PDBi (Protein Data Bank in India)

All in One Protein Databank
Home About Help Resources External Links Contact Us
Advanced Search
FASTA Sequence PDB Format mmCIF Format
FASTA Sequence PDB Format PDB Format(gz) PDBx/mmCIF Format PDBx/mmCIF Format(gz) PDBML/XML Format Validation Full PDF Validation CIF

8RJD

Structure of the rabbit 80s ribosome stalled on a 2-tmd rhodopsin intermediate in complex with sec61-trap, open conformation 2

PDB DOI: 10.2210/pdb8rjd/pdb

Classification: RIBOSOME
Organism(s): Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa

Deposited: 2023-12-20
Deposition Author(s): Hegde, R.S. , Lewis, A.J.O.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.78574 Å

8rjd
Literature

Structure of the rabbit 80s ribosome stalled on a 2-tmd rhodopsin intermediate in complex with sec61-trap, open conformation 2

Hegde, R.S. , Lewis, A.J.O.

Primary Citation of Related Structures: 8RJD


Proteins
Molecule Chains Sequence Length Organism Sequence
Protein transport protein Sec61 subunit alpha isoform 1 1 476 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MAIKFLEVIKPFCVILPEIQKPERKIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFGMIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGISLFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLPNLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSNLYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFGSVLEDPVHAVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTAAAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF
60S ribosomal protein L27a A 148 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MPSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFCPTVNLDKLWTLVSEQTRVNAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGVGGACVLVA
60S ribosomal protein L29 B 226 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQANNAKAMAARAEAIKALVKPKEVKPTIPKGVSRKLHRLAYIAHPKLGRRARARIARGLRLSRPQTKAKAKTEPQIKGKVKAQIKAQAQAQIKSKGKGKAQAETKPKAQAETKPKAQAQAKPKAQAQGKPKAQAQGKPKAQAQAKPKAQAQAKPKAQAQTKPKAQATPA
Large ribosomal subunit protein eL30 C 115 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MVAAKKTKKSLESINSRLQLVMKSGKYVLGYKQSLKMIRQGKAKLVILANNCPALRKSEIEYYAMLAKTGVHHYSGNNIELGTACGKYYRVCTLSIIDPGDSDIIRSMPEQTGEK
60S ribosomal protein L31 D 125 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MAPAKKGGEKKKGRSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNKAVWAKGIRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNLQTVNVDEN
Ribosomal protein L32 E 135 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHMLPSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPNARLRSEENE
60S ribosomal protein L35a F 110 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MSGRLWCKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTPGGKPNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI
60S ribosomal protein L34 G 116 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MVQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLMRLSKTKKHVSRAYGGSMCAKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQKA
60S ribosomal protein L35 H 123 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MAKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVINQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEESLKTKKQQRKERLYPLRKYAVKA
60S ribosomal protein L36 I 105 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MALRYPMAVGLNKGHKVTKNVSKPRHSRRRGRLTKHTKFVRDMIREVCGFAPYERRAMELLKVSKDKRALKFIKKRVGTHIRAKRKREELSSVLAAMRKAAAKKD
Ribosomal protein L37 J 97 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MTKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGRMRHLKIVYRRFRHGFREGTTPKPKRAAVAASSSS
Protein transport protein Sec61 subunit beta 2 96 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS
Large ribosomal subunit protein eL38 K 70 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MPRKIEEIKDFLLTARRKDAKSVKIKKNKDNVKFKVRCSRYLYTLVITDKEKAEKLKQSLPPGLAVKELK
60S ribosomal protein L39-like L 51 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MSSHKTFRIKRFLAKKQKQNRPIPQWIWMKTGNKIRYNSKRRHWRRTKLGL
eL40 M 102 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MGDPESGGCIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKKVK
60S ribosomal protein L41 N 25 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MRAKWRKKRMRRLKRKRRKMRQRSK
60S ribosomal protein L36a-like O 106 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIFRKKAKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
60S ribosomal protein L37a P 92 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MAKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRAVGIWHCGSCMKTVAGGAWTYNTTSAVTVKSAIRRLKELKDQ
60S ribosomal protein L28 R 137 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MSAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGVEPAADGKGVVVVMKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKNKYHPDLRMAAIRRASAILRSQKPVMVKRKRTRPTKSS
60S ribosomal protein L18a S 176 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MKASGTLREYKVVGRCLPTPKCRTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGEIVYCGQVFEKSPLRVKNFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRRPAVKQFHDSKIKFPLPHRVLRRQHKPRFTTKRPNTFF
60S ribosomal protein L21 T 160 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKGMPHKCYHGKTGRVYNVTQHAVGIVVNKQVKGKILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHFVRTNGKEPELLEPIPYEFMA
Protein transport protein Sec61 subunit gamma 3 68 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIPINNIIVGG
Ribosomal protein L3 W 403 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA
Large ribosomal subunit protein uL23 N-terminal domain-containing protein X 156 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MAPKAKKEAPAPPKVEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII
Ribosomal protein L26 Y 145 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEETIEKMQE
60S ribosomal protein L27 Z 136 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MGKFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRSKIKSFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF
Stress-associated endoplasmic reticulum protein 4 66 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MVAKQRIRMANEKHSKNITQRGNVAKTSRNAPEEKASVGPWLLALFIFVVCGSAIFQIIQSIRMGM
Translocon-associated protein subunit alpha 5 286 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MRVLPRLLLLLLLAFPAAVLLRGGPGGSLVAAQDLTEDEETVEDSIIEDEDDEAEVEEDEPTDLAEDKEEEDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESLDASFRYPQDYQFYIQNFTALPLNTVVPPQRQATFEYSFIPAEPMGGRPFGLVINLNYKDLNGNVFQDAVFNQTVTIIEREDGLDGETIFMYMFLAGLGLLVVVGLHQLLESRKRKRPIQKVEMGTSSQNDVDMSWIPQETLNQINKASPRRLPRKRAQKRSVGSDE
Translocon-associated protein subunit beta 6 183 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MRLLASVLLALFAVSHAEEGARLLASKSLLNRYAVEGRDLTLQYNIYNVGSSAALDVELSDDSFPPEDFGIVSGMLNVKWDRIAPASNVSHTVVLRPLKAGYFNFTSATVTYLAQEDGPVVIGFTSAPGQGGILAQREFDRRFSPHFLDWAAFGVMTLPSIGIPLLLWYSSKRKYDTPKSKKN
Translocon-associated protein subunit gamma 7 185 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MAPKGGSKQQSEEDLLLQDFSRNLSAKSSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAVLYSVMTLVSTYLVAFAYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDERILWKKNEVADYEATTFSIFYNNTLFLVLVIVASFFILKNFNPTVNYILSISASSGLIALLSTGSK
Translocon-associated protein subunit delta 8 173 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MAALASLGALALLLLSSLSCCSAEACVEPQITPSYYTTSDAVISTETVFIVEISLTCKNRVQNMALYADVSGKQFPVTRGQDVGRYQVSWSLDHKSAHAGTYEVRFFDEESYSLLRKAQRNNEDISIIPPLFTVSVDHRGTWNGPWVSTEVLAAAIGLVIYYLAFSAKSHIQA
Calnexin 9 593 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MEGKWLLCMLLVLGTTIVQAHEGHDDDMIDIEDDLDDVIEEVEDSKSKPDTSAPTSPKVTYKAPVPTGEVYFADSFDRGTLSGWILSKAKKDDTDDEIAKYDGKWEVDEMKETKLPGDKGLVLMSRAKHHAISAKLNKPFLFDTKPLIVQYEVNFQNGIECGGAYVKLLSKTPELNLDQFHDKTPYTIMFGPDKCGEDYKLHFIFRHKNPKTGVYEEKHAKRPDADLKTYFTDKKTHLYTLILNPDNSFEILVDQSIVNSGNLLNDMTPPVNPSREIEDPEDQKPEDWDERPKIPDPDAVKPDDWNEDAPAKIPDEEATKPDGWLDDEPEYVPDPDAEKPEDWDEDMDGEWEAPQIANPKCESAPGCGVWQRPMIDNPNYKGKWKPPMIDNPNYQGIWKPRKIPNPDFFEDLEPFKMTPFSAIGLELWSMTSDIFFDNFIVCGDRRVVDDWANDGWGLKKAADGAAEPGVVGQMIEAAEERPWLWVVYVLTVALPVFLVILFCCSGKKQSSPVEYKKTDAPQPDVKEEEEEKEEEKDKGDEEEEGEEKLEEKQKSDAEEDGGTASQEEDDRKPKAEEDEILNRSPRNRKPRRE

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
P-site tRNA q 76 NA GUCUCCGUAGUGUAGCGGUUAUCACGUUCGCCUAACACGCGAAAGGUCCUCGGUUCGAAACCGGGCGGAAACACCA
5S rRNA u 120 NA GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
5.8S rRNA v 156 NA CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2023-12-20
Deposition Author(s): Hegde, R.S. , Lewis, A.J.O.