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FASTA Sequence PDB Format mmCIF Format
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8RJB

Structure of the rabbit 80s ribosome stalled on a 2-tmd rhodopsin intermediate in complex with sec61-ramp4

PDB DOI: 10.2210/pdb8rjb/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: 2.69243 Å

8rjb
Literature

Structure of the rabbit 80s ribosome stalled on a 2-tmd rhodopsin intermediate in complex with sec61-ramp4

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

Primary Citation of Related Structures: 8RJB


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 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
60S ribosomal protein L38 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
Protein transport protein Sec61 subunit beta 2 96 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS
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
Ribosomal protein L3 W 403 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA
Ribosomal_L23eN 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
Protein transport protein Sec61 subunit gamma 3 68 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIPINNIIVGG
60S ribosomal protein L27 Z 136 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MGKFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPRKVTAAMGKKKIAKRSKIKSFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF
Ribosomal protein L8 A 257 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPGDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAARRTGRLRGTKTVQEKEN
Nascent chain B 229 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVTASAWSHPQFEKGGGSGGGSGGSAWSHPQFEKAGGSAGSGGGSAGGSALSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLFGSAGSGGGSAGGGSAAEPWQFSMLAAYMFLLIMLGFPINCLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGMPGPTPSGTNVGSSGRSPSV
Large ribosomal subunit protein uL4 C 425 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLAPGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAAKSDPKEAPAKKKPVVGKKVKKPRAVGIKQKKKPVVGRKAAAAKKPAADKKAADKRAGPEDKKPAA
Ribosomal_L18_c domain-containing protein D 297 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
60S ribosomal protein L6 E 291 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYSRSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTGPLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEKEKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF
Stress-associated endoplasmic reticulum protein 4 66 Bos Taurus , Canis Lupus Familiaris , Oryctolagus , Oryctolagus Cuniculus , Sus Scrofa MVAKQRIRMANEKHSKNITQRGNVAKTSRNAPEEKASVGPWLLALFIFVVCGSAIFQIIQSIRMGM

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.