6P5I: Mammalian 80S ribosome

Name: PDB 6P5I: Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1)
Published: 2019-09-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1). Determined by electron microscopy at 3.1 Å resolution. Released 18 Sept 2019.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Oryctolagus cuniculus, Israeli acute paralysis virus
Chains: 81
Atoms: 215,974
Mol. weight: 3411.88 kDa
Released: 18 Sept 2019

Explore 6P5I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P5I contains 548 α-helices and 563 β-strands across 76 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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	1
β-strand	50	1	143
α-helix	52-58	7
β-strand	68	1	2
α-helix	72-77	6
β-strand	79	1	1
α-helix	81-90	10
β-strand	97-102	6	2
β-strand	107-111	5	2
α-helix	112-113	2

Chain Aa: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	29	1	92
β-strand	31	1	92
α-helix	42-47	6
β-strand	72-74	3	93
α-helix	75-80	6
α-helix	84-92	9
β-strand	97-98	2	172
α-helix	99	1
β-strand	100-102	3	94
α-helix	103-106	4
β-strand	110-112	3	93
β-strand	123-126	4	94
β-strand	128-129	2	93
α-helix	131-140	10
β-strand	143-146	4	94

Chain AA: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-12	7
β-strand	18	1	97
α-helix	28-32	5
α-helix	34-37	4
β-strand	40-49	10	98
α-helix	57	1
β-strand	58-64	7	98
β-strand	71-77	7	98
α-helix	78	1
β-strand	79	1	99
β-strand	83	1	8
α-helix	86	1
β-strand	87-91	5	98
β-strand	101-103	3	98
α-helix	104-106	3
β-strand	111-114	4	98
β-strand	116	1	100
β-strand	126	1	100
β-strand	134-140	7	98
β-strand	145-149	5	98
β-strand	155-158	4	98
β-strand	163-166	4	98
β-strand	169	1	99
α-helix	174-176	3
α-helix	178-179	2
α-helix	182-189	8
β-strand	193	1	97
α-helix	201-203	3
β-strand	224-225	2	101
α-helix	229-230	2
β-strand	237-238	2	101

Chain Ab: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	37-48	12
α-helix	55-69	15
α-helix	91-100	10
α-helix	106-115	10

Chain AB: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	32-35	4
α-helix	40-41	2
β-strand	42-43	2	103
β-strand	45-55	11	104
β-strand	56-59	4	105
β-strand	71-72	2	105
β-strand	75-80	6	104
α-helix	82-83	2
β-strand	84-95	12	106
β-strand	98-106	9	106
α-helix	112-117	6
α-helix	134-137	4
α-helix	140-153	14
β-strand	159-165	7	106
α-helix	168-170	3
β-strand	180-184	5	106
β-strand	185-186	2	103
α-helix	190-199	10
β-strand	203-205	3	106
α-helix	207-209	3
β-strand	216-222	7	104
β-strand	228-229	2	107
α-helix	231-234	4
α-helix	237-241	5
β-strand	270-271	2	107
β-strand	276-287	12	104
α-helix	288-291	4
β-strand	292-293	2	108
β-strand	298-299	2	108
β-strand	320	1	109
β-strand	324	1	109
β-strand	330-334	5	104
β-strand	344-349	6	104
β-strand	365-368	4	105
α-helix	382-389	8

Chain Ac: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-23	13
β-strand	26-29	4	110
α-helix	31-39	9
β-strand	45-48	4	110
α-helix	54-67	14
β-strand	70-73	4	110
α-helix	78-84	7
β-strand	93-98	6	110

Chain AC: 25 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	111
β-strand	17-23	7	111
α-helix	24-25	2
α-helix	26-29	4
α-helix	34-44	11
α-helix	45-48	4
β-strand	65-66	2	112
β-strand	77-78	2	112
β-strand	79	1	113
α-helix	80-81	2
β-strand	87	1	113
α-helix	100-101	2
α-helix	104-106	3
α-helix	117-132	16
α-helix	134-139	6
β-strand	153-154	2	111
α-helix	156-160	5
α-helix	164-174	11
α-helix	177-186	10
β-strand	188-189	2	114
α-helix	190-191	2
α-helix	193-195	3
β-strand	201-202	2	114
β-strand	208-211	4	111
α-helix	217-221	5
β-strand	228-231	4	111
α-helix	237-240	4
α-helix	242-244	3
β-strand	250-253	4	111
α-helix	254-257	4
α-helix	260-263	4
α-helix	279-282	4
α-helix	289-293	5
α-helix	296-300	5
α-helix	303-305	3
α-helix	322-328	7
α-helix	332-362	31

Chain Ad: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	115
α-helix	29-31	3
α-helix	38-40	3
α-helix	41-56	16
β-strand	62-64	3	115
α-helix	66-72	7
β-strand	83-92	10	115
α-helix	93-94	2
β-strand	102-108	7	115

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
18S rRNA	2	RNA	1869	Oryctolagus cuniculus
uS2	B	protein	295	Oryctolagus cuniculus
eS1	C	protein	264	Oryctolagus cuniculus	G1SS70 (AlphaFold model)
uS5	D	protein	255	Oryctolagus cuniculus
uS3	E	protein	281	Oryctolagus cuniculus	G1TNM3 (AlphaFold model)
eS4	F	protein	263	Oryctolagus cuniculus	G1TK17 (AlphaFold model)
uS7	G	protein	204	Oryctolagus cuniculus	G1TFM5 (AlphaFold model)
eS6	H	protein	249	Oryctolagus cuniculus	G1TM55
eS7	I	protein	194	Oryctolagus cuniculus	G1SVB0
eS8	J	protein	207	Oryctolagus cuniculus
uS4	K	protein	194	Oryctolagus cuniculus	B7NZS8
eS10	L	protein	149	Oryctolagus cuniculus	G1TPV3

69 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>6P5I_1 18S rRNA (chains 2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCCACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAA
GGAUCAUUA

Sequence of entity 2 (B), FASTA

>6P5I_2 uS2 (chains B)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPQADHQPLMEASYVNLPTIALCNTDSPLHYVDIAIPCNNKGAHSVGLMWWMLAQ
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPEPEFTA
TQPEVADWSEGMQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWMGTTTEWS

Sequence of entity 3 (C), FASTA

>6P5I_3 eS1 (chains C)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 4 (D), FASTA

>6P5I_4 uS5 (chains D)
MADDAGAAGGPGGPGGPGNKEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFCL
GAALKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGLKCSKEVATAIRGAIILA
KLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLLMAG
IDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTNHLMKTHT
RVSVQRTQAPAVATT

Sequence of entity 5 (E), FASTA

>6P5I_5 uS3 (chains E)
MSARRRRRRAAFRRRAEPFIPISVREPLPFLSAARGGKMAVQISKKRKFVADGIFKAELN
EFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEG
SVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKL
RGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKK
PLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPVPTA

Sequence of entity 6 (F), FASTA

>6P5I_6 eS4 (chains F)
MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 7 (G), FASTA

>6P5I_7 uS7 (chains G)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 8 (H), FASTA

>6P5I_8 eS6 (chains H)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 9 (I), FASTA

>6P5I_9 eS7 (chains I)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 10 (J), FASTA

>6P5I_10 eS8 (chains J)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKG

Sequence of entity 11 (K), FASTA

>6P5I_11 uS4 (chains K)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Sequence of entity 12 (L), FASTA

>6P5I_12 eS10 (chains L)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATE

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 G1SS70 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O7Y 2.2 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
7OYD 2.3 Å, Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b
11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
7O7Z 2.4 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
8SCB 2.5 Å, Terminating ribosome with SRI-41315
9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
7JQB 2.7 Å, SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex
8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
7ZJW 2.8 Å, Rabbit 80S ribosome as it decodes the Sec-UGA codon

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