8EWB: Hypopseudouridylated yeast 80S

Name: PDB 8EWB: Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III
Published: 2023-09-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III. Determined by electron microscopy at 2.87 Å resolution. Released 6 Sept 2023.

Method: Electron microscopy
Resolution: 2.87 Å
Organisms: Saccharomyces cerevisiae, Taura syndrome virus
Chains: 82
Atoms: 213,196
Mol. weight: 3318.66 kDa
Ligands: GDP, ZN, MG
Released: 6 Sept 2023

Explore 8EWB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EWB contains 550 α-helices and 592 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 Aa: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	42-48	7
β-strand	53	1	6
β-strand	72-73	2	101
α-helix	75-77	3
α-helix	84-91	8
β-strand	99-100	2	163
β-strand	101-103	3	102
β-strand	111-112	2	101
β-strand	124-127	4	102
β-strand	129-130	2	101
α-helix	132-140	9
β-strand	144-147	4	102

Chain AA: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	14-16	3
β-strand	18	1	82
α-helix	34-38	5
β-strand	40-50	11	83
β-strand	57-64	8	83
β-strand	71-77	7	83
α-helix	78	1
β-strand	79	1	84
β-strand	83	1	85
β-strand	87-91	5	83
β-strand	101-103	3	83
α-helix	104-106	3
β-strand	112-114	3	83
β-strand	116	1	86
β-strand	126	1	86
β-strand	134-140	7	83
β-strand	145-149	5	83
β-strand	155-159	5	83
β-strand	163-166	4	83
β-strand	169	1	84
α-helix	174-176	3
α-helix	182-189	8
β-strand	193	1	82
α-helix	201-203	3
β-strand	224-225	2	87
β-strand	237-238	2	87

Chain Ab: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-18	7
α-helix	37-56	20

Chain AB: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
α-helix	40-41	2
β-strand	42-43	2	91
β-strand	45-59	15	92
β-strand	71-80	10	92
α-helix	82-83	2
β-strand	84-95	12	93
β-strand	98-106	9	93
α-helix	112-115	4
α-helix	116-118	3
α-helix	134-137	4
α-helix	142-153	12
β-strand	157-163	7	93
β-strand	178-182	5	93
β-strand	183-184	2	91
α-helix	188-197	10
β-strand	202-203	2	93
α-helix	205-207	3
β-strand	214-220	7	92
β-strand	225-227	3	94
α-helix	229-233	5
α-helix	235-239	5
β-strand	268-270	3	94
β-strand	274-286	13	92
β-strand	311	1	95
β-strand	315	1	95
β-strand	321-325	5	92
β-strand	335-339	5	92
β-strand	356-359	4	92
α-helix	373-380	8

Chain Ac: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-19	10
β-strand	22-25	4	108
α-helix	27-36	10
β-strand	41-44	4	108
α-helix	50-62	13
β-strand	66-69	4	108
α-helix	74-80	7
β-strand	89-94	6	108

Chain AC: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	98
β-strand	13-20	8	98
α-helix	32-42	11
β-strand	63-64	2	99
β-strand	75-76	2	99
β-strand	88	1	99
α-helix	115-128	14
α-helix	132-138	7
β-strand	150-152	3	98
α-helix	154-158	5
α-helix	162-169	8
α-helix	170-174	5
α-helix	175-178	4
β-strand	186-187	2	100
α-helix	191-194	4
β-strand	199-200	2	100
β-strand	206-209	4	98
α-helix	215-218	4
β-strand	226-229	4	98
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	98
α-helix	252-262	11
α-helix	276-279	4
α-helix	286-290	5
α-helix	293-296	4
α-helix	300-301	2
α-helix	321-326	6
α-helix	331-336	6
α-helix	339-341	3
α-helix	343-345	3
α-helix	349-352	4
α-helix	353-359	7

Chain Ad: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	112
α-helix	16-19	4
α-helix	25-27	3
α-helix	28-44	17
β-strand	48-51	4	112
α-helix	53-59	7
α-helix	60-62	3
β-strand	70-79	10	112
β-strand	89-95	7	112
α-helix	96	1
β-strand	107-109	3	112

Chain AD: 20 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	21-25	5
α-helix	30-37	8
β-strand	50-55	6	114
β-strand	60-66	7	114
β-strand	73-79	7	114
α-helix	80-85	6
α-helix	95-113	19
α-helix	133-135	3
α-helix	139-142	4
β-strand	143	1	115
β-strand	145-147	3	114
α-helix	151-153	3
α-helix	159-168	10
β-strand	172	1	115
α-helix	177-179	3
β-strand	183	1	116
β-strand	190	1	116
α-helix	192-199	8
α-helix	202-214	13
α-helix	216-221	6
α-helix	224-229	6
α-helix	233-235	3
α-helix	236-249	14
α-helix	254-256	3
α-helix	262-270	9
α-helix	276-278	3
α-helix	279-294	16

69 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
40S ribosomal protein S0-A	BA	protein	252	Saccharomyces cerevisiae	P32905 (AlphaFold model)
RPS1A isoform 1	BB	protein	255	Saccharomyces cerevisiae	A0A6A5PRY4
RPS2 isoform 1	BC	protein	254	Saccharomyces cerevisiae	A0A6A5PWF7
40S ribosomal protein S4-A	BE	protein	261	Saccharomyces cerevisiae	P0CX35 (AlphaFold model)
40S ribosomal protein S6-A	BG	protein	236	Saccharomyces cerevisiae	P0CX37
40S ribosomal protein S7-A	BH	protein	190	Saccharomyces cerevisiae	P26786
40S ribosomal protein S8-A	BI	protein	200	Saccharomyces cerevisiae	P0CX39
40S ribosomal protein S9-A	BJ	protein	197	Saccharomyces cerevisiae	O13516
40S ribosomal protein S11-A	BL	protein	156	Saccharomyces cerevisiae	P0CX47
40S ribosomal protein S13	BN	protein	151	Saccharomyces cerevisiae	P05756
40S ribosomal protein S14-A	BO	protein	137	Saccharomyces cerevisiae	P06367
40S ribosomal protein S21-A	BV	protein	87	Saccharomyces cerevisiae	P0C0V8

70 more molecules are not listed.

Sequence of entity 1 (BA), FASTA

>8EWB_1 40S ribosomal protein S0-A (chains BA)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 2 (BB), FASTA

>8EWB_2 RPS1A isoform 1 (chains BB)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 3 (BC), FASTA

>8EWB_3 RPS2 isoform 1 (chains BC)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF

Sequence of entity 4 (BE), FASTA

>8EWB_4 40S ribosomal protein S4-A (chains BE)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL

Sequence of entity 5 (BG), FASTA

>8EWB_5 40S ribosomal protein S6-A (chains BG)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Sequence of entity 6 (BH), FASTA

>8EWB_6 40S ribosomal protein S7-A (chains BH)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH

Sequence of entity 7 (BI), FASTA

>8EWB_7 40S ribosomal protein S8-A (chains BI)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 8 (BJ), FASTA

>8EWB_8 40S ribosomal protein S9-A (chains BJ)
MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK
AEASGEAADEADEADEE

Sequence of entity 9 (BL), FASTA

>8EWB_9 40S ribosomal protein S11-A (chains BL)
MSTELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPF
TGLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVG
DIVTVGQCRPISKTVRFNVVKVSAAAGKANKQFAKF

Sequence of entity 10 (BN), FASTA

>8EWB_10 40S ribosomal protein S13 (chains BN)
MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGV
TQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIES
RIHRLARYYRTVAVLPPNWKYESATASALVN

Sequence of entity 11 (BO), FASTA

>8EWB_11 40S ribosomal protein S14-A (chains BO)
MSNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAA
MLAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTP
VPSDSTRKKGGRRGRRL

Sequence of entity 12 (BV), FASTA

>8EWB_12 40S ribosomal protein S21-A (chains BV)
MENDKGQLVELYVPRKCSATNRIIKADDHASVQINVAKVDEEGRAIPGEYVTYALSGYVR
SRGESDDSLNRLAQNDGLLKNVWSYSR

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	242

Primary citation

Regulation of translation by ribosomal RNA pseudouridylation. Zhao, Y., Rai, J., Li, H. Sci Adv (2023) 9:eadg8190-eadg8190. DOI 10.1126/sciadv.adg8190 · PubMed

Other PDB entries of the same protein (UniProt P32905 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
8EVT 2.2 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8CGN 2.28 Å, Non-rotated 80S S. cerevisiae ribosome with ligands
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
8EVP 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
7ZW0 2.4 Å, FAP-80S Complex - Rotated state
8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing

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