6FT6: Nop53 pre-60S particle

Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors. Determined by electron microscopy at 3.9 Å resolution. Released 28 Mar 2018.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 57
Atoms: 157,395
Mol. weight: 2670.69 kDa
Ligands: ZN, GTP, MG
Released: 28 Mar 2018

Explore 6FT6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FT6 contains 493 α-helices and 469 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: 19 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	31-45	15
α-helix	61-76	16
β-strand	87-97	11	139
β-strand	100-102	3	140
α-helix	110-118	9
α-helix	126-129	4
α-helix	132-134	3
β-strand	139-147	9	139
β-strand	150-158	9	139
α-helix	171-172	2
β-strand	176	1	141
α-helix	179-199	21
α-helix	220-234	15
β-strand	236-238	3	139
α-helix	239	1
β-strand	243-246	4	139
β-strand	248	1	142
β-strand	251	1	142
β-strand	266-268	3	139
α-helix	273-276	4
β-strand	316-325	10	139
β-strand	333-339	7	140
β-strand	360-362	3	143
α-helix	375-378	4
β-strand	390	1	143
α-helix	407-426	20
β-strand	432-434	3	143
α-helix	435-437	3
β-strand	438-444	7	140
α-helix	446-450	5
β-strand	475	1	144
β-strand	480	1	144
α-helix	482-490	9
β-strand	497	1	140
β-strand	500-510	11	139
β-strand	521-525	5	139
α-helix	533-535	3
β-strand	537	1	141
α-helix	548-559	12
β-strand	569-571	3	139
α-helix	572-576	5

Chain 5: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	43-89	47
α-helix	91-96	6
α-helix	101-111	11

Chain a: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	72-73	2	1
α-helix	84-91	8
β-strand	99-100	2	59
β-strand	101-103	3	2
β-strand	111-112	2	1
β-strand	124-127	4	2
β-strand	129	1	1
α-helix	132-141	10
β-strand	145-147	3	2
α-helix	148	1

Chain A: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-9	4
α-helix	10-12	3
α-helix	29-31	3
β-strand	42-49	8	3
β-strand	58-64	7	3
β-strand	71-77	7	3
α-helix	78	1
β-strand	79	1	4
β-strand	83	1	5
β-strand	87-89	3	3
β-strand	90	1	6
β-strand	101-103	3	6
α-helix	104-106	3
α-helix	108	1
β-strand	112-114	3	6
β-strand	116	1	7
β-strand	126	1	7
β-strand	134-140	7	6
β-strand	145-149	5	6
β-strand	155-159	5	6
β-strand	163-166	4	6
α-helix	168	1
β-strand	169	1	4
α-helix	174-176	3
α-helix	182-192	11
α-helix	198-200	3

Chain b: 29 helices, 7 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	122-142	21
α-helix	144-158	15
β-strand	169-174	6	8
α-helix	180-187	8
β-strand	206-210	5	8
β-strand	215-219	5	8
α-helix	234-245	12
β-strand	248-255	8	8
α-helix	264-274	11
α-helix	275-277	3
β-strand	284-288	5	8
α-helix	300-309	10
β-strand	317-318	2	8
α-helix	325-347	23
α-helix	354-361	8
α-helix	363	1
β-strand	364	1	9
α-helix	380-383	4
α-helix	385-387	3
α-helix	400-406	7
α-helix	426-428	3
α-helix	430-432	3
α-helix	441-443	3
α-helix	450-464	15
α-helix	485-508	24
α-helix	513-516	4
α-helix	531-536	6
α-helix	543-556	14
α-helix	562-566	5
α-helix	596-607	12
α-helix	610-616	7
α-helix	632-635	4

Chain B: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	27-29	3
α-helix	32-34	3
α-helix	40-41	2
β-strand	43	1	10
β-strand	46-50	5	11
β-strand	54-60	7	11
β-strand	63	1	12
β-strand	65	1	12
β-strand	70-81	12	11
β-strand	84-94	11	13
β-strand	99-106	8	13
α-helix	112-118	7
α-helix	122-124	3
α-helix	133-137	5
α-helix	144-153	10
β-strand	157-163	7	13
α-helix	166-168	3
α-helix	176-177	2
β-strand	178-182	5	13
β-strand	183	1	10
α-helix	188-197	10
β-strand	202-203	2	13
β-strand	214-221	8	11
β-strand	226-227	2	14
α-helix	229-233	5
α-helix	235-238	4
β-strand	268-269	2	14
β-strand	273-286	14	11
α-helix	306-307	2
β-strand	311	1	15
β-strand	314	1	15
β-strand	320-325	6	11
β-strand	334-339	6	11
α-helix	348-351	4
β-strand	355-359	5	11
α-helix	373-380	8

Chain c: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-17	8
β-strand	23-25	3	16
α-helix	27-36	10
β-strand	41-44	4	16
α-helix	50-63	14
β-strand	66-69	4	16
α-helix	74-81	8
β-strand	89-92	4	16

Chain C: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
β-strand	7-9	3	17
β-strand	15-19	5	17
α-helix	32-42	11
β-strand	63	1	18
α-helix	75	1
β-strand	76	1	18
α-helix	77	1
β-strand	88	1	18
α-helix	98-99	2
α-helix	115-128	14
α-helix	133-138	6
β-strand	150-152	3	17
α-helix	154-158	5
α-helix	162-172	11
α-helix	175-180	6
β-strand	186-187	2	19
α-helix	191-195	5
β-strand	199-200	2	19
β-strand	206-209	4	17
α-helix	215-218	4
β-strand	226-229	4	17
α-helix	240-242	3
β-strand	248-251	4	17
α-helix	252-262	11
α-helix	286-290	5
α-helix	293-298	6
α-helix	299-301	3
α-helix	321-326	6
α-helix	330-336	7
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
7S ribosomal RNA	2	RNA	162	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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
Bud site selection protein 20	I	protein	166	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q08004
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

45 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>6FT6_1 7S ribosomal RNA (chains 2)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUAAAAUU

Sequence of entity 2 (A), FASTA

>6FT6_2 60S ribosomal protein L2-A (chains A)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD

Sequence of entity 3 (B), FASTA

>6FT6_3 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL

Sequence of entity 4 (C), FASTA

>6FT6_4 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD

Sequence of entity 5 (D), FASTA

>6FT6_5 60S ribosomal protein L5 (chains D)
MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI
ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK
GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF
PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY
TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Sequence of entity 6 (E), FASTA

>6FT6_6 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Sequence of entity 7 (F), FASTA

>6FT6_7 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Sequence of entity 8 (G), FASTA

>6FT6_8 60S ribosomal protein L8-A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA

Sequence of entity 9 (H), FASTA

>6FT6_9 60S ribosomal protein L9-A (chains H)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL

Sequence of entity 10 (I), FASTA

>6FT6_10 Bud site selection protein 20 (chains I)
MGRYSVKRYKTKRRTRDLDLIYNDLSTKESVQKLLNQPLDETKPGLGQHYCIHCAKYMET
AIALKTHLKGKVHKRRVKELRGVPYTQEVSDAAAGYNLNKFLNRVQEITQSVGPEKESNE
ALLKEHLDSTLANVKTTEPTLPWAAADAEANTAAVTEAESTASAST

Sequence of entity 11 (J), FASTA

>6FT6_11 60S ribosomal protein L11-A (chains J)
MSAKAQNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVRTFGIR
RNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFGIDEHIDLGIKYDPSI
GIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTTKEDTVSWFKQKYDADVLDK

Sequence of entity 12 (L), FASTA

>6FT6_12 60S ribosomal protein L13-A (chains L)
MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRA
PTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFR
GIREKRAREKAEAEAEKKK

Ligands and cofactors

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

Primary citation

Structure of the nuclear exosome captured on a maturing preribosome. Schuller, J.M., Falk, S., Fromm, L. et al. Science (2018) 360:219-222. DOI 10.1126/science.aar5428 · 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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