7BT6: 60S ribosomal protein L2-A

Name: PDB 7BT6: Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1)
Published: 2020-10-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1). Determined by electron microscopy at 3.12 Å resolution. Released 28 Oct 2020.

Method: Electron microscopy
Resolution: 3.12 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 47
Atoms: 133,299
Mol. weight: 2215.43 kDa
Ligands: GTP, MG, ZN
Released: 28 Oct 2020

Explore 7BT6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BT6 contains 315 α-helices and 381 β-strands across 44 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: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	72-73	2	113
α-helix	84-91	8
β-strand	99-100	2	42
β-strand	101-103	3	114
β-strand	111-112	2	113
β-strand	124-127	4	114
β-strand	129-130	2	113
α-helix	132-141	10
β-strand	144-147	4	114

Chain A: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	29-32	4
α-helix	34-38	5
β-strand	42-49	8	1
β-strand	58-63	6	1
β-strand	72-77	6	1
β-strand	79	1	2
β-strand	83	1	3
β-strand	87-89	3	1
β-strand	101-103	3	4
α-helix	104-106	3
β-strand	112-114	3	4
β-strand	134-140	7	4
β-strand	145-149	5	4
β-strand	155-159	5	4
β-strand	163-166	4	4
β-strand	169	1	2
α-helix	174-176	3
α-helix	182-189	8

Chain b: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-27	14
α-helix	39-65	27
α-helix	78-86	9
α-helix	88-116	29
α-helix	122-140	19
α-helix	146-157	12
β-strand	169-173	5	115
α-helix	180-187	8
β-strand	205-211	7	115
β-strand	214-220	7	115
α-helix	236-245	10
β-strand	248-252	5	115
β-strand	253-254	2	116
α-helix	264-274	11
α-helix	275-278	4
β-strand	284-287	4	116
α-helix	295-297	3
α-helix	300-307	8
β-strand	316-319	4	116
α-helix	328-349	22
α-helix	353-357	5
β-strand	364	1	117
α-helix	380-383	4
α-helix	400-406	7
β-strand	435	1	118
β-strand	440	1	118
α-helix	441-444	4
α-helix	450-466	17
α-helix	487-511	25

Chain B: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	6
β-strand	47-59	13	7
β-strand	71-80	10	7
β-strand	84-96	13	8
β-strand	98-106	9	8
α-helix	112-115	4
α-helix	116-118	3
α-helix	131-134	4
α-helix	135-137	3
α-helix	145-153	9
β-strand	157-163	7	8
α-helix	166-168	3
β-strand	178-182	5	8
β-strand	183	1	6
α-helix	188-197	10
β-strand	202-203	2	8
α-helix	205-207	3
β-strand	214-221	8	7
β-strand	225-227	3	9
α-helix	229-233	5
α-helix	235-238	4
β-strand	242	1	10
β-strand	245	1	10
β-strand	268-270	3	9
β-strand	273-285	13	7
β-strand	321-325	5	7
β-strand	335-339	5	7
β-strand	356-359	4	7
α-helix	373-380	8

Chain c: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-19	10
β-strand	21-25	5	5
α-helix	27-36	10
β-strand	41-44	4	5
α-helix	50-62	13
β-strand	66-69	4	5
α-helix	74-80	7
β-strand	89-95	7	5

Chain C: 20 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	12
β-strand	9	1	13
β-strand	20-21	2	12
α-helix	25-27	3
α-helix	32-42	11
α-helix	98-99	2
α-helix	115-127	13
α-helix	134-137	4
β-strand	150-152	3	13
α-helix	154-158	5
α-helix	162-170	9
α-helix	175-180	6
β-strand	186-187	2	14
α-helix	193-195	3
β-strand	199-200	2	14
β-strand	206-209	4	13
β-strand	226-229	4	13
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	13
α-helix	254-262	9
α-helix	286-291	6
α-helix	293-298	6
α-helix	300-301	2
α-helix	307-309	3
α-helix	321-326	6
α-helix	331-334	4
α-helix	350-352	3
α-helix	353-360	8

Chain d: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	11
α-helix	25-27	3
α-helix	29-44	16
β-strand	49-51	3	11
α-helix	53-59	7
β-strand	70-79	10	11
β-strand	89-95	7	11
β-strand	108	1	11

Chain D: 14 helices, 8 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	16
β-strand	59-66	8	16
β-strand	73-79	7	16
α-helix	80-85	6
α-helix	95-112	18
α-helix	141-142	2
β-strand	143	1	17
β-strand	146-147	2	16
α-helix	160-169	10
β-strand	172	1	17
β-strand	184	1	18
β-strand	189	1	18
α-helix	192-199	8
α-helix	202-214	13
α-helix	217-220	4
α-helix	224-227	4
α-helix	235-249	15
α-helix	262-269	8
α-helix	279-291	13

36 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 (strain ATCC 204508 / S288c)	P0CX45 (AlphaFold model)
60S ribosomal protein L3	B	protein	387	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P14126 (AlphaFold model)
60S ribosomal protein L4-A	C	protein	362	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P10664 (AlphaFold model)
60S ribosomal protein L5	D	protein	297	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P26321 (AlphaFold model)
60S ribosomal protein L6-A	E	protein	176	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q02326
60S ribosomal protein L7-A	F	protein	244	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05737
60S ribosomal protein L8-A	G	protein	256	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P17076
60S ribosomal protein L9-A	H	protein	191	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05738
60S ribosomal protein L11-A	J	protein	174	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0C0W9
60S ribosomal protein L13-A	L	protein	199	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12690
60S ribosomal protein L14-A	M	protein	138	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P36105
60S ribosomal protein L15-A	N	protein	204	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05748

35 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7BT6_1 60S ribosomal protein L2-A (chains A)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD

Sequence of entity 2 (B), FASTA

>7BT6_2 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL

Sequence of entity 3 (C), FASTA

>7BT6_3 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD

Sequence of entity 4 (D), FASTA

>7BT6_4 60S ribosomal protein L5 (chains D)
MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI
ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK
GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF
PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY
TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Sequence of entity 5 (E), FASTA

>7BT6_5 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Sequence of entity 6 (F), FASTA

>7BT6_6 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Sequence of entity 7 (G), FASTA

>7BT6_7 60S ribosomal protein L8-A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA

Sequence of entity 8 (H), FASTA

>7BT6_8 60S ribosomal protein L9-A (chains H)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL

Sequence of entity 9 (J), FASTA

>7BT6_9 60S ribosomal protein L11-A (chains J)
MSAKAQNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVRTFGIR
RNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFGIDEHIDLGIKYDPSI
GIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTTKEDTVSWFKQKYDADVLDK

Sequence of entity 10 (L), FASTA

>7BT6_10 60S ribosomal protein L13-A (chains L)
MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRA
PTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFR
GIREKRAREKAEAEAEKKK

Sequence of entity 11 (M), FASTA

>7BT6_11 60S ribosomal protein L14-A (chains M)
MSTDSIVKASNWRLVEVGRVVLIKKGQSAGKLAAIVEIIDQKKVLIDGPKAGVPRQAINL
GQVVLTPLTFALPRGARTATVSKKWAAAAVCEKWAASSWAKKIAQRERRAALTDFERFQV
MVLRKQKRYTVKKALAKA

Sequence of entity 12 (N), FASTA

>7BT6_12 60S ribosomal protein L15-A (chains N)
MGAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFV
IYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYW
VNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGINKGHKF
NNTKAGRRKTWKRQNTLSLWRYRK

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	3

Primary citation

Structural insights into assembly of the ribosomal nascent polypeptide exit tunnel. Wilson, D.M., Li, Y., LaPeruta, A. et al. Nat Commun (2020) 11:5111-5111. DOI 10.1038/s41467-020-18878-8 · 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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