7O81: 40S ribosomal protein S27

Name: PDB 7O81: Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknot
Published: 2021-06-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknot. Determined by electron microscopy at 3.1 Å resolution. Released 2 Jun 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Oryctolagus cuniculus, Severe acute respiratory syndrome coronavirus 2, Bos taurus
Chains: 87
Atoms: 228,361
Mol. weight: 4089.29 kDa
Ligands: ZN, SPD, MG
Released: 2 Jun 2021

Explore 7O81 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7O81 contains 611 α-helices and 567 β-strands across 80 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: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	28-34	7	96
β-strand	43-50	8	96
α-helix	51-52	2
β-strand	53	1	97
β-strand	56	1	97
α-helix	58-62	5
β-strand	66-70	5	96
α-helix	71-73	3
β-strand	82-92	11	96
β-strand	95-105	11	96
α-helix	107-113	7
β-strand	118	1	98
β-strand	120-128	9	96
β-strand	134-143	10	96
α-helix	144-146	3
β-strand	154	1	98
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
β-strand	207-219	13	96
α-helix	221-223	3
α-helix	225-232	8

Chain AA: 2 helices, 6 β-strands

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

Chain Ab: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	65-71	7
α-helix	78-84	7
α-helix	86-88	3
α-helix	91-98	8
β-strand	103-116	14	100
β-strand	119-131	13	100
β-strand	136-144	9	100
α-helix	147-160	14
β-strand	162-164	3	100
β-strand	168	1	101
β-strand	179	1	101
β-strand	184-188	5	102
β-strand	191-197	7	102
β-strand	204-205	2	102
α-helix	208-217	10
β-strand	222-227	6	102
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: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	17
β-strand	27-34	8	17
β-strand	41-47	7	17
β-strand	55-58	4	17
α-helix	65-67	3

Chain Ac: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-42	9	107
β-strand	45-52	8	107
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	107
α-helix	98-111	14
α-helix	115-129	15
β-strand	133-141	9	108
β-strand	147-155	9	108
α-helix	163-167	5
β-strand	168-176	9	108
β-strand	181-189	9	108
α-helix	190-192	3
β-strand	209	1	109
α-helix	212-214	3
β-strand	223-226	4	54

Chain AC: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	88-89	2
α-helix	91-93	3
α-helix	101-105	5
β-strand	106-108	3	22
β-strand	114-116	3	22
α-helix	119	1
β-strand	120	1	23
α-helix	121	1
β-strand	131	1	23
β-strand	132-134	3	24
β-strand	138-141	4	24
β-strand	146-149	4	24

Chain Ad: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	111
α-helix	16-18	3
β-strand	27	1	111
α-helix	30-32	3
β-strand	42-43	2	112
α-helix	44-46	3
α-helix	47-51	5
α-helix	58-66	9
β-strand	71-72	2	113
β-strand	75-76	2	113
β-strand	83-84	2	112
β-strand	89-92	4	113
β-strand	97-103	7	113
β-strand	109-114	6	113
α-helix	118-120	3
β-strand	121-125	5	114
β-strand	126-132	7	115
α-helix	133-135	3
β-strand	136-141	6	115
β-strand	146-148	3	115
β-strand	159-163	5	114
β-strand	169-173	5	114
β-strand	180-183	4	116
β-strand	192-199	8	116
β-strand	207-211	5	116
β-strand	217-221	5	116
α-helix	222-224	3
β-strand	225-229	5	116
α-helix	248-262	15

Chain AD: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	85-89	5
α-helix	91-92	2
α-helix	94-97	4
α-helix	99-102	4
α-helix	105-115	11
β-strand	116-119	4	29

72 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
A-site Met-tRNA(Met)	AJ	RNA	76	Bos taurus
P-site tRNA(Pro)	AT	RNA	75	Bos taurus
EDF1	AU	protein	148	Oryctolagus cuniculus

75 more molecules are not listed.

Sequence of entity 1 (A2), FASTA

>7O81_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

>7O81_2 40S ribosomal protein S27 (chains AA)
MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS
TVLCQPTGGKARLTEGCSFRRKQH

Sequence of entity 3 (AB), FASTA

>7O81_3 Ribosomal protein S28 (chains AB)
MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLE
SEREARRLR

Sequence of entity 4 (AC), FASTA

>7O81_4 Ribosomal protein S27a (chains AC)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRE
CPSDECGAGVFMASHFDRHYCGKCCLTYCFNKPEDK

Sequence of entity 5 (AD), FASTA

>7O81_5 40S ribosomal protein S30 (chains AD)
MQLFVRAQELHTLEVTGRETVAQIKAHVASLEGIAPEDQVVLLAGTPLEDEATLGQCGVE
ALSTLEVAGRMLGGKVHGSLARVGKVRGQTLKVAKQEKKKKRTGRAKRRMQYNRRFVNVV
PTFGKKKGPNANS

Sequence of entity 6 (AE), FASTA

>7O81_6 Ribosomal protein eS26 (chains AE)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

Sequence of entity 7 (AF), FASTA

>7O81_7 RACK1 (chains AF)
MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALR
GHSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQI
VSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLA
NCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALC
FSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFA
GYTDNLVRVWQVTIGTR

Sequence of entity 8 (AG), FASTA

>7O81_8 uS14 (chains AG)
MGHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD

Sequence of entity 9 (AH), FASTA

>7O81_9 mRNA containing SARS-CoV-2 sequence (chains AH)
CAACUUGUGCUAAUGACCCUGUGGGUUUUACACUUAAAAACACAGUCUGUACCGUCUGCG
GUAUGUGGAAAGGUUAUGGCUGUAGUUGUGAUCAACUCCGCGAACCCAUGCUUCAGUCAG
CUGAUGCACAAUCGUUUUUAUAAGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUG
CGGCACAGGCACUAGUACUGAUGUCGUAUACAGGGCU

Sequence of entity 10 (AJ), FASTA

>7O81_10 A-site Met-tRNA(Met) (chains AJ)
GCCUUCUUAGCGCAGUAGGCAGCGCGUCAGUCUCAUAAUCUGAAGGUCCUGAGUUCGAGC
CUCAGAGAGGGCACCA

Sequence of entity 11 (AT), FASTA

>7O81_11 P-site tRNA(Pro) (chains AT)
GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUC
CCGGACGAGCCCCCA

Sequence of entity 12 (AU), FASTA

>7O81_12 EDF1 (chains AU)
MAESDWDTVTVLRKKGPTAAQAKSKQAILAAQRRGDDVETSKKWAAGQNKQHSITKNTAK
LDRETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQV
LGKIERAIGLKLRGRDVGKPIEKGPRAK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
SPD	Spermidine	C7 H19 N3	1
MG	Magnesium ion	Mg	349

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

Browse structure collections

About this viewer

MolViewer shows 7O81 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.