7O80: Rabbit 80S ribosome

Name: PDB 7O80: Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery site
Published: 2021-06-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery site. Determined by electron microscopy at 2.9 Å resolution. Released 2 Jun 2021.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Oryctolagus cuniculus, Severe acute respiratory syndrome coronavirus 2, Bos taurus
Chains: 88
Atoms: 235,677
Mol. weight: 4156.66 kDa
Ligands: SPD, MG, ZN, GTP
Released: 2 Jun 2021

Explore 7O80 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7O80 contains 662 α-helices and 622 β-strands across 81 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 Aa: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-34	7	109
β-strand	43-50	8	109
α-helix	51-52	2
β-strand	53	1	110
β-strand	56	1	110
α-helix	58-62	5
β-strand	66-70	5	109
α-helix	71-73	3
β-strand	82-92	11	109
β-strand	95-105	11	109
α-helix	107-113	7
β-strand	118	1	111
β-strand	120-128	9	109
β-strand	134-143	10	109
α-helix	144-146	3
β-strand	154	1	111
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
α-helix	201-203	3
β-strand	207-219	13	109
α-helix	221-223	3
α-helix	225-232	8

Chain AA: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	11
β-strand	43-47	5	11
α-helix	54	1
β-strand	55	1	12
α-helix	56	1
β-strand	62	1	12
β-strand	64-65	2	13
α-helix	71	1
β-strand	72-73	2	13
α-helix	74	1
β-strand	78-81	4	11

Chain Ab: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
α-helix	65-71	7
α-helix	78-83	6
α-helix	86-88	3
α-helix	91-98	8
β-strand	103-115	13	113
β-strand	120-131	12	113
β-strand	136-144	9	113
α-helix	147-160	14
β-strand	163-164	2	113
β-strand	168	1	114
β-strand	179	1	114
β-strand	184-188	5	115
β-strand	191-197	7	115
β-strand	204-205	2	115
α-helix	208-216	9
β-strand	222-227	6	115
α-helix	233-245	13
α-helix	253-255	3
α-helix	258-259	2
α-helix	265-268	4
α-helix	270-275	6

Chain AB: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	10-21	12	18
β-strand	27-34	8	18
β-strand	41-47	7	18
β-strand	55-58	4	18
α-helix	65-67	3

Chain Ac: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-42	9	120
β-strand	45-52	8	120
α-helix	55-59	5
α-helix	61-63	3
α-helix	64-77	14
α-helix	79-80	2
β-strand	84-89	6	120
α-helix	98-111	14
α-helix	115-129	15
β-strand	133-141	9	121
β-strand	147-155	9	121
α-helix	163-167	5
β-strand	168-177	10	121
β-strand	180-189	10	121
α-helix	190-192	3
α-helix	203-204	2
β-strand	209-210	2	122
α-helix	211-214	4
β-strand	223-226	4	60

Chain AC: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	91-93	3
α-helix	101-104	4
β-strand	106-108	3	23
β-strand	114-116	3	23
α-helix	119	1
β-strand	120	1	24
α-helix	121	1
β-strand	131	1	24
β-strand	132-134	3	25
β-strand	139-141	3	25
β-strand	147-148	2	25

Chain Ad: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	124
α-helix	16-18	3
β-strand	27	1	124
α-helix	30-32	3
α-helix	38-40	3
β-strand	42-43	2	125
α-helix	44-45	2
α-helix	46-51	6
α-helix	58-66	9
β-strand	70-72	3	126
β-strand	75-76	2	126
β-strand	83-84	2	125
β-strand	89-92	4	126
β-strand	97-100	4	126
β-strand	102-103	2	127
β-strand	109-110	2	127
β-strand	113	1	126
α-helix	118-120	3
β-strand	121-125	5	128
β-strand	126-132	7	129
α-helix	133-135	3
β-strand	136-141	6	129
β-strand	146-148	3	129
β-strand	159-163	5	128
β-strand	168-173	6	128
β-strand	180-183	4	130
β-strand	192-199	8	130
β-strand	207-211	5	130
β-strand	217-221	5	130
α-helix	222-224	3
β-strand	225-230	6	130
β-strand	233-234	2	130
α-helix	248-262	15

Chain AD: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	85-89	5
α-helix	91-92	2
α-helix	94-97	4
α-helix	99-102	4
α-helix	105-116	12
α-helix	119-121	3

73 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	A2	RNA	1870	Oryctolagus cuniculus
40S ribosomal protein S27	AA	protein	84	Oryctolagus cuniculus	G1TZ76 (AlphaFold model)
Ribosomal protein S28	AB	protein	69	Oryctolagus cuniculus	G1TIB4 (AlphaFold model)
Ribosomal protein S27a	AC	protein	156	Oryctolagus cuniculus	G1SK22 (AlphaFold model)
40S ribosomal protein S30	AD	protein	133	Oryctolagus cuniculus	G1T8A2 (AlphaFold model)
Ribosomal protein eS26	AE	protein	115	Oryctolagus cuniculus
RACK1	AF	protein	317	Oryctolagus cuniculus	G1SJB4
uS14	AG	protein	56	Oryctolagus cuniculus	G1U7M4
mRNA containing SARS-CoV-2 sequence	AH	RNA	217	Severe acute respiratory syndrome coronavirus 2
E-site tRNA	AI	RNA	76	Bos taurus
P-site Leu-tRNA(Leu)	AT	RNA	86	Bos taurus
40S ribosomal protein SA	AZ	protein	295	Oryctolagus cuniculus	G1TLT8

76 more molecules are not listed.

Sequence of entity 1 (A2), FASTA

>7O80_1 18S rRNA (chains A2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCUCCCCCCGGCCCCGGCCGGGGGGGUGGGCGCCGGCGGCUUUGGUGACUCUAGA
UAACCUCGGGCCGAUCGCACGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCU
AUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAG
GGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGC
GCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUC
UUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGA
GGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUG
CUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCG
AGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUG
UCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGC
CGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUU
CGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGG
UGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUC
AUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACC
AUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCC
GGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGA
AUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGAA
ACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGU
GGGUGGUGGUGCAUGGCNGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAA
CGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAA
CUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAU
GCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCC
UACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCA
AUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAA
GUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCC
CUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCG
AACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCNGUAGGUGAACCUGCGGA
AGGAUCAUUA

Sequence of entity 2 (AA), FASTA

>7O80_2 40S ribosomal protein S27 (chains AA)
MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS
TVLCQPTGGKARLTEGCSFRRKQH

Sequence of entity 3 (AB), FASTA

>7O80_3 Ribosomal protein S28 (chains AB)
MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLE
SEREARRLR

Sequence of entity 4 (AC), FASTA

>7O80_4 Ribosomal protein S27a (chains AC)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRE
CPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPEDK

Sequence of entity 5 (AD), FASTA

>7O80_5 40S ribosomal protein S30 (chains AD)
MQLFVRAQELHTLEVTGRETVAQIKAHVASLEGIAPEDQVVLLAGTPLEDEATLGQCGVE
ALSTLEVAGRMLGGKVHGSLARVGKVRGQTLKVAKQEKKKKRTGRAKRRMQYNRRFVNVV
PTFGKKKGPNANS

Sequence of entity 6 (AE), FASTA

>7O80_6 Ribosomal protein eS26 (chains AE)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

Sequence of entity 7 (AF), FASTA

>7O80_7 RACK1 (chains AF)
MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALR
GHSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQI
VSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLA
NCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALC
FSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFA
GYTDNLVRVWQVTIGTR

Sequence of entity 8 (AG), FASTA

>7O80_8 uS14 (chains AG)
MGHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD

Sequence of entity 9 (AH), FASTA

>7O80_9 mRNA containing SARS-CoV-2 sequence (chains AH)
CAACUUGUGCUAAUGACCCUGUGGGUUUUACACUUAAAAACACAGUCUGUACCGUCUGCG
GUAUGUGGAAAGGUUAUGGCUGUAGUUGUGAUCAACUCCGCGAACCCAUGCUUCAGUCAG
CUGAUGCACAAUCGUUUUUAUAAGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUG
CGGCACAGGCACUAGUACUGAUGUCGUAUACAGGGCU

Sequence of entity 10 (AI), FASTA

>7O80_10 E-site tRNA (chains AI)
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNCCA

Sequence of entity 11 (AT), FASTA

>7O80_11 P-site Leu-tRNA(Leu) (chains AT)
ACCGGGAUGGCCGAGUGGUUAAGGCGUUGGACUUAAGAUCCAAUGGGCUAGUGCCCGCGU
GGGUUCGAACCCCACUCUCGGUACCA

Sequence of entity 12 (AZ), FASTA

>7O80_12 40S ribosomal protein SA (chains AZ)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS

Ligands and cofactors

ID	Name	Formula	Copies
SPD	Spermidine	C7 H19 N3	1
MG	Magnesium ion	Mg	355
ZN	Zinc ion	Zn	8
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
SF4	Iron/sulfur cluster	Fe4 S4	2

Water and common crystallization additives (UNX) are not listed.

Primary citation

Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Bhatt, P.R., Scaiola, A., Loughran, G. et al. Science (2021) 372:1306-1313. DOI 10.1126/science.abf3546 · PubMed

Other PDB entries of the same protein (UniProt G1TZ76 (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
9BDL 2.8 Å, 80S ribosome with angiogenin

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