8Y0U: Dormant ribosome with STM1

Name: PDB 8Y0U: dormant ribosome with STM1
Published: 2024-02-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

dormant ribosome with STM1. Determined by electron microscopy at 3.59 Å resolution. Released 7 Feb 2024.

Method: Electron microscopy
Resolution: 3.59 Å
Organism: Saccharomyces cerevisiae
Chains: 77
Atoms: 196,269
Mol. weight: 3092.55 kDa
Ligands: ZN, MG
Released: 7 Feb 2024

Explore 8Y0U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y0U contains 456 α-helices and 468 β-strands across 73 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 5: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	19-20	2	88
α-helix	23-25	3
β-strand	33-34	2	89
β-strand	37-38	2	89
β-strand	39-48	10	90
β-strand	55-63	9	90
β-strand	69-75	7	90
β-strand	81-82	2	88
β-strand	90-92	3	91
β-strand	102-103	2	91
α-helix	119-128	10
β-strand	134-139	6	91
β-strand	146-152	7	91

Chain La: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	8-11	4
α-helix	42-48	7
β-strand	72-74	3	29
α-helix	84-92	9
β-strand	99-100	2	87
β-strand	101-103	3	30
α-helix	104-107	4
β-strand	111-113	3	29
β-strand	124-127	4	30
β-strand	129-130	2	29
α-helix	132-141	10
β-strand	144-147	4	30

Chain LA: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-9	4
α-helix	35-37	3
β-strand	41-49	9	1
α-helix	57	1
β-strand	58-62	5	1
β-strand	73-77	5	1
β-strand	79	1	2
β-strand	83	1	3
β-strand	87-90	4	1
β-strand	101-103	3	1
α-helix	104-106	3
β-strand	112-114	3	1
β-strand	134-136	3	1
β-strand	140	1	1
β-strand	145-149	5	1
β-strand	155-159	5	1
β-strand	163-166	4	1
β-strand	169	1	2
α-helix	174-176	3
α-helix	182-190	9
α-helix	201-203	3
α-helix	206-208	3
β-strand	224-225	2	4
α-helix	229-230	2
β-strand	237-238	2	4

Chain Lb: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
α-helix	37-58	22

Chain LB: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	21-22	2
α-helix	27-29	3
α-helix	33-35	3
α-helix	40-41	2
β-strand	45-59	15	18
β-strand	71-80	10	18
α-helix	82-83	2
β-strand	84-95	12	19
β-strand	98-105	8	19
α-helix	112-115	4
α-helix	116-118	3
α-helix	134-136	3
α-helix	142-153	12
β-strand	157-163	7	19
α-helix	166-168	3
β-strand	178-182	5	19
α-helix	188-198	11
β-strand	202-203	2	19
α-helix	205-207	3
β-strand	214-220	7	18
α-helix	221-223	3
β-strand	227	1	20
α-helix	229-233	5
α-helix	235-239	5
α-helix	260-261	2
β-strand	268	1	20
β-strand	274-286	13	18
α-helix	307	1
β-strand	311	1	21
β-strand	315	1	21
β-strand	321-325	5	18
β-strand	335-340	6	18
β-strand	356-359	4	18
α-helix	373-380	8

Chain Lc: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	22-25	4	35
α-helix	27-36	10
β-strand	41-44	4	35
α-helix	50-63	14
β-strand	66-69	4	35
α-helix	74-80	7
β-strand	89-94	6	35

Chain LC: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	36
α-helix	8	1
β-strand	9	1	37
β-strand	10	1	38
β-strand	13	1	38
β-strand	19-20	2	36
α-helix	32-42	11
α-helix	43-45	3
β-strand	63-64	2	39
β-strand	75-76	2	39
β-strand	88	1	39
α-helix	115-129	15
α-helix	132-138	7
β-strand	151-152	2	37
α-helix	154-158	5
α-helix	162-172	11
α-helix	175-183	9
β-strand	186-187	2	40
α-helix	191-194	4
β-strand	199-200	2	40
β-strand	206-209	4	37
α-helix	215-219	5
β-strand	226-229	4	37
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	37
α-helix	252-262	11
α-helix	287-290	4
α-helix	300-301	2
α-helix	321-327	7
α-helix	330-337	8
α-helix	342-346	5
α-helix	353-360	8

Chain Ld: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	41
α-helix	16-20	5
α-helix	28-44	17
β-strand	49-51	3	41
α-helix	53-59	7
α-helix	60-62	3
β-strand	70-79	10	41
β-strand	89-95	7	41
β-strand	107-108	2	41

65 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
Large ribosomal subunit protein uL2A	LA	protein	254	Saccharomyces cerevisiae	P0CX45 (AlphaFold model)
Small ribosomal subunit protein uS2A	SA	protein	252	Saccharomyces cerevisiae	P32905 (AlphaFold model)
Large ribosomal subunit protein uL3	LB	protein	387	Saccharomyces cerevisiae	P14126 (AlphaFold model)
40S ribosomal protein S1-A	SB	protein	255	Saccharomyces cerevisiae	P33442 (AlphaFold model)
25S rRNA	C1	RNA	3396	Saccharomyces cerevisiae
5S rRNA	C4	RNA	121	Saccharomyces cerevisiae
5.8S rRNA	C3	RNA	158	Saccharomyces cerevisiae
Large ribosomal subunit protein uL4A	LC	protein	362	Saccharomyces cerevisiae	P10664
Large ribosomal subunit protein uL18	LD	protein	297	Saccharomyces cerevisiae	P26321
Large ribosomal subunit protein eL6B	LE	protein	176	Saccharomyces cerevisiae	P05739
Large ribosomal subunit protein uL30A	LF	protein	244	Saccharomyces cerevisiae	P05737
Large ribosomal subunit protein eL8A	LG	protein	256	Saccharomyces cerevisiae	P17076

65 more molecules are not listed.

Sequence of entity 1 (LA), FASTA

>8Y0U_1 Large ribosomal subunit protein uL2A (chains LA)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD

Sequence of entity 2 (SA), FASTA

>8Y0U_2 Small ribosomal subunit protein uS2A (chains SA)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 3 (LB), FASTA

>8Y0U_3 Large ribosomal subunit protein uL3 (chains LB)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL

Sequence of entity 4 (SB), FASTA

>8Y0U_4 40S ribosomal protein S1-A (chains SB)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 5 (C1), FASTA

>8Y0U_5 25S rRNA (chains C1)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUC
UCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCU
UGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACG
UAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGA
GUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUA
GGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGA
GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCC
AGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUG
GGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCU
CAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUUCCGGG
GUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUACUUAA
UUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGAACUGG
CGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGACACCA
CAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAA
GGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGC
GUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGGCGUGG
AGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUG
GUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACG
UCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAG
GCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAU
AUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAG
UUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUU
AUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAA
UCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCCAAG
GUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGU
AACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCAGACGCAGC
GGGCGUGCUUGUGGACUGCUUGGUGGGGCUUGCUCUGCUAGGCGGACUACUUGCGUGCCU
UGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGACCGUCGCUUGCUACAAUUAACGAUCAA
CUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUG
GUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAA
GAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAA
AUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCU
AUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAG
AAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAU
AAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAA
UGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGA
UCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGA
UAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGG
UAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUC
GAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCU
CUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUA
CCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGC
GGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUC
UAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUA
CGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGC
GGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAU
UUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUAC
GAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU

Sequence of entity 6 (C4), FASTA

>8Y0U_6 5S rRNA (chains C4)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U

Sequence of entity 7 (C3), FASTA

>8Y0U_7 5.8S rRNA (chains C3)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU

Sequence of entity 8 (LC), FASTA

>8Y0U_8 Large ribosomal subunit protein uL4A (chains LC)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD

Sequence of entity 9 (LD), FASTA

>8Y0U_9 Large ribosomal subunit protein uL18 (chains LD)
MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI
ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK
GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF
PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY
TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Sequence of entity 10 (LE), FASTA

>8Y0U_10 Large ribosomal subunit protein eL6B (chains LE)
MTAQQAPKWYPSEDVAAPKKTRKAVRPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLVTGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQTKEIKTERVEDQKVVDKALLAEIKKTPLLKQYLSASFSLKNGDKPHLLKF

Sequence of entity 11 (LF), FASTA

>8Y0U_11 Large ribosomal subunit protein uL30A (chains LF)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Sequence of entity 12 (LG), FASTA

>8Y0U_12 Large ribosomal subunit protein eL8A (chains LG)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7
MG	Magnesium ion	Mg	281

Primary citation

Implication of Stm1 in the protection of eIF5A, eEF2 and tRNA through dormant ribosomes. Du, M., Li, X., Dong, W. et al. Front Mol Biosci (2024) 11:1395220-1395220. DOI 10.3389/fmolb.2024.1395220 · PubMed

Other PDB entries of the same protein (UniProt P0CX45 (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…
8P8N 2.15 Å, Mouse RPL39 integrated into the yeast 60S ribosomal subunit
8PFR 2.15 Å, Mouse RPL39L integrated into the yeast 60S ribosomal subunit
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,…
8P8U 2.23 Å, Yeast 60S ribosomal subunit
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
7UOO 2.34 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state

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