Cryo-EM reconstruction of the small subunit of the chloroplast ribosome

2024-05-15 REL PDBe PDBe PDBe 2016-12-10 2017-01-11 2017-01-11 2024-05-15 Cryo-EM reconstruction of the small subunit of the chloroplast ribosome Bieri P Leibundgut M chloroplast, translation, ribosome, cryo-EM Bieri P Leibundgut M Saurer M Boehringer D Ban N The complete structure of the chloroplast 70S ribosome in complex with translation factor pY. EMBO J. UK 36 475 486 2017 28007896 doi:10.15252/embj.201695959 1460-2075 0897 EMJODG 5mmj FULLOVERLAP Chloroplast 70S ribosome Chloroplast 70S ribosome 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Spinacia oleracea leaf chloroplast 2.4 50S ribosomal protein L31 Spinacia oleracea 0.014748200999999999 1 LEVO MVLTLSNQFLAKIPATPKTLTLPKTSSSTLRPQWSCRKSDIHPEFREDAKVYCNGELVMTTGGTQKDYTVEVWSGNHPFY LGNRSALLLDADQVEKFRKKYGELTQIMEIPVLKGEIILPPKKKSKAKKK A0A0K9R0R6 plastid ribosomal protein bS1c Spinacia oleracea 0.014826253

Residues were built as poly-alanine and deposited as UNK.

1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) 16S ribosomal RNA Spinacia oleracea 0.48346649999999997 1 UCUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGGACGGGAAGUGGUGU UUCCAGUGGCGGACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGAACAACAGCUGGAAACGGCUGCUAAUACC CCGUAGGCUGAGAAGCAAAAGGAGGAAUCCGCCCGAGGAGGGGCUCGCGUCUGAUUAGCUAGUUGGUGAGGUAAUAGCUU ACCAAGGCGAUGAUCAGUAGCUGGUCCGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGA GGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGGAGGCAGAAGGCCCACGGGUCGU GAACUUCUUUUCCCGGAGAAGAAGCAAUGACGGUAUCCGGGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUA AGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUUAAGUCCGCCGUCAAAUCC CAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGU GAAAUGCGUAGAGAUCGGAAAGAACACCAACGGCGAAAGCACUCUGCUGGGCCGACACUGACACUGAGAGACGAAAGCUA GGGGAGCGAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGCGCUGUGCGUAUCGACCCGUGC AGUGUUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCC CGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUACCAGGGCUUGACAUGCCGCGAAUCCUCU UGAAAGAGAGGGGUGCCUUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUU AAGUCCCGCAACGAGCGCAACCCUCGUGUUUAGUUGCCAACGUUGAGUUUGGAACCCUGAACAGACUGCCGGUGAUAAGC CGGAGGAAGGUGAGGAUGACGUCAAGUCAUCAUGCCCCUUAUGCCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAA GGGUCGCGAUCCCGCGAGGGUGAGCUAACCCCAAAAACCCGUCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGA AGCCGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACAC UAUGGGAGCUGGCCAUGCCCGAAGUCGUUACCUUAACCGCAAGGAGGGGGAUGCCGAAGGCAGGGCUAGUGACUGGAGUG AAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU AJ400848.1 30S ribosomal protein S2, chloroplastic Spinacia oleracea 0.026736140999999998 1 LEVO MTRRYWNINLEEMMEAGVHFGHGTRKWNPRMSPYISAKCKGIHIINLTRTARFLSEACDLVFDASSRGKQFLIVGTKNKA ADSVARAAIRARCHYVNKKWLGGMLTNWSTTETRLHKFRDLRMEQTAGRLARLPKRDAAVVKRQLSHLQTYLGGIKYMTG LPDIVIIVDQQEEYTALRECITLGIPTICLIDTNCNPDLADISIPANDDAIASIRLILTKLVFAICEGRSSYIRNP P08242 30S ribosomal protein S3, chloroplastic Spinacia oleracea 0.024965156 1 LEVO MGQKINPLGFRLGTTQSHYSLWFSQPKNYAEGLQEDQKIRDCIKNYVQKNTKTSSGVEGIARIEIQKRIDLIQVIIHMGF PKLLIENRPQGVEDLKINVQKELNCVNRKLNIAITRIAKPYGDPNILAEFIAGQLKSRVSFRKAMKKAIELTEQADTKGI QIQIAGRIDGKEIARIEWIREGRVPLQTIRAKIDYCAYTVRTIYGVLGIKIWIFMGEE P09595 30S ribosomal protein S4, chloroplastic Spinacia oleracea 0.023454530999999997 1 LEVO MSRYRGPRFKKIRRLGALPGLTNKRPRAGSDLRNQSRSGKRSQYRIRLEEKQKLRFHYGITERQLLKYVRIARKAKGSTG QVLLQLLEMRLDNILFRLGMAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMARDEQKSIALIQNSLDLSPREEL PKHLTLNPFPYKGLVNQIIDSKWVGLKINELLVVEYYSRQT P13788 30S ribosomal protein S5, chloroplastic Spinacia oleracea 0.033626363

Residues 122-150 were built as poly-alanine and deposited as UNK.

1 LEVO MATTATTTPSATSLTTLHRRIPLFPTTTTLLSLSSSSKPLFLSLSSTRSFPTHLYCIKKDDIDITFFEQDNPDEEITFDP PEKPEGYIPPRAVDEPPFESEEEIALAYEELYGAAYSGESLLGNDVYAMDSKIKKATGFGSKSKKEKIRDGFEENVVQVR RVTKVVKGGKHMRFRAIVVVGDKKGQVGVGVGKAKEVVSAVQKAAVDARRNIITVPMTKYLTFPHRNEADYGAARVMLRP AAPGTGVIAGGAVRTVLEMAGVENALGKQLGSNNALNNARATIVAVQTMRQFSDVARDRGIPMEELWK Q9ST69 plastid ribosomal protein bS6c Spinacia oleracea 0.023510664 1 LEVO MATFSLTSTLPSSSPTTSLHSIPKPKLKPSTINFTHNLNPFNPNLKPSRHHYLSNYGPYVKAIALDFSGSFFEGGFGGLD EDPPSTPPAGLAVEEKPEPQCPPGLRQYETMAVLRPDMTEDERLTLTQKYEELLVAGGAMYVEVFNRGVIPLAYSIKRKN KAGETNNYLDGIYLLFTYFTKPESISPLEAALVTDDDVIRSSSFKIRKRKY A0A0K9R0H2 30S ribosomal protein S7, chloroplastic Spinacia oleracea 0.017378309 1 LEVO MSRRGTVEEKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQILYRAVKKIQQKTETNPLSVLRQAIRGVTPDIAVKARRV GGSTHQVPIEIGSTQGKALAIRWLLGAARKRPGRNMAFKLSSELVDAAKGSGDAVRKKEETHRMAEANRAFAHFR P82129 30S ribosomal protein S8, chloroplastic Spinacia oleracea 0.015527255999999998 1 LEVO MGKDTIADIITCIRNADMNRKGTVRIVSTNITENIVKILLREGFIENARKHQERNKYFLVLTLRHRRNKKGPYLNTFHLK RVSRPGLRIYSNYQRIPRILGGMGIAILSTSRGIMTDREARLEGIGGEILCYIW P09597 plastid ribosomal protein uS9c Spinacia oleracea 0.022415057 1 LEVO MAVSISSLTSSFASLSFTSNLTPKPQTLPMARTKPFSLSNPAVVKPLVITATSATAPVEVAETADLEKFVKSRLPGGFAA QTVIGTGRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYVKTPLATLGYETNYDVFVKAHGGGLSGQAQAISLG VARALLKVSASHRAPLKQEGLLTRDSRIVERKKPGLKKARKAPQFSKR A0A0K9RY17 plastid ribosomal protein uS10c Spinacia oleracea 0.021440538999999998 1 LEVO MATSSISAALLSPLTLRNASSSSTKQDFSTLSSLNLRRTLTPTLQSGHTLSNSSNFATFAAPGALEVLETSPDSFEDGSE TSKISIAADSDQMAPKQKIRIKLRSYWVPLIEDSCKQIMDAARTTNAKIMGPVPLPTKKRIYCVLKSPHVHKDARFHFEI RTHQRLIDILYPTAQTIDSLMQLDLPAGVDVEVKL A0A0K9RWE7 30S ribosomal protein S11, chloroplastic Spinacia oleracea 0.014927550999999999 1 LEVO MAKPIPKIGSRRNGRISSRKSARKIPKGVIHVQASFNNTIVTVTDVRGRVVSWASAGTCGFRGTKRGTPFAAQTAAGNAI RTVVEQGMQRAEVMIKGPGLGRDAALRAIRRSGILLSFVRDVTPMPHNGCRPPKKRRV P06506 30S ribosomal protein S12, chloroplastic Spinacia oleracea 0.013794261 1 LEVO MPTIKQLIRNTRQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQEHSVV LVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQQGRSKYGVKKPK P62128 plastid ribosomal protein uS13c Spinacia oleracea 0.019310641 1 LEVO MAHTLATPVAPSVSLICNTKLSVSLSSSSLAFRPVNPKNGGGLSIKCVRVGNVEIPNNKRVEYSLQYIHGIGRSRARQIL CDLTLENKLTKELSEDELLQVRDEVTKYMIEGDLRRFNAIAIRRLKEIQCYRGVRHIQGLPCRGQRTKNNCRTLKRGKRV QIAGKKKPPGPK A0A0K9R024 30S ribosomal protein S14, chloroplastic Spinacia oleracea 0.011809832 1 LEVO MARKSLIQREKKRRNLEQKYHLIRRSSKQEIRKVTSLSDKWEIHGKLQSPPRNSAPARLHRRCFLTGRPRANIRDFGLSG HILREMVHTCLLPGATRSSW P06507 30S ribosomal protein S15, chloroplastic Spinacia oleracea 0.010778763 1 LEVO MKKNSFISVISDEKKEENKGSVEFQVFCFTNKIRRLTLHLELHKKDYSSQRGLRKTLGKRQRLLAYLLKINGVRYKELIS KLNIRELKTR Q9M3I4 30S ribosomal protein S16, chloroplastic Spinacia oleracea 0.010454236999999998 1 LEVO MVKLRLKRCGRKQRAVYRIVAIDVRSRREGRDLQKVGFYDPIKSQTYLNVPAILDFLEKGAQPTETVYDILKRAEVFKEF RLNQTKFN P28807 plastid ribosomal protein uS17c Spinacia oleracea 0.018151936 1 LEVO MSLSFSLLKPPLSSSNPNPFLHGTTTKLSLLPSFSALSLSSSPPSSSTTYTFPVIKAMRSMQGKVICATNDKTVNVEVVR LAPHPKYKRRVRKKKKYQAHDPDNQFKVGDWVQLDKCRPISKTKTFLAVAPEGRQSSATRPKPIQAASDELGIPLESQVE GDKTV A0A0K9RRR0 30S ribosomal protein S18, chloroplastic Spinacia oleracea 0.012079137 1 LEVO MDKSKRPFIKSKRSFRRRLPPIQSGDRIDYRNMSLISRFISEQGKILSRRVNRLTLKQQRLITSAIKQARILSLLPFLNN EKQFERTESTTRTANFRTKNK Q9M3K7 30S ribosomal protein S19 alpha, chloroplastic Spinacia oleracea 0.0106325 1 LEVO MTRSLKKNPFVANHLLRKIEKLNKKAEKEIIVTWSRASTIIPTMIGHTIAIHNGREHLPIYITDRMVGHKLGEFAPTLNF RGHAKNDNKSRR P06508 plastid ribosomal protein bS20c Spinacia oleracea 0.020147291 1 LEVO MAAISMACVSSQCLSISSKLHNLSFSSTQFPNSSLKPLTFSANLSQPLFSQGCSSLGSFQRRGFSVVCEVATLKKADSAA KRTRQAETRRLRNKARKSEVKTRMRKVFEALDALKKKSGASTEELVPIDNLIAEAYSAIDKAVVKGTLHRNTAARRKSRL ARNKKVVEIHHGWYTPSLAPTNV plastid ribosomal protein bS21c Spinacia oleracea 0.02061615 1 LEVO MASTSSLLNFLSPLFPSNTSLPPSSNPKFPNPNSLSSQQNSISISSKKHENAAIAKKEEYPGDLMAVVCPSLAFSNTLYF RSAYNVQVLVDDNENEERLLNRFRREVMRAGVIQECKRRRYFENKQEEKKRKHREAAKRNSRRRRGPFRGPFPGKEEATK VDKKEDDGDNWDMPEGGAPF A0A0K9RHF9 30S ribosomal protein 2, chloroplastic Spinacia oleracea 0.028327863 1 LEVO MATISSILPCHGLLQHCSSSSSSSKPKFSSQNLVQLQSFSNGFGLKLKTRVSTNPPLLKVRAVVTEETSSSSTASSSSDG EGARRLYVGNIPRNLNNDELRTIVEEHGAIEIAEVMYDKYSGRSRRFGFVTMKTVEDANAVIEKLNDTEIGGRKIKVNIT EKPLEGMDIATTQAEDSQFVESPYKVYIGNLAKTVTNELLKDFFSEKGKVLGAKVQRTPGTSKSNGFGFVSFSSEEEVEA AIQALNNSVLEGQKIRVNKA P82277 30S ribosomal protein 3, chloroplastic Spinacia oleracea 0.020312749999999997 1 LEVO MLSMAVQPNINAIAKPSIYQSPKLSLKPFKTPAFANPKPFFSSPSFSQLKKKNNWSLFVAPETISDVAIMGNEVDIDDDL LVNKEKLKVLVKPMDKPRLVLKFIWMEKNIGLALDQTIPGHGTVPLSPYYFWPRKDAWEELKVLLENKPWISQKQMIILL NQATDIINLWQQSGGNLAS P82412 30S ribosomal protein S31, chloroplastic Spinacia oleracea 0.010602075999999998 1 LEVO MASLLLGTPSMACHSVSFSFSHSQSVAGVSLSSPPTLSLSSSVSTSPALPLIYCGRGDRKTAKGKRFNHSFGNARPKNKN KGRGPPKAPIFPKGDPSQKED P47910 Ribosome-binding factor PSRP1, chloroplastic Spinacia oleracea 0.033799266 1 LEVO MATLCTSAINMNPNLTNSLSNSINLSSTPTNLSSLRSTFTNSCSLGLNVAVKSVQISRNKPNVVCMSWDGPLSSVKLILQ GRNLEVSDNVRSHVEDKVGKSVAKHSHLVREVDVRLSARGGDLSKGPKLRRCEVTLFTKRHGVIRAEEDAESLYSSIDLV SSIIQRKLRKIKDKVSDHGRHMKGFNRSKVRDPEPVRITREEVLEEVESAPAPVSVEDDDFIEEVVRTKYFDMPPLTITE AVEQLENVDHDFYAFRNEETGDINILYKRKEGGYGLIIPKDGKTEKLESLPVQTDKQPSFAE P19954 MAGNESIUM ION 2.4305e-05 185 MG singleParticle particle 0.12 7.6 25.0 Tris-HCl Tris hydrochloride 25.0 KCl Potassium chloride 25.0 Mg(CH3COO)2 Magnesium acetate 2.0 DTT Dithiothreitol 0.05 Spermine 2.0 Spermidine Quantifoil R2/2 COPPER CARBON CONTINUOUS GLOW DISCHARGE ETHANE-PROPANE 100 278 FEI VITROBOT MARK I FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 3.5 59000.0 FEI TITAN KRIOS AUTOGRID HOLDER FEI FALCON II (4k x 4k) INTEGRATING 2-8 2796 20.0 1 326094 EMD-2847 C1 3.6 FSC 0.143 CUT-OFF RELION 1.4 127031 PROJECTION MATCHING RELION 1.4 PROJECTION MATCHING RELION 1.4 RELION 1.4 emd_3532.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 444.8 444.8 444.8 90.0 90.0 90.0 X Y Z -0.10384296 0.34530732 0.0009308014 0.010387902 1.39 1.39 1.39 0.06 AUTHOR ::::EMDATABANK.org::::D_1200002691:::: Cryo-EM reconstruction of the 30S small subunit of the chloroplast ribosome OTHER RECIPROCAL 111.599999999999994