5T6R
Nmd3 is a structural mimic of eif5a, and activates the cpgtpase lsg1 during 60s ribosome biogenesis: 60s-nmd3 complex
PDB DOI: 10.2210/pdb5t6r/pdb
Classification: RIBOSOME Organism(s): Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C)
Deposited: 2016-09-01 Deposition Author(s): Frank, J. , Johnson, A.W. , Malyutin, A.G. , Musalgaonkar, S. , Patchett, S.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 4.2 Å
Nmd3 is a structural mimic of eif5a, and activates the cpgtpase lsg1 during 60s ribosome biogenesis: 60s-nmd3 complex
Frank, J. , Johnson, A.W. , Malyutin, A.G. , Musalgaonkar, S. , Patchett, S.
Primary Citation of Related Structures: 5T6R
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 60S ribosomal protein L15-A | A | 204 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MGAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFVIYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYWVNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGINKGHKFNNTKAGRRKTWKRQNTLSLWRYRK |
| 60S ribosomal protein L24-A | J | 155 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIAWTVLFRKHHKKGITEEVAKKRSRKTVKAQRPITGASLDLIKERRSLKPEVRKANREEKLKANKEKKKAEKAARKAEKAKSAGTQSSKFSKQQAKGAFQKVAATSR |
| 60S ribosomal protein L25 | K | 142 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYKVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTKKAYVRLTADYDALDIANRIGYI |
| 60S ribosomal protein L26-A | L | 127 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHPSKLVITKLHLDKDRKALIQRKGGKLE |
| 60S ribosomal protein L27-A | M | 136 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAKKVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEERHQAGKNQWFFSKLRF |
| 60S ribosomal protein L28 | N | 149 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MPSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPGYFGKVGMRYFHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDTLAAGYGKILGKGRIPNVPVIVKARFVSKLAEEKIRAAGGVVELIA |
| 60S ribosomal protein L29 | O | 59 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAKSKNHTAHNQTRKAHRNGIKKPKTYKYPSLKGVDPKFRRNHKHALHGTAKALAAAKK |
| 60S ribosomal protein L2-A | D | 254 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAKVVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKPGDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLLKAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAARRTGLLRGSQKTQD |
| 60S ribosomal protein L3 | E | 387 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL |
| 60S ribosomal protein L4-A | F | 362 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRPAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLKHD |
| 60S ribosomal protein L5 | G | 297 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYKGVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ |
| 60S ribosomal protein L6-A | H | 176 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDNTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEANLFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF |
| 60S ribosomal protein L7-A | I | 244 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLVKSMN |
| 60S ribosomal protein L30 | P | 105 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAPVKSQESINQKLALVIKSGKYTLGYKSTVKSLRQGKSKLIIIAANTPVLRKSELEYYAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA |
| 60S ribosomal protein L42-A | Q | 106 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MVNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHKKAKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKGQALQF |
| 60S ribosomal protein L43-A | R | 92 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAKRTKKVGITGKYGVRYGSSLRRQVKKLEIQQHARYDCSFCGKKTVKRGAAGIWTCSCCKKTVAGGAYTVSTAAAATVRSTIRRLREMVEA |
| Ribosomal Protein uL1 | S | 210 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
| 60S ribosomal protein L34-A | T | 121 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSALQGISTLRPRQYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIVKKVVKEQTEAAKKSEKKAKK |
| 60S ribosomal protein L35-A | U | 120 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPSLPKIKTVRKSIACVLTVINEQQREAVRQLYKGKKYQPKDLRAKKTRALRRALTKFEASQVTEKQRKKQIAFPQRKYAIKA |
| Maltose binding protein, 60S ribosomal export protein Nmd3 fusion | V | 917 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNSSSNNNNNNNNNNLGHHHHHHHHHHENLYFQGEFTPIDPHQHQNAATLLCCNCGTPIDGSTGLVMCYDCIKLTVDITQGIPREANISFCRNCERFLQPPGQWIRAELESRELLAICLRRLKGLTKVRLVDASFIWTEPHSRRIRIKLTVQGEAMTNTIIQQTFEVEYIVIAMQCPDCARSYTTNTWRATVQIRQKVPHKRTFLFLEQLILKHNAHVDTISISEAKDGLDFFYAQKNHAVKMIDFLNAVVPIKHKKSEELISQDTHTGASTYKFSYSVEIVPICKDDLVVLPKKLAKSMGNISQFVLCSKISNTVQFMDPTTLQTADLSPSVYWRAPFNALADVTQLVEFIVLDVDSTGISRGNRVLADITVARTSDLGVNDQVYYVRSHLGGICHAGDSVMGYFIANSNYNSDLFDGLNIDYVPDVVLVKKLYQRKSKKSRHWKLKRMAKEHKDIDASLDYNSRAQKQEMERAEKDYELFLQELEEDAELRQSVNLYKNREANVPPEEHEMDEDEDEDAPQINIDELLDELDEMTLEDGVENTPVESQQ |
| 60S ribosomal protein L37-A | W | 88 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MGKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA |
| 60S ribosomal protein L38 | X | 78 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAREITDIKQFLELTRRADVKTATVKINKKLNKAGKPFRQTKFKVRGSSSLYTLVINDAGKAKKLIQSLPPTLKVNRL |
| 60S ribosomal protein L39 | Y | 51 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MAAQKSFRIKQKMAKAKKQNRPLPQWIRLRTNNTIRYNAKRRNWRRTKMNI |
| Ubiquitin-60S ribosomal protein L40 | Z | 128 | Saccharomyces Cerevisiae , Saccharomyces Cerevisiae (Strain Atcc 204508 / S288C) | MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQLRPKKKLK |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 5S Ribosomal RNA | b | 121 | NA | GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUGGUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU |
| 5.8S Ribosomal RNA | c | 158 | NA | AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAUACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCCUUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2016-09-01 Deposition Author(s): Frank, J. , Johnson, A.W. , Malyutin, A.G. , Musalgaonkar, S. , Patchett, S.