4V8T: 60S Ribosomal Subunit

Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1. Determined by electron microscopy at 8.1 Å resolution. Released 9 Jul 2014.

Method: Electron microscopy
Resolution: 8.1 Å
Organisms: Saccharomyces cerevisiae S288C, SACCHAROMYCES CEREVISIAE
Chains: 50
Atoms: 130,050
Mol. weight: 2101.46 kDa
Ligands: ZN
Released: 9 Jul 2014

Explore 4V8T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V8T contains 356 α-helices and 312 β-strands across 46 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 a: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-11	5
β-strand	12	1	6
β-strand	14	1	6
α-helix	42-45	4
β-strand	72-74	3	7
α-helix	79-81	3
α-helix	84-93	10
β-strand	99-100	2	57
β-strand	101-103	3	8
α-helix	104-107	4
β-strand	111-113	3	7
β-strand	124-127	4	8
β-strand	130	1	7
α-helix	132-140	9
β-strand	144-147	4	8

Chain A: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	10-12	3
α-helix	14-16	3
β-strand	18	1	1
α-helix	29-31	3
α-helix	34-38	5
β-strand	41-51	11	2
β-strand	54-64	11	2
β-strand	71-77	7	2
α-helix	78	1
β-strand	83	1	3
β-strand	87-90	4	2
β-strand	101-103	3	2
α-helix	104-106	3
β-strand	112-114	3	2
β-strand	116	1	4
β-strand	126	1	4
β-strand	134-140	7	2
β-strand	145-149	5	2
β-strand	155-159	5	2
β-strand	163-166	4	2
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	1
α-helix	201-203	3
α-helix	206-208	3
β-strand	224	1	5
α-helix	229-230	2
β-strand	237	1	5

Chain b: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	21	1	78
α-helix	37-56	20

Chain B: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	33-35	3
β-strand	43	1	9
β-strand	45-59	15	10
β-strand	60	1	11
β-strand	68	1	11
β-strand	71-80	10	10
β-strand	84-93	10	12
β-strand	100-106	7	12
α-helix	112-115	4
α-helix	116-118	3
α-helix	122-124	3
α-helix	131-135	5
α-helix	142-153	12
β-strand	157-164	8	12
α-helix	166-168	3
α-helix	176-177	2
β-strand	178-182	5	12
β-strand	183	1	9
α-helix	188-198	11
β-strand	202-203	2	12
α-helix	205-207	3
β-strand	214-220	7	10
α-helix	221-223	3
β-strand	226-227	2	13
α-helix	229-233	5
α-helix	236-239	4
β-strand	268-269	2	13
β-strand	274-286	13	10
α-helix	307	1
β-strand	311	1	14
β-strand	315	1	14
β-strand	321-325	5	10
β-strand	335-340	6	10
α-helix	352-354	3
β-strand	358-359	2	10
α-helix	373-380	8

Chain c: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	22-25	4	20
α-helix	27-36	10
β-strand	41-44	4	20
α-helix	50-61	12
β-strand	66-69	4	20
α-helix	74-80	7
β-strand	89-94	6	20

Chain C: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	15
β-strand	10-11	2	16
β-strand	13	1	16
β-strand	19-20	2	15
α-helix	25-27	3
α-helix	32-42	11
β-strand	63-64	2	17
β-strand	75-76	2	17
β-strand	88	1	17
α-helix	98-99	2
α-helix	115-128	14
α-helix	132-137	6
β-strand	150-152	3	18
α-helix	156-158	3
α-helix	162-169	8
α-helix	170-174	5
α-helix	175-182	8
β-strand	186-187	2	19
α-helix	192-194	3
β-strand	199-200	2	19
β-strand	206-209	4	18
α-helix	215-219	5
β-strand	226-229	4	18
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	18
α-helix	252-262	11
α-helix	276-279	4
α-helix	286-289	4
α-helix	293-298	6
α-helix	307-309	3
α-helix	321-326	6
α-helix	331-336	6
α-helix	354-359	6

Chain d: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	24
α-helix	17-20	4
α-helix	25-27	3
α-helix	28-42	15
β-strand	49-51	3	24
α-helix	53-59	7
β-strand	70-79	10	24
β-strand	89-95	7	24
β-strand	107-108	2	24

Chain D: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	10-15	6
α-helix	18-20	3
α-helix	21-24	4
α-helix	30-37	8
α-helix	38-40	3
α-helix	41-43	3
β-strand	50-55	6	21
β-strand	60-66	7	21
β-strand	73-79	7	21
α-helix	80-86	7
α-helix	95-112	18
α-helix	133-135	3
α-helix	139-142	4
β-strand	143	1	22
β-strand	145-147	3	21
α-helix	159-168	10
β-strand	172	1	22
β-strand	183-184	2	23
β-strand	189-190	2	23
α-helix	192-199	8
α-helix	202-214	13
α-helix	216-222	7
α-helix	224-228	5
α-helix	233-235	3
α-helix	236-249	14
α-helix	262-269	8
α-helix	274-278	5
α-helix	279-293	15

38 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 L2-A	A	protein	254	Saccharomyces cerevisiae S288C	P0CX45 (AlphaFold model)
60S ribosomal protein L3	B	protein	387	Saccharomyces cerevisiae S288C	P14126 (AlphaFold model)
60S ribosomal protein L4-A	C	protein	362	Saccharomyces cerevisiae S288C	P10664 (AlphaFold model)
60S ribosomal protein L5	D	protein	297	Saccharomyces cerevisiae S288C	P26321 (AlphaFold model)
60S ribosomal protein L6-A	E	protein	176	Saccharomyces cerevisiae S288C	Q02326
60S ribosomal protein L7-A	F	protein	244	Saccharomyces cerevisiae S288C	P05737
60S ribosomal protein L8-A	G	protein	256	Saccharomyces cerevisiae S288C	P17076
60S ribosomal protein L9-A	H	protein	191	Saccharomyces cerevisiae S288C	P05738
60S ribosomal protein L10	I	protein	221	Saccharomyces cerevisiae S288C	P41805
60S ribosomal protein L11-A	J	protein	174	Saccharomyces cerevisiae S288C	P0C0W9
60S ribosomal protein L12	K	protein	155	SACCHAROMYCES CEREVISIAE
60S ribosomal protein L13-A	L	protein	199	Saccharomyces cerevisiae S288C	Q12690

38 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>4V8T_1 60S ribosomal protein L2-A (chains A)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD

Sequence of entity 2 (B), FASTA

>4V8T_2 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL

Sequence of entity 3 (C), FASTA

>4V8T_3 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD

Sequence of entity 4 (D), FASTA

>4V8T_4 60S ribosomal protein L5 (chains D)
MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI
ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK
GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF
PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY
TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Sequence of entity 5 (E), FASTA

>4V8T_5 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Sequence of entity 6 (F), FASTA

>4V8T_6 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Sequence of entity 7 (G), FASTA

>4V8T_7 60S ribosomal protein L8-A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA

Sequence of entity 8 (H), FASTA

>4V8T_8 60S ribosomal protein L9-A (chains H)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL

Sequence of entity 9 (I), FASTA

>4V8T_9 60S ribosomal protein L10 (chains I)
MARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQL
SSEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWG
KPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPE
YLKKREAGEVKDDGAFVKFLSKKGSLENNIREFPEYFAAQA

Sequence of entity 10 (J), FASTA

>4V8T_10 60S ribosomal protein L11-A (chains J)
MSAKAQNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVRTFGIR
RNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFGIDEHIDLGIKYDPSI
GIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTTKEDTVSWFKQKYDADVLDK

Sequence of entity 11 (K), FASTA

>4V8T_11 60S RIBOSOMAL PROTEIN L12 (chains K)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 12 (L), FASTA

>4V8T_12 60S ribosomal protein L13-A (chains L)
MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRA
PTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFR
GIREKRAREKAEAEAEKKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Cryo-Em Structures of Arx1 and Maturation Factors Rei1 and Jjj1 Bound to the 60S Ribosomal Subunit. Greber, B.J., Boehringer, D., Montellese, C. et al. Nat Struct Mol Biol (2012) 19:1228. DOI 10.1038/NSMB.2425 · 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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