADVSGIGNALAARIKADVGGLEVESETEAEVEEEGGEEAPDEDVETELQARGLTEKTPDLSDEDARLLTQRHRVGKPQFNRQDHHKKKRVSTSWRKPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFEEVRVHNVDDLEGVDGDTEAVRIASKVGARKRERIEEEAEDAGIRVLNPTYVEVEVSE |
| RPL37AE | Z | 92 | Methanothermobacter Thermautotrophicus | MASKSGKTGSSGRFGARYGRVSRRRVAEIESEMNEDHACPNCGEDRVDRQGTGIWQCSYCDYKFTGGSYKPETPGGKTVRRSIRAALSEDEE |
| RPL44E | 3 | 92 | Methanothermobacter Thermautotrophicus | MQMPRRFNTYCPHCNEHQEHEVEKVRSGRQTGMKWIDRQRERNSGIGNDGKFSKVPGGDKPTKKTDLKYRCGECGKAHLREGWRAGRLEFQE |
| RPL34E | 4 | 123 | Methanothermobacter Thermautotrophicus | MAQRITYRRRCSYNTRSNKVRKVKTPGGRLVAQYVKKVVNYTKCSEAGCNVALNGIAQVRPAEYATIARSAKTVSRVYGGELCHTCVRSRIIRAFLTEEVKIVKRKMISKPKTDKKKKRSQKK |
| RPL40E | 5 | 129 | Methanothermobacter Thermautotrophicus | MQIFVKTLTGKTITLDVEASDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGMEPTIAALAKKYNCEKKVCRDCYARLPPKATNCRKRKCGHSNSLRLKKKPKE |
| RPL30E | 6 | 104 | Methanothermobacter Thermautotrophicus | MVKKVTQDNIQSKLALVMRSGKATLGYKSTIKAIRNGTAKLVFISNNCPTVRKSEIEYYASLAQISIHHFVGSNVELGTACGKYHRCSTMAILDAGDSDILKTE |
| RPL14E | 7 | 126 | Methanothermobacter Thermautotrophicus | MVFNKFVQVGRVVYINYGADKGKLAVIVNIINQNRILIDGEHIVRQVIPIRRVHLTKFQIDNVELNQRTVLLKKKIAKFDLTKKYAETSFAKKQAIKTKRANLGDFDRFRVMVLKKKLARTSAKSK |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2012-01-04 Deposition Author(s): Ban, N. , Boehringer, D. , Crnkovic, A. , Godinic-Mikulcic, V. , Greber, B.J. , Ibba, M. , Weygand-Durasevic, I.