3JCT: Eukaryotic pre-60S ribosomal subunits

Name: PDB 3JCT: Cryo-em structure of eukaryotic pre-60S ribosomal subunits
Published: 2016-06-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-em structure of eukaryotic pre-60S ribosomal subunits. Determined by electron microscopy at 3.08 Å resolution. Released 1 Jun 2016.

Method: Electron microscopy
Resolution: 3.08 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 58
Atoms: 156,562
Mol. weight: 2679.63 kDa
Ligands: MG, GTP, ZN
Released: 1 Jun 2016

Explore 3JCT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JCT contains 475 α-helices and 472 β-strands across 54 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 4: 22 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	27-30	4
α-helix	32-45	14
α-helix	61-76	16
β-strand	87-88	2	26
β-strand	94-97	4	26
β-strand	100-102	3	27
α-helix	110-118	9
α-helix	126-130	5
β-strand	139-147	9	26
β-strand	150-158	9	26
α-helix	162-164	3
α-helix	171-172	2
β-strand	176	1	28
α-helix	179-200	22
α-helix	220-234	15
β-strand	236-238	3	26
α-helix	239	1
β-strand	243-247	5	26
β-strand	248	1	29
β-strand	251	1	29
β-strand	266-268	3	26
α-helix	271-276	6
β-strand	315-325	11	26
β-strand	333-340	8	27
β-strand	360-361	2	30
α-helix	373-384	12
β-strand	390	1	30
α-helix	406-428	23
β-strand	433-434	2	30
β-strand	437-444	8	27
α-helix	445-450	6
β-strand	474	1	31
β-strand	481	1	31
α-helix	482-490	9
α-helix	496	1
β-strand	497	1	27
α-helix	498-499	2
β-strand	500-510	11	26
β-strand	521-524	4	26
α-helix	529-532	4
α-helix	533-536	4
β-strand	537	1	28
α-helix	548-559	12
β-strand	569-571	3	26
α-helix	572-576	5

Chain 5: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	43-98	56
α-helix	101-111	11

Chain a: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	72-73	2	5
α-helix	79-81	3
α-helix	84-91	8
β-strand	99-100	2	66
β-strand	101-103	3	6
α-helix	104-107	4
β-strand	111-112	2	5
β-strand	124-127	4	6
β-strand	129-130	2	5
α-helix	132-141	10
β-strand	145-147	3	6
α-helix	148	1

Chain A: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-9	4
α-helix	18-19	2
α-helix	29-31	3
α-helix	34-38	5
β-strand	41-49	9	1
α-helix	57	1
β-strand	58-64	7	1
β-strand	71-77	7	1
α-helix	78	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	108	1
β-strand	112-114	3	1
β-strand	116	1	4
β-strand	126	1	4
β-strand	134-140	7	1
β-strand	145-149	5	1
β-strand	155-158	4	1
β-strand	163-166	4	1
β-strand	169	1	2
α-helix	174-176	3
α-helix	182-192	11
α-helix	198-200	3
α-helix	201-203	3
α-helix	206-208	3

Chain b: 28 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-28	15
α-helix	39-67	29
α-helix	76-86	11
α-helix	88-116	29
α-helix	122-141	20
α-helix	144-158	15
α-helix	161-162	2
β-strand	170-174	5	14
α-helix	180-187	8
β-strand	205-207	3	14
β-strand	210	1	15
β-strand	215	1	15
β-strand	218-220	3	14
α-helix	234-245	12
β-strand	249-255	7	14
α-helix	264-274	11
α-helix	275-280	6
β-strand	283-288	6	14
α-helix	300-309	10
β-strand	317-319	3	14
α-helix	327-347	21
α-helix	354-361	8
α-helix	380-384	5
α-helix	385-387	3
α-helix	398-406	9
α-helix	412-414	3
α-helix	427-429	3
β-strand	435	1	16
β-strand	440	1	16
α-helix	441-444	4
α-helix	450-466	17
α-helix	484-511	28
α-helix	518-520	3
α-helix	530-538	9
α-helix	543-556	14
α-helix	562-566	5
α-helix	596-615	20
α-helix	632-635	4

Chain B: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
α-helix	40-41	2
β-strand	43	1	7
β-strand	45-47	3	8
β-strand	49-50	2	9
β-strand	54-59	6	10
β-strand	71-76	6	10
β-strand	78-80	3	9
α-helix	82-83	2
β-strand	84-94	11	11
β-strand	99-106	8	11
α-helix	112-118	7
α-helix	129-136	8
α-helix	143-153	11
β-strand	157-163	7	11
α-helix	166-168	3
β-strand	178-182	5	11
β-strand	183	1	7
α-helix	187-196	10
β-strand	202-203	2	11
α-helix	206-208	3
β-strand	214-220	7	8
β-strand	223	1	12
β-strand	227	1	13
α-helix	229-233	5
β-strand	268	1	13
β-strand	271	1	12
β-strand	274-281	8	8
β-strand	285-286	2	9
β-strand	321-323	3	9
β-strand	337-339	3	8
β-strand	356-359	4	10
α-helix	373-380	8

Chain c: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-19	10
β-strand	23-25	3	21
α-helix	27-36	10
β-strand	41-44	4	21
α-helix	50-63	14
β-strand	66-69	4	21
α-helix	74-81	8
β-strand	89-92	4	21
α-helix	100-102	3

Chain C: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	17
β-strand	9	1	18
β-strand	19-20	2	17
α-helix	32-43	12
β-strand	63	1	19
β-strand	76	1	19
β-strand	88	1	19
α-helix	97-99	3
α-helix	115-129	15
α-helix	133-138	6
β-strand	150-152	3	18
α-helix	154-158	5
α-helix	162-172	11
α-helix	175-183	9
β-strand	186-187	2	20
α-helix	191-195	5
β-strand	199-200	2	20
β-strand	206-209	4	18
α-helix	215-220	6
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	286-291	6
α-helix	294-298	5
α-helix	300-302	3
α-helix	321-326	6
α-helix	330-337	8
α-helix	350-352	3
α-helix	353-360	8

46 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
Bud site selection protein 20	I	protein	166	Saccharomyces cerevisiae S288c	Q08004
60S ribosomal protein L11-A	J	protein	174	Saccharomyces cerevisiae S288c	P0C0W9
Proteasome-interacting protein CIC1	K	protein	376	Saccharomyces cerevisiae S288c	P38779
60S ribosomal protein L13-A	L	protein	199	Saccharomyces cerevisiae S288c	Q12690

46 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>3JCT_1 60S ribosomal protein L2-A (chains A)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD

Sequence of entity 2 (B), FASTA

>3JCT_2 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL

Sequence of entity 3 (C), FASTA

>3JCT_3 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD

Sequence of entity 4 (D), FASTA

>3JCT_4 60S ribosomal protein L5 (chains D)
MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI
ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK
GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF
PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY
TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Sequence of entity 5 (E), FASTA

>3JCT_5 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Sequence of entity 6 (F), FASTA

>3JCT_6 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Sequence of entity 7 (G), FASTA

>3JCT_7 60S ribosomal protein L8-A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA

Sequence of entity 8 (H), FASTA

>3JCT_8 60S ribosomal protein L9-A (chains H)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL

Sequence of entity 9 (I), FASTA

>3JCT_9 Bud site selection protein 20 (chains I)
MGRYSVKRYKTKRRTRDLDLIYNDLSTKESVQKLLNQPLDETKPGLGQHYCIHCAKYMET
AIALKTHLKGKVHKRRVKELRGVPYTQEVSDAAAGYNLNKFLNRVQEITQSVGPEKESNE
ALLKEHLDSTLANVKTTEPTLPWAAADAEANTAAVTEAESTASAST

Sequence of entity 10 (J), FASTA

>3JCT_10 60S ribosomal protein L11-A (chains J)
MSAKAQNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVRTFGIR
RNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFGIDEHIDLGIKYDPSI
GIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTTKEDTVSWFKQKYDADVLDK

Sequence of entity 11 (K), FASTA

>3JCT_11 Proteasome-interacting protein CIC1 (chains K)
MAKKSNSKKSTPVSTPSKEKKKVIEKKSSTAIPRERVIKAVNELIKFTSKPQDENNEEGN
NGKKNLLEDDEEELKKDLQLIVVNNKSFTGTSKSFKLKLLNVKHSFYKPWKEASATAVKD
FKVLLILKDSDIKKVSEDDLFDQLDSEGIKVDEIICGKDLKTVYKAYEARNAFISQFSLI
LADDSIVTSLPKLMGGKAYNKVETTPISIRTHANKEFSLTTLTNNIKKVYMNQLPVKLPR
GTTLNVHLGNLEWLRPEEFVDNVELISEQLIKAYQIRSIFIKTNRSPVLPLYYNQDVLDE
LEAKKDKIEETHEDDMVTIDGVQVHLSTFNKGLMEIANPSELGSIFSKQINNAKKRSSSE
LEKESSESEAVKKAKS

Sequence of entity 12 (L), FASTA

>3JCT_12 60S ribosomal protein L13-A (chains L)
MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRA
PTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFR
GIREKRAREKAEAEAEKKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
ZN	Zinc ion	Zn	4

Primary citation

Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes. Wu, S., Tutuncuoglu, B., Yan, K. et al. Nature (2016) 534:133-137. DOI 10.1038/nature17942 · 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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