7BTB: 60S ribosomal protein L13-A

Name: PDB 7BTB: Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.22 Angstroms resolution(state R2)
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 3.22 Angstroms resolution(state R2). Determined by electron microscopy at 3.22 Å resolution. Released 28 Oct 2020.

Method: Electron microscopy
Resolution: 3.22 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 53
Atoms: 147,931
Mol. weight: 2517.11 kDa
Ligands: GTP, ZN, MG
Released: 28 Oct 2020

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

Secondary structure: helices and β-sheets

7BTB contains 378 α-helices and 416 β-strands across 49 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: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	72-73	2	8
α-helix	84-90	7
β-strand	99	1	5
β-strand	101-103	3	9
α-helix	104-107	4
β-strand	111-112	2	8
β-strand	124-127	4	9
β-strand	129-130	2	8
α-helix	132-141	10
β-strand	144-147	4	9

Chain A: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	11
α-helix	34-38	5
β-strand	40-49	10	11
β-strand	58-64	7	11
β-strand	71-77	7	11
β-strand	79	1	12
β-strand	83	1	13
β-strand	87-91	5	11
β-strand	101-103	3	11
α-helix	104-106	3
β-strand	112-114	3	11
β-strand	116	1	14
β-strand	126	1	14
β-strand	134-140	7	11
β-strand	145-149	5	11
β-strand	157-158	2	11
β-strand	163-166	4	11
β-strand	169	1	12
α-helix	182-189	8

Chain b: 20 helices, 8 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
β-strand	169-172	4	6
α-helix	180-187	8
β-strand	189	1	6
β-strand	205-210	6	6
β-strand	215-220	6	6
α-helix	235-245	11
β-strand	248	1	6
β-strand	253	1	7
α-helix	266-274	9
α-helix	275-277	3
β-strand	285-287	3	7
α-helix	295-297	3
α-helix	300-311	12
β-strand	317-319	3	7
α-helix	327-348	22
α-helix	358-361	4
α-helix	380-383	4
α-helix	400-403	4
α-helix	425-427	3
α-helix	441-443	3
α-helix	450-465	16
α-helix	485-511	27

Chain B: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	27-29	3
α-helix	40-41	2
β-strand	43	1	17
β-strand	45-60	16	18
β-strand	70-80	11	18
β-strand	84-95	12	19
β-strand	98-106	9	19
α-helix	112-117	6
α-helix	131-135	5
α-helix	144-153	10
β-strand	157-163	7	19
α-helix	166-168	3
β-strand	178-182	5	19
β-strand	183	1	17
α-helix	188-197	10
β-strand	202-203	2	19
β-strand	214-220	7	18
β-strand	225-226	2	20
α-helix	229-233	5
β-strand	269-270	2	20
β-strand	274-286	13	18
α-helix	307	1
β-strand	321-325	5	18
β-strand	335-339	5	18
β-strand	356-359	4	18
α-helix	373-380	8

Chain c: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-17	8
β-strand	21-25	5	10
α-helix	28-36	9
β-strand	41-44	4	10
α-helix	50-63	14
β-strand	66-69	4	10
α-helix	74-81	8
β-strand	89-95	7	10

Chain C: 18 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	22
β-strand	19-20	2	22
α-helix	32-43	12
α-helix	115-127	13
α-helix	128-130	3
α-helix	136-138	3
β-strand	151-152	2	23
α-helix	154-156	3
α-helix	162-165	4
α-helix	167-170	4
α-helix	175-178	4
β-strand	186-187	2	24
α-helix	191-194	4
β-strand	199-200	2	24
β-strand	206-209	4	23
α-helix	215-218	4
β-strand	226-229	4	23
β-strand	248-251	4	23
α-helix	252-256	5
α-helix	258-262	5
α-helix	286-289	4
α-helix	296-298	3
α-helix	321-326	6
α-helix	331-336	6
α-helix	344-346	3
α-helix	355-358	4

Chain d: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	15
β-strand	15	1	16
α-helix	16-18	3
α-helix	25-27	3
α-helix	28-44	17
β-strand	49-51	3	15
α-helix	53-60	8
β-strand	70	1	16
β-strand	73-79	7	15
β-strand	89-95	7	15
β-strand	107-108	2	15

Chain D: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	21-24	4
α-helix	30-37	8
β-strand	50-56	7	26
β-strand	59-66	8	26
β-strand	73-79	7	26
α-helix	83-85	3
α-helix	95-112	18
β-strand	143	1	27
β-strand	145-147	3	26
α-helix	158-169	12
β-strand	172	1	27
β-strand	183	1	28
β-strand	190	1	28
α-helix	192-199	8
α-helix	202-212	11
α-helix	218-221	4
α-helix	224-229	6
α-helix	233-249	17
α-helix	254-256	3
α-helix	262-272	11
α-helix	279-292	14

41 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 L13-A	L	protein	199	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12690 (AlphaFold model)
60S ribosomal protein L28	a	protein	149	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P02406 (AlphaFold model)
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
60S ribosomal protein L5	D	protein	297	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P26321
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
Proteasome-interacting protein CIC1	K	protein	376	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38779

41 more molecules are not listed.

Sequence of entity 1 (L), FASTA

>7BTB_1 60S ribosomal protein L13-A (chains L)
MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRA
PTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFR
GIREKRAREKAEAEAEKKK

Sequence of entity 2 (a), FASTA

>7BTB_2 60S ribosomal protein L28 (chains a)
MPSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPGYFGKVGMRY
FHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDTLAAGYGKILGKGRIPN
VPVIVKARFVSKLAEEKIRAAGGVVELIA

Sequence of entity 3 (A), FASTA

>7BTB_3 60S ribosomal protein L2-A (chains A)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD

Sequence of entity 4 (B), FASTA

>7BTB_4 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL

Sequence of entity 5 (C), FASTA

>7BTB_5 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD

Sequence of entity 6 (D), FASTA

>7BTB_6 60S ribosomal protein L5 (chains D)
MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI
ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK
GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF
PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY
TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Sequence of entity 7 (E), FASTA

>7BTB_7 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Sequence of entity 8 (F), FASTA

>7BTB_8 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Sequence of entity 9 (G), FASTA

>7BTB_9 60S ribosomal protein L8-A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA

Sequence of entity 10 (H), FASTA

>7BTB_10 60S ribosomal protein L9-A (chains H)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL

Sequence of entity 11 (J), FASTA

>7BTB_11 60S ribosomal protein L11-A (chains J)
MSAKAQNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVRTFGIR
RNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFGIDEHIDLGIKYDPSI
GIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTTKEDTVSWFKQKYDADVLDK

Sequence of entity 12 (K), FASTA

>7BTB_12 Proteasome-interacting protein CIC1 (chains K)
MAKKSNSKKSTPVSTPSKEKKKVIEKKSSTAIPRERVIKAVNELIKFTSKPQDENNEEGN
NGKKNLLEDDEEELKKDLQLIVVNNKSFTGTSKSFKLKLLNVKHSFYKPWKEASATAVKD
FKVLLILKDSDIKKVSEDDLFDQLDSEGIKVDEIICGKDLKTVYKAYEARNAFISQFSLI
LADDSIVTSLPKLMGGKAYNKVETTPISIRTHANKEFSLTTLTNNIKKVYMNQLPVKLPR
GTTLNVHLGNLEWLRPEEFVDNVELISEQLIKAYQIRSIFIKTNRSPVLPLYYNQDVLDE
LEAKKDKIEETHEDDMVTIDGVQVHLSTFNKGLMEIANPSELGSIFSKQINNAKKRSSSE
LEKESSESEAVKKAKS

Ligands and cofactors

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

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 Q12690 (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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