6P5N: Mammalian 80S ribosome

Structure of a mammalian 80S ribosome in complex with a single translocated Israeli Acute Paralysis Virus IRES and eRF1. Determined by electron microscopy at 3.2 Å resolution. Released 25 Sept 2019.

Method
Electron microscopy
Resolution
3.2 Å
Organisms
Oryctolagus cuniculus, Homo sapiens, Israeli acute paralysis virus
Chains
82
Atoms
219,295
Mol. weight
3460.27 kDa
Released
25 Sept 2019

Explore 6P5N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P5N contains 499 α-helices and 585 β-strands across 77 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain a: 3 helices, 6 β-strands

ElementResiduesLengthSheet
β-strand471151
β-strand501107
α-helix52-609
β-strand681152
α-helix73-764
β-strand791151
α-helix81-9414
β-strand98-1025152
β-strand107-1104152
Chain Aa: 7 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix8-103
β-strand29122
β-strand31122
α-helix42-487
β-strand72-73223
α-helix75-806
α-helix84-929
α-helix971
β-strand981106
α-helix991
β-strand100-102324
β-strand110-111223
β-strand123-126424
β-strand128-129223
α-helix131-1399
β-strand143-146424
Chain AA: 8 helices, 19 β-strands
ElementResiduesLengthSheet
α-helix6-105
β-strand18133
α-helix30-323
α-helix34-374
β-strand40-491034
β-strand58-63634
β-strand72-77634
α-helix781
β-strand79135
β-strand83136
β-strand87-91534
β-strand101-103334
β-strand113-114234
β-strand116137
β-strand126137
β-strand136-138338
β-strand146-149438
β-strand155-158438
β-strand163-166434
α-helix1681
β-strand169135
α-helix182-1898
β-strand193133
α-helix201-2033
β-strand224-225239
α-helix229-2302
β-strand237-238239
Chain Ab: 8 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix12-187
α-helix22-243
α-helix37-4812
α-helix51-533
α-helix55-6410
α-helix66-7510
α-helix91-999
α-helix108-1147
Chain AB: 17 helices, 21 β-strands
ElementResiduesLengthSheet
α-helix9-102
α-helix32-343
α-helix40-412
β-strand42-43244
β-strand45-591545
β-strand71-801045
α-helix82-832
β-strand84-951246
β-strand98-106946
α-helix112-1154
α-helix116-1183
α-helix134-1374
α-helix143-1464
α-helix148-1514
β-strand159-165746
α-helix178-1792
β-strand180-184546
β-strand185-186244
α-helix190-19910
β-strand204-205246
α-helix207-2104
β-strand216-222745
β-strand228-229247
α-helix231-2344
α-helix237-2404
α-helix262-2632
β-strand270-271247
β-strand276-283845
β-strand286-287245
β-strand292-294348
β-strand297-299348
β-strand320149
β-strand324149
β-strand330-334545
β-strand344-348545
α-helix361-3633
β-strand365-368445
α-helix382-3898
Chain Ac: 4 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix11-2414
β-strand26-29450
α-helix32-398
β-strand45-48450
α-helix54-6714
β-strand70-73450
α-helix78-847
β-strand93-98650
Chain AC: 20 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand7-11553
β-strand17-23753
α-helix26-294
α-helix34-4411
α-helix45-473
β-strand65-66254
β-strand77-78254
α-helix79-813
α-helix100-1012
α-helix104-1063
α-helix117-13216
α-helix134-1385
β-strand154153
α-helix164-17310
α-helix177-18610
β-strand188-189255
α-helix193-1953
β-strand201-202255
β-strand208-211456
α-helix217-2215
β-strand228-231456
β-strand234156
β-strand250-252356
β-strand253153
α-helix254-2585
α-helix260-2634
α-helix278-2825
α-helix289-2946
α-helix296-3005
α-helix303-3053
α-helix322-3287
α-helix331-36232
Chain Ad: 4 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand22-28757
α-helix29-335
α-helix38-403
α-helix42-5615
β-strand62-64357
α-helix66-727
β-strand74158
β-strand76158
β-strand83-921057
β-strand102-108757
β-strand120-122357

69 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
28S rRNA5RNA3594Oryctolagus cuniculus
5S rRNA7RNA119Oryctolagus cuniculus
5.8S rRNA8RNA156Oryctolagus cuniculus
uL2AAprotein257Oryctolagus cuniculusG1TT27 (AlphaFold model)
uL3ABprotein402Oryctolagus cuniculusG1TL06 (AlphaFold model)
uL4ACprotein392Oryctolagus cuniculusG1SVW5 (AlphaFold model)
uL18ADprotein297Oryctolagus cuniculusP19949 (AlphaFold model)
eL6AEprotein291Oryctolagus cuniculusG1SKF7
L30AFprotein249Oryctolagus cuniculusG1SV32
eL8AGprotein242Oryctolagus cuniculusG1STW0
uL6AHprotein192Oryctolagus cuniculusG1SWI6
uL16AIprotein214Oryctolagus cuniculusB7NZQ2

70 more molecules are not listed.

Sequence of entity 1 (5), FASTA
>6P5N_1 28S rRNA (chains 5)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAA
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCCCGCGGCGGGGCGCGGGAAAUGUGGCGUACGGAAGACCCACUCCCCGGCGC
CGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCGGUAGCG
GCCCCCGGCGCGCCGGGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCAGCCCAA
AGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAACAAGUA
CCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAACCGUUA
AGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGCGGGUCC
GGCCGUGCCGGCGGGGCGGAUCUCCCGCUCCCGUCGGCGGGGGACCGCCCCCCGGCCGGC
GACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCGGGACG
GCUGGGAAGGCCCGGCGGGGAAGGUGGCCCGGGGGCCCCGGGUGUUACAGCCCACCCGGC
AGCAGCAGCUCGCCGAAUCCCGGGGCCGAGGGAGCGAGACCUGUGUCGCCGCGCUCUCCC
CCCUGGGGGGGCCGGGCCACCCCUCCCACGGCGCGACCGCUGGGGCGGACUGUCCAGUGC
GCCCCGGGCGGGUCGCGCCGUCGGGCCCGGGGGGCCACGCGUCCCCCGCGAGCGCACGGG
GUCGGCGGCGAUGUCGGCUACCCACCCGACCCGUCUUGAAACACGGACCAAGGAGUCUAA
CACGUGCGCGAGUCGGGGGCUACGAAAGCCGCCGUGGCGCAAUGAAGGUGAAGGCCGGCG
CCGCCGGCCGAGGUGGGAUCCCGAGGCCUUCCAGUCCGCCGAGGGCGCACCACCGGCCCG
UCUCGCCCGCCGCGCCGGGGAGGUGGAGCACGAGCGCACGUGUUAGGACCCGAAAGAUGG
UGAACUAUGCCUGGGCAGGGCGAAGCCAGAGGAAACUCUGGUGGAGGUCCGUAGCGGUCC
UGACGUGCGAAUCGGUCGUCCGACCUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUA
GUAGCUGGUUCCCUCCAAAGUUUCCCUCAGGAUAGCUGGCGCUCUCCGCAGUUUUAUCCG
GUAAAGCGAAUGAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUA
AAUGGGUAAGAAGCCCGGCUCGCUGGUGUGGAGCCGGGCGUGGAAUGCGAGUGCCUAGUG
GGCCACUUUUGGUAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGC
CCGAUGCCGACGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGAUGG
UGGCCAUGGAAGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUA
GCCCUGAAAAUGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCUGGCAGUCGG
CAGAGCGAGAAAGAGAGUGGCGCGGACGCUACGCCGCGACGAGUAGGAGGGCCGCUGCGG
UGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGCCGCAGGUGCAGAUCUUGGUG
GUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAGUGGAGAAGGGUUCCAUGUGA
ACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGGCGAGCGCCGUUCCGAAGGGA
CGGGCGAUGGCCUCCGUUGCCCUCAGCCGAUCGAAAGGGAGUCGGGUUCAGAUCCCCGAA
UCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGCGGUAACGCGACCGAUCCCGG
AGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUUGUGAAGGGCAGGGCGCCCUG
GAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAAGCGUCGCGGUUCCGGCGGCG
UCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGAGGGUGUAAAUCUCGCGCCGG
GCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGCCUCUGGCAUGUUGGAACAAU
GUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGG
GCUGGCAGCCGACUUAGAACUGGUGCGGACCAGGGGAAUCCGACUGUUUAAUUAAAACAA
AGCAUCGCGAAGGCCCGCGGCGGGUGUUGACGCGAUGUGAUUUCUGCCCAGUGCUCUGAA
UGUCAAAGUGAAGAAAUUCAAUGAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCU
UAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUGAACGAGAUU
CCCACUGUCCCUACCUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAU
CAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGA
GAGGUGUAGAAUAAGUGGGAGGCCCGGGCCGCCGGUGAAAUACCACUACUCUGAUCGUUU
UUUCACUGACCCGGUGAGGCGGGGGGGCGAGCCGGGCUCUCGCUUCUGGCGCCAAGCGCC
CGGCCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCG
GUACACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCU
CCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCG
UGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAA
AGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUG
AUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGU
UCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUAC
CCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUU
CAGACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGG
AUUAUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGGAACGAUAGCGCCGGAGCC
UCGGUUGGCCUCGGAUAGCCGGUCCCCCGCCGGGGUCCGGUGCGGAGAGCCCUUCGUCCC
GGGAAACGGGGCGGCCGGAAAGGGGGCCGCCCUCUCGCCCGUCACGCACCGCACGUUCGU
GGGGAACCUGGCGCUAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGGUUUCGUACGU
AGCAGAGCAGCUGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACAAGGGUUUGU
Sequence of entity 2 (7), FASTA
>6P5N_2 5S rRNA (chains 7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCU
Sequence of entity 3 (8), FASTA
>6P5N_3 5.8S rRNA (chains 8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU
Sequence of entity 4 (AA), FASTA
>6P5N_4 uL2 (chains AA)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN
Sequence of entity 5 (AB), FASTA
>6P5N_5 uL3 (chains AB)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 6 (AC), FASTA
>6P5N_6 uL4 (chains AC)
AAGRRGAWLSPLPAMACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRK
NNRQPYAVSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTK
TWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKE
AVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPG
ITLLNVTKLNILKLAPGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLN
TDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARN
HKLRVERAAAALAAKSDPKEAPAKKKPVVGKK
Sequence of entity 7 (AD), FASTA
>6P5N_7 uL18 (chains AD)
KGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES
Sequence of entity 8 (AE), FASTA
>6P5N_8 eL6 (chains AE)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF
Sequence of entity 9 (AF), FASTA
>6P5N_9 L30 (chains AF)
LFANNIREKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHK
EYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFN
GTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSL
GKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQ
INRLIRRMN
Sequence of entity 10 (AG), FASTA
>6P5N_10 eL8 (chains AG)
KKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFT
QVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVT
TLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGKARLCRLVHRKTCTTVAF
TQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATK
LG
Sequence of entity 11 (AH), FASTA
>6P5N_11 uL6 (chains AH)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE
Sequence of entity 12 (AI), FASTA
>6P5N_12 uL16 (chains AI)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Primary citation

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs. Acosta-Reyes, F., Neupane, R., Frank, J. et al. EMBO J (2019) 38:e102226-e102226. DOI 10.15252/embj.2019102226 · PubMed

Other PDB entries of the same protein (UniProt G1TT27 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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