8T3D: Hypomethylated yeast 80S

Name: PDB 8T3D: Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III
Published: 2024-12-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure III. Determined by electron microscopy at 2.95 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 2.95 Å
Organisms: Saccharomyces cerevisiae, Taura syndrome virus
Chains: 81
Atoms: 211,084
Mol. weight: 3279.02 kDa
Ligands: ZN, GDP, MG, SO1
Released: 11 Dec 2024

Explore 8T3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T3D contains 528 α-helices and 584 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 Aa: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	42-47	6
β-strand	72-73	2	110
α-helix	76-80	5
α-helix	84-91	8
β-strand	99-100	2	167
β-strand	101-103	3	111
β-strand	111-112	2	110
β-strand	124-127	4	111
β-strand	129-130	2	110
α-helix	132-141	10
β-strand	144-147	4	111

Chain AA: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	18	1	89
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-49	10	90
α-helix	57	1
β-strand	58-64	7	90
β-strand	71-77	7	90
α-helix	78	1
β-strand	79	1	91
β-strand	83	1	92
α-helix	86	1
β-strand	87-91	5	90
β-strand	101-103	3	93
α-helix	108	1
β-strand	112-114	3	93
β-strand	116	1	94
β-strand	126	1	94
β-strand	134-140	7	93
β-strand	145-149	5	93
β-strand	155-159	5	93
β-strand	163-166	4	93
β-strand	169	1	91
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	89
α-helix	201-203	3
β-strand	224-225	2	95
β-strand	237-238	2	95

Chain Ab: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	12-18	7
β-strand	22	1	50
α-helix	37-58	22

Chain AB: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	20-22	3
β-strand	42-43	2	100
β-strand	45-59	15	101
β-strand	71-80	10	101
β-strand	84-95	12	102
β-strand	98-106	9	102
α-helix	112-115	4
α-helix	116-118	3
α-helix	131-134	4
α-helix	142-153	12
β-strand	157-163	7	102
β-strand	178-182	5	102
β-strand	183-184	2	100
α-helix	188-197	10
β-strand	199	1	102
β-strand	202-203	2	102
α-helix	205-207	3
β-strand	214-220	7	101
α-helix	221-223	3
β-strand	225-227	3	103
α-helix	229-233	5
α-helix	235-239	5
β-strand	268-270	3	103
β-strand	274-285	12	101
α-helix	307	1
β-strand	311	1	104
β-strand	315	1	104
β-strand	321-325	5	101
β-strand	335-340	6	101
β-strand	356-359	4	101
α-helix	373-380	8

Chain Ac: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-17	7
β-strand	22-25	4	117
α-helix	27-36	10
β-strand	41-45	5	117
α-helix	50-63	14
β-strand	66-70	5	117
α-helix	74-81	8
β-strand	89-94	6	117

Chain AC: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	107
β-strand	13-20	8	107
α-helix	25-27	3
α-helix	32-42	11
β-strand	63-64	2	108
β-strand	75-76	2	108
β-strand	88	1	108
α-helix	98-99	2
α-helix	115-128	14
α-helix	132-138	7
β-strand	150-152	3	107
α-helix	154-158	5
α-helix	162-169	8
α-helix	170-174	5
α-helix	175-180	6
β-strand	186-187	2	109
α-helix	188-189	2
α-helix	191-194	4
β-strand	199-200	2	109
β-strand	206-209	4	107
α-helix	215-218	4
β-strand	226-229	4	107
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	107
α-helix	252-261	10
α-helix	276-279	4
α-helix	286-290	5
α-helix	293-297	5
α-helix	321-326	6
α-helix	331-337	7
α-helix	339-341	3
α-helix	353-360	8

Chain Ad: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	120
α-helix	25-27	3
α-helix	28-44	17
β-strand	50	1	120
α-helix	53-60	8
β-strand	70-79	10	120
β-strand	89-95	7	120
β-strand	107-108	2	120

Chain AD: 18 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	21-24	4
α-helix	30-37	8
β-strand	50-56	7	122
β-strand	59-67	9	122
β-strand	72-79	8	122
α-helix	83-85	3
α-helix	95-112	18
α-helix	133-135	3
α-helix	139-142	4
β-strand	143	1	123
β-strand	145-147	3	122
α-helix	151-153	3
α-helix	158-168	11
β-strand	172	1	123
α-helix	177-179	3
α-helix	192-199	8
α-helix	202-214	13
α-helix	217-221	5
α-helix	224-228	5
α-helix	233-235	3
α-helix	236-249	14
α-helix	262-272	11
α-helix	279-293	15

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
40S ribosomal protein S0-A	BA	protein	252	Saccharomyces cerevisiae	P32905 (AlphaFold model)
RPS1A isoform 1	BB	protein	255	Saccharomyces cerevisiae	P33442 (AlphaFold model)
RPS2 isoform 1	BC	protein	254	Saccharomyces cerevisiae	P25443 (AlphaFold model)
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

69 more molecules are not listed.

Sequence of entity 1 (BA), FASTA

>8T3D_1 40S ribosomal protein S0-A (chains BA)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 2 (BB), FASTA

>8T3D_2 RPS1A isoform 1 (chains BB)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 3 (BC), FASTA

>8T3D_3 RPS2 isoform 1 (chains BC)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF

Sequence of entity 4 (BE), FASTA

>8T3D_4 40S ribosomal protein S4-A (chains BE)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL

Sequence of entity 5 (BG), FASTA

>8T3D_5 40S ribosomal protein S6-A (chains BG)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Sequence of entity 6 (BH), FASTA

>8T3D_6 40S ribosomal protein S7-A (chains BH)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH

Sequence of entity 7 (BI), FASTA

>8T3D_7 40S ribosomal protein S8-A (chains BI)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 8 (BJ), FASTA

>8T3D_8 40S ribosomal protein S9-A (chains BJ)
MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK
AEASGEAADEADEADEE

Sequence of entity 9 (BL), FASTA

>8T3D_9 40S ribosomal protein S11-A (chains BL)
MSTELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPF
TGLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVG
DIVTVGQCRPISKTVRFNVVKVSAAAGKANKQFAKF

Sequence of entity 10 (BN), FASTA

>8T3D_10 40S ribosomal protein S13 (chains BN)
MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGV
TQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIES
RIHRLARYYRTVAVLPPNWKYESATASALVN

Sequence of entity 11 (BO), FASTA

>8T3D_11 40S ribosomal protein S14-A (chains BO)
MSNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAA
MLAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTP
VPSDSTRKKGGRRGRRL

Sequence of entity 12 (BV), FASTA

>8T3D_12 40S ribosomal protein S21-A (chains BV)
MENDKGQLVELYVPRKCSATNRIIKADDHASVQINVAKVDEEGRAIPGEYVTYALSGYVR
SRGESDDSLNRLAQNDGLLKNVWSYSR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	1
SO1	[1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-deox…	C27 H42 O8	1

Primary citation

Regulation of Translation by Ribosome RNA 2'-O-Methylation. Zhao, Y., Li, H. To be published.

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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