8HFR: NPC-trapped pre-60S particle

NPC-trapped pre-60S particle. Determined by electron microscopy at 2.64 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 2.64 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 61
Atoms: 152,374
Mol. weight: 2639.6 kDa
Ligands: MG
Released: 12 Apr 2023

Explore 8HFR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HFR contains 450 α-helices and 452 β-strands across 58 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 AN: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	102-114	13
β-strand	115-116	2	128
β-strand	121-123	3	128
α-helix	131-136	6
α-helix	148-158	11
β-strand	166-168	3	128
α-helix	180-182	3
α-helix	183-186	4
β-strand	192-194	3	128
α-helix	207-209	3
β-strand	218-220	3	128
α-helix	225-228	4
α-helix	232-239	8
β-strand	245-246	2	128
β-strand	250	1	128
β-strand	252	1	129
α-helix	254-260	7
β-strand	270	1	130
α-helix	275-294	20
α-helix	296-302	7
β-strand	309-314	6	130
α-helix	317-319	3
β-strand	322	1	131
α-helix	334-336	3
α-helix	347-352	6
β-strand	355	1	130
α-helix	358-366	9
β-strand	369	1	132
β-strand	372	1	130
α-helix	379-381	3
β-strand	383-389	7	130
β-strand	394-404	11	130
β-strand	409	1	132
α-helix	433-435	3
β-strand	442-452	11	130
β-strand	459-468	10	130
β-strand	473	1	24

Chain As: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
β-strand	20	1	8
β-strand	24	1	8
β-strand	33-38	6	9
β-strand	50-52	3	10
β-strand	67-68	2	11
α-helix	72-79	8
β-strand	84-85	2	11
α-helix	87-95	9
α-helix	97-106	10
β-strand	111-113	3	12
α-helix	134-135	2
β-strand	136-138	3	12
α-helix	144-153	10
β-strand	156-158	3	10
β-strand	164-167	4	9
α-helix	176-193	18
β-strand	201-207	7	9

Chain aw: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	42-48	7
α-helix	65-68	4
β-strand	72-73	2	61
α-helix	75-81	7
α-helix	84-92	9
β-strand	99	1	123
β-strand	101-103	3	62
α-helix	104-107	4
β-strand	111-112	2	61
β-strand	124-127	4	62
β-strand	129-130	2	61
α-helix	132-141	10
β-strand	144-147	4	62

Chain b3: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	12-18	7
β-strand	22	1	13
α-helix	23-25	3
β-strand	33	1	14
β-strand	35	1	14
α-helix	37-57	21

Chain B4: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-49	10	26
β-strand	58-64	7	26
β-strand	71-77	7	26
α-helix	78	1
β-strand	79	1	27
β-strand	83	1	28
β-strand	87-91	5	26
β-strand	101-103	3	26
α-helix	104-106	3
β-strand	112-114	3	26
β-strand	116	1	29
β-strand	126	1	29
β-strand	134-140	7	26
β-strand	145-149	5	26
β-strand	155-159	5	26
β-strand	163-166	4	26
β-strand	169	1	27
α-helix	174-176	3
α-helix	182-189	8
α-helix	201-203	3
β-strand	224	1	30
α-helix	225-226	2
β-strand	237	1	30

Chain Bt: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	39-44	6
β-strand	51-54	4	24
β-strand	58-59	2	24
α-helix	62-71	10
β-strand	76-82	7	24
β-strand	86	1	24
β-strand	93-104	12	24
β-strand	109	1	25
β-strand	115	1	25
β-strand	117	1	129
β-strand	145-154	10	24
β-strand	168-175	8	24
β-strand	177	1	131

Chain cC: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
β-strand	21-25	5	88
α-helix	27-35	9
β-strand	41-45	5	88
α-helix	50-63	14
β-strand	66-70	5	88
α-helix	74-81	8
β-strand	89-95	7	88

Chain CD: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
α-helix	33-35	3
α-helix	40-41	2
β-strand	43	1	90
β-strand	45-60	16	91
β-strand	70-80	11	91
β-strand	84-95	12	92
β-strand	98-106	9	92
α-helix	112-118	7
α-helix	133-137	5
α-helix	143-153	11
β-strand	157-163	7	92
α-helix	166-168	3
β-strand	178-182	5	92
β-strand	183	1	90
α-helix	188-197	10
β-strand	202-203	2	92
α-helix	205-207	3
β-strand	214-220	7	91
α-helix	221-223	3
β-strand	225-227	3	93
α-helix	229-233	5
α-helix	235-238	4
β-strand	268-270	3	93
β-strand	274-286	13	91
β-strand	311	1	94
β-strand	315	1	94
β-strand	321-325	5	91
β-strand	335-339	5	91
β-strand	356-359	4	91
α-helix	373-380	8

50 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 L35-A	h1	protein	120	Saccharomyces cerevisiae S288C	P0CX84 (AlphaFold model)
60S ribosomal protein L34-A	g2	protein	121	Saccharomyces cerevisiae S288C	P87262 (AlphaFold model)
60S ribosomal protein L29	b3	protein	59	Saccharomyces cerevisiae S288C	P05747 (AlphaFold model)
60S ribosomal protein L2-A	B4	protein	254	Saccharomyces cerevisiae S288C	P0CX45 (AlphaFold model)
60S ribosomal protein L23-A	V5	protein	137	Saccharomyces cerevisiae S288C	P0CX41
60S ribosomal protein L16-A	O6	protein	199	Saccharomyces cerevisiae S288C	P26784
60S ribosomal protein L33-A	f7	protein	107	Saccharomyces cerevisiae S288C	P05744
60S ribosomal protein L6-A	F8	protein	176	Saccharomyces cerevisiae S288C	Q02326
Nucleolar GTP-binding protein 2	v9	protein	486	Saccharomyces cerevisiae S288C	P53742
Nucleolar GTP-binding protein 1	rA	protein	647	Saccharomyces cerevisiae S288C	Q02892
Ribosome biogenesis protein RLP24	tB	protein	199	Saccharomyces cerevisiae S288C	Q07915
60S ribosomal protein L30	cC	protein	105	Saccharomyces cerevisiae S288C	P14120

45 more molecules are not listed.

Sequence of entity 1 (h1), FASTA

>8HFR_1 60S ribosomal protein L35-A (chains h1)
MAGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPSLPKIKTVRKSIACVLTVINE
QQREAVRQLYKGKKYQPKDLRAKKTRALRRALTKFEASQVTEKQRKKQIAFPQRKYAIKA

Sequence of entity 2 (g2), FASTA

>8HFR_2 60S ribosomal protein L34-A (chains g2)
MAQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSALQGISTLRPR
QYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIVKKVVKEQTEAAKKSEKKAK
K

Sequence of entity 3 (b3), FASTA

>8HFR_3 60S ribosomal protein L29 (chains b3)
MAKSKNHTAHNQTRKAHRNGIKKPKTYKYPSLKGVDPKFRRNHKHALHGTAKALAAAKK

Sequence of entity 4 (B4), FASTA

>8HFR_4 60S ribosomal protein L2-A (chains B4)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD

Sequence of entity 5 (V5), FASTA

>8HFR_5 60S ribosomal protein L23-A (chains V5)
MSGNGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMA
TVKKGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGK
ECADLWPRVASNSGVVV

Sequence of entity 6 (O6), FASTA

>8HFR_6 60S ribosomal protein L16-A (chains O6)
MSVEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRK
ATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVV
PQALRVLRLKPGRKYTTLGKLSTSVGWKYEDVVAKLEAKRKVSSAEYYAKKRAFTKKVAS
ANATAAESDVAKQLAALGY

Sequence of entity 7 (f7), FASTA

>8HFR_7 60S ribosomal protein L33-A (chains f7)
MAESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVR
GSKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI

Sequence of entity 8 (F8), FASTA

>8HFR_8 60S ribosomal protein L6-A (chains F8)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Sequence of entity 9 (v9), FASTA

>8HFR_9 Nucleolar GTP-binding protein 2 (chains v9)
MGTGKKEKSRRIREGDTKDGNLRVKGENFYRDSKRVKFLNMYTSGKEIRNKKGNLIRAAS
FQDSTIPDARVQPDRRWFGNTRVISQDALQHFRSALGETQKDTYQVLLRRNKLPMSLLEE
KDADESPKARILDTESYADAFGPKAQRKRPRLAASNLEDLVKATNEDITKYEEKQVLDAT
LGLMGNQEDKENGWTSAAKEAIFSKGQSKRIWNELYKVIDSSDVVIHVLDARDPLGTRCK
SVEEYMKKETPHKHLIYVLNKCDLVPTWVAAAWVKHLSKERPTLAFHASITNSFGKGSLI
QLLRQFSQLHTDRKQISVGFIGYPNTGKSSIINTLRKKKVCQVAPIPGETKVWQYITLMK
RIFLIDCPGIVPPSSKDSEEDILFRGVVRVEHVTHPEQYIPGVLKRCQVKHLERTYEISG
WKDATEFIEILARKQGRLLKGGEPDESGVSKQILNDFNRGKIPWFVLPPEKEGEEKPKKK
EVEKTA

Sequence of entity 10 (rA), FASTA

>8HFR_10 Nucleolar GTP-binding protein 1 (chains rA)
MQLSWKDIPTVAPANDLLDIVLNRTQRKTPTVIRPGFKITRIRAFYMRKVKYTGEGFVEK
FEDILKGFPNINDVHPFHRDLMDTLYEKNHYKISLAAISRAKSLVEQVARDYVRLLKFGQ
SLFQCKQLKRAALGRMATIVKKLRDPLAYLEQVRQHIGRLPSIDPNTRTLLICGYPNVGK
SSFLRCITKSDVDVQPYAFTTKSLYVGHFDYKYLRFQAIDTPGILDRPTEEMNNIEMQSI
YAIAHLRSCVLYFMDLSEQCGFTIEAQVKLFHSIKPLFANKSVMVVINKTDIIRPEDLDE
ERAQLLESVKEVPGVEIMTSSCQLEENVMEVRNKACEKLLASRIENKLKSQSRINNVLNK
IHVAQPQARDDVKRTPFIPESVKNLKKYDPEDPNRRKLARDIEAENGGAGVFNVNLKDKY
LLEDDEWKNDIMPEILDGKNVYDFLDPEIAAKLQALEEEEEKLENEGFYNSDDEEEIYDG
FEASEVDDIKEKAAWIRNRQKTMIAEARNRKSLKNKAIMPRSKLTKSFGKMEEHMSTLGH
DMSALQDKQNRAARKNRYVERGSDVVFGDQDALTASTENGVKLRQTDRLLDGVADGSMRS
KADRMAKMERRERNRHAKQGESDRHNAVSLSKHLFSGKRGVGKTDFR

Sequence of entity 11 (tB), FASTA

>8HFR_11 Ribosome biogenesis protein RLP24 (chains tB)
MRIYQCHFCSSPCYPGHGIMFVRNDAKEFRFCRSKCHKAFKQRRNPRKLKWTKAFRKAAG
KELAVDSTLTFAQRRNVPVRYNRELVATTLKAMARIEEIRQKRERAFYKNRMRGNKEKDF
LRDKKLVESNPELLRIREVEIARKLAKEQERAESVSEQEESEEEEEDMEIDSDEEEEEQL
EKQKILLKNRRRNTKKIAF

Sequence of entity 12 (cC), FASTA

>8HFR_12 60S ribosomal protein L30 (chains cC)
MAPVKSQESINQKLALVIKSGKYTLGYKSTVKSLRQGKSKLIIIAANTPVLRKSELEYYA
MLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	237

Primary citation

Nuclear export of pre-60S particles through the nuclear pore complex. Li, Z., Chen, S., Zhao, L. et al. Nature (2023) 618:411-418. DOI 10.1038/s41586-023-06128-y · PubMed

Other PDB entries of the same protein (UniProt P0CX84 (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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