8P8U: Yeast 60S ribosomal subunit

Yeast 60S ribosomal subunit. Determined by electron microscopy at 2.23 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 2.23 Å
Organism: Saccharomyces cerevisiae
Chains: 43
Atoms: 119,919
Mol. weight: 1932.04 kDa
Ligands: MG, SPM, SPD, ZN
Released: 12 Jun 2024

Explore 8P8U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P8U contains 311 α-helices and 272 β-strands across 40 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 2: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-18	12
α-helix	25-29	5

Chain JT: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
β-strand	22-24	3	30
α-helix	28-46	19
β-strand	54	1	31
β-strand	57-59	3	32
α-helix	62-65	4
β-strand	69-71	3	32
β-strand	75	1	33
α-helix	77-83	7
α-helix	87-91	5
β-strand	95	1	31
β-strand	97	1	33
β-strand	105	1	34
α-helix	106-121	16
β-strand	124-126	3	35
α-helix	136-138	3
α-helix	149-151	3
β-strand	156-157	2	36
α-helix	166-178	13
α-helix	180-189	10

Chain JU: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	39
α-helix	12-14	3
β-strand	15	1	55
β-strand	19-23	5	56
β-strand	32-38	7	56
β-strand	43-48	6	56
β-strand	53-59	7	56
α-helix	60-62	3
β-strand	63-69	7	56
α-helix	78-88	11
α-helix	90-95	6
α-helix	98-110	13
α-helix	114-135	22

Chain JV: 12 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
α-helix	17-31	15
β-strand	36-39	4	68
α-helix	45-50	6
β-strand	59-67	9	68
α-helix	76-78	3
α-helix	84-86	3
α-helix	98-109	12
β-strand	114-123	10	68
β-strand	127-135	9	68
α-helix	140-143	4
α-helix	149-152	4
α-helix	154-156	3
α-helix	166-172	7
α-helix	178-180	3
α-helix	187-194	8
β-strand	197-199	3	30

Chain JW: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	75
β-strand	14	1	76
β-strand	15	1	77
α-helix	16-28	13
β-strand	32-36	5	75
α-helix	38-40	3
β-strand	42-44	3	77
α-helix	47-58	12
α-helix	76-85	10
α-helix	93-99	7
β-strand	102-104	3	75
β-strand	118	1	75
β-strand	119	1	78
α-helix	121-123	3
β-strand	124	1	76
α-helix	125-128	4
α-helix	130	1
β-strand	135-137	3	77
α-helix	138-144	7
α-helix	150-184	35
α-helix	189-196	8

Chain LF: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	10-12	3
α-helix	34-38	5
β-strand	40-49	10	24
β-strand	58-64	7	24
β-strand	71-77	7	24
α-helix	78	1
β-strand	79	1	25
β-strand	83	1	66
β-strand	87-91	5	24
β-strand	101-103	3	24
α-helix	104-106	3
β-strand	112-114	3	24
β-strand	116	1	26
β-strand	126	1	26
β-strand	134-140	7	24
α-helix	142-144	3
β-strand	145-149	5	24
β-strand	155-159	5	24
β-strand	163-166	4	24
β-strand	169	1	25
α-helix	174-176	3
α-helix	182-190	9
α-helix	201-203	3
β-strand	224-225	2	27
α-helix	229-230	2
β-strand	237-238	2	27

Chain LG: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	33-35	3
β-strand	42-43	2	42
β-strand	45-59	15	43
β-strand	71-80	10	43
α-helix	82-83	2
β-strand	84-93	10	44
β-strand	100-106	7	44
α-helix	112-117	6
α-helix	133-138	6
α-helix	142-154	13
β-strand	157-163	7	44
α-helix	166-168	3
α-helix	176-177	2
β-strand	178-182	5	44
β-strand	183-184	2	42
α-helix	188-197	10
β-strand	202-203	2	44
α-helix	205-207	3
β-strand	214-220	7	43
α-helix	221-222	2
β-strand	223-227	5	45
α-helix	229-232	4
α-helix	235-239	5
β-strand	268-271	4	45
β-strand	274-286	13	43
α-helix	307	1
β-strand	311	1	46
β-strand	315	1	46
β-strand	321-325	5	43
β-strand	335-340	6	43
β-strand	356-359	4	43
α-helix	373-380	8

Chain LH: 23 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	52
α-helix	10	1
β-strand	15-21	7	52
α-helix	25-27	3
α-helix	32-42	11
β-strand	63-64	2	53
β-strand	75-76	2	53
β-strand	88	1	53
α-helix	115-128	14
α-helix	132-137	6
β-strand	150-152	3	52
α-helix	154-158	5
α-helix	162-172	11
α-helix	175-182	8
β-strand	186-187	2	54
α-helix	191-194	4
β-strand	199-200	2	54
β-strand	206-209	4	52
α-helix	215-218	4
β-strand	226-229	4	52
α-helix	230-232	3
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	52
α-helix	252-262	11
α-helix	276-279	4
α-helix	286-290	5
α-helix	293-296	4
α-helix	307-309	3
α-helix	314-316	3
α-helix	321-326	6
α-helix	331-336	6
α-helix	339-341	3
α-helix	353-360	8

32 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
60S ribosomal protein L39	2	protein	51	Saccharomyces cerevisiae	P04650 (AlphaFold model)
60S ribosomal protein L7-A	LK	protein	244	Saccharomyces cerevisiae	P05737 (AlphaFold model)
60S ribosomal protein L25	QX	protein	142	Saccharomyces cerevisiae	P04456 (AlphaFold model)
60S ribosomal protein L38	RM	protein	78	Saccharomyces cerevisiae	P49167 (AlphaFold model)
25S rRNA	A	RNA	3396	Saccharomyces cerevisiae
60S ribosomal protein L8-A	LL	protein	256	Saccharomyces cerevisiae	P17076
60S ribosomal protein L26-A	QY	protein	127	Saccharomyces cerevisiae	P05743
Ubiquitin-60S ribosomal protein L40	RO	protein	128	Saccharomyces cerevisiae	P0CH08
60S ribosomal protein L13-A	JT	protein	199	Saccharomyces cerevisiae	Q12690
60S ribosomal protein L9-A	LM	protein	191	Saccharomyces cerevisiae	P05738
60S ribosomal protein L27-A	QZ	protein	136	Saccharomyces cerevisiae	P0C2H6
60S ribosomal protein L42-A	RQ	protein	106	Saccharomyces cerevisiae	P0CX27

31 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>8P8U_1 60S ribosomal protein L39 (chains 2)
MAAQKSFRIKQKMAKAKKQNRPLPQWIRLRTNNTIRYNAKRRNWRRTKMNI

Sequence of entity 2 (LK), FASTA

>8P8U_2 60S ribosomal protein L7-A (chains LK)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Sequence of entity 3 (QX), FASTA

>8P8U_3 60S ribosomal protein L25 (chains QX)
MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSY
KVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTK
KAYVRLTADYDALDIANRIGYI

Sequence of entity 4 (RM), FASTA

>8P8U_4 60S ribosomal protein L38 (chains RM)
MAREITDIKQFLELTRRADVKTATVKINKKLNKAGKPFRQTKFKVRGSSSLYTLVINDAG
KAKKLIQSLPPTLKVNRL

Sequence of entity 5 (A), FASTA

>8P8U_5 25S rRNA (chains A)
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 (LL), FASTA

>8P8U_6 60S ribosomal protein L8-A (chains LL)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA

Sequence of entity 7 (QY), FASTA

>8P8U_7 60S ribosomal protein L26-A (chains QY)
MAKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIRRDDEVLVVR
GSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHPSKLVITKLHLDKDRKALIQ
RKGGKLE

Sequence of entity 8 (RO), FASTA

>8P8U_8 Ubiquitin-60S ribosomal protein L40 (chains RO)
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGIIEPSLKALASKYNCDKSVCRKCYARLPPRATNCRKRKCGHTNQ
LRPKKKLK

Sequence of entity 9 (JT), FASTA

>8P8U_9 60S ribosomal protein L13-A (chains JT)
MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRA
PTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFR
GIREKRAREKAEAEAEKKK

Sequence of entity 10 (LM), FASTA

>8P8U_10 60S ribosomal protein L9-A (chains LM)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL

Sequence of entity 11 (QZ), FASTA

>8P8U_11 60S ribosomal protein L27-A (chains QZ)
MAKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAK
KVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEE
RHQAGKNQWFFSKLRF

Sequence of entity 12 (RQ), FASTA

>8P8U_12 60S ribosomal protein L42-A (chains RQ)
MVNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFGGQTKPVFHK
KAKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKGQALQF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	129
SPM	Spermine	C10 H26 N4	1
SPD	Spermidine	C7 H19 N3	1
ZN	Zinc ion	Zn	5

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

Primary citation

Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains. Banerjee, A., Ataman, M., Smialek, M.J. et al. Nucleic Acids Res (2024) 52:9028-9048. DOI 10.1093/nar/gkae630 · PubMed

Other PDB entries of the same protein (UniProt P04650 (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
7UOO 2.34 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state
7V08 2.36 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1…
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…

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