5JCS: RIX1-REA1 pre-60S particle
cryo-EM structure of the RIX1-REA1 pre-60S particle. Determined by electron microscopy at 9.5 Å resolution. Released 16 Nov 2016.
- Method
- Electron microscopy
- Resolution
- 9.5 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae
- Chains
- 48
- Atoms
- 118,855
- Mol. weight
- 2814.4 kDa
- Released
- 16 Nov 2016
Explore 5JCS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5JCS contains 369 α-helices and 360 β-strands across 45 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: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 101-102 | 2 | 126 |
| β-strand | 124-125 | 2 | 126 |
| α-helix | 136-139 | 4 | |
Chain A: 2 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 40 | 1 | 1 |
| β-strand | 49-50 | 2 | 2 |
| α-helix | 51 | 1 | |
| β-strand | 57-59 | 3 | 2 |
| β-strand | 76-77 | 2 | 2 |
| β-strand | 80 | 1 | 3 |
| β-strand | 91 | 1 | 1 |
| β-strand | 101 | 1 | 4 |
| β-strand | 146-150 | 5 | 5 |
| β-strand | 154-158 | 5 | 5 |
| β-strand | 165 | 1 | 4 |
| β-strand | 168 | 1 | 3 |
| α-helix | 206-208 | 3 | |
| β-strand | 224-225 | 2 | 6 |
| β-strand | 237-238 | 2 | 6 |
Chain B: 8 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-35 | 3 | |
| β-strand | 42-43 | 2 | 12 |
| β-strand | 45-48 | 4 | 13 |
| β-strand | 49-54 | 6 | 14 |
| β-strand | 56-59 | 4 | 15 |
| β-strand | 71-72 | 2 | 15 |
| β-strand | 76-81 | 6 | 14 |
| β-strand | 86-88 | 3 | 16 |
| β-strand | 89-90 | 2 | 17 |
| β-strand | 91 | 1 | 18 |
| β-strand | 104-105 | 2 | 17 |
| α-helix | 131-134 | 4 | |
| α-helix | 145-151 | 7 | |
| β-strand | 158 | 1 | 18 |
| β-strand | 159-162 | 4 | 16 |
| β-strand | 179-182 | 4 | 16 |
| β-strand | 183-184 | 2 | 12 |
| α-helix | 192-196 | 5 | |
| β-strand | 199 | 1 | 16 |
| β-strand | 214-218 | 5 | 13 |
| β-strand | 220 | 1 | 19 |
| α-helix | 229 | 1 | |
| α-helix | 230-234 | 5 | |
| α-helix | 248-250 | 3 | |
| β-strand | 274 | 1 | 19 |
| β-strand | 277-281 | 5 | 13 |
| β-strand | 282-285 | 4 | 14 |
| β-strand | 320-324 | 5 | 14 |
| β-strand | 336-339 | 4 | 13 |
| β-strand | 356-359 | 4 | 15 |
| α-helix | 373-380 | 8 | |
Chain c: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-17 | 4 | |
| β-strand | 24 | 1 | 9 |
| α-helix | 28-31 | 4 | |
| β-strand | 41-44 | 4 | 9 |
| α-helix | 54-57 | 4 | |
| β-strand | 66-69 | 4 | 9 |
| α-helix | 77-80 | 4 | |
| β-strand | 90-92 | 3 | 9 |
| α-helix | 100-102 | 3 | |
Chain C: 16 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-9 | 4 | |
| α-helix | 32-42 | 11 | |
| α-helix | 115-124 | 10 | |
| α-helix | 127-129 | 3 | |
| β-strand | 151-152 | 2 | 36 |
| α-helix | 155-158 | 4 | |
| α-helix | 163-167 | 5 | |
| α-helix | 175-177 | 3 | |
| β-strand | 205-207 | 3 | 37 |
| α-helix | 215-217 | 3 | |
| β-strand | 227 | 1 | 37 |
| α-helix | 235-238 | 4 | |
| β-strand | 247-249 | 3 | 37 |
| β-strand | 250-251 | 2 | 36 |
| α-helix | 259-262 | 4 | |
| α-helix | 286-289 | 4 | |
| α-helix | 300-302 | 3 | |
| α-helix | 324-327 | 4 | |
| α-helix | 331-334 | 4 | |
| α-helix | 339-341 | 3 | |
| α-helix | 354-359 | 6 | |
Chain d: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-10 | 2 | 23 |
| α-helix | 28-43 | 16 | |
| α-helix | 53-59 | 7 | |
| β-strand | 75-76 | 2 | 23 |
| β-strand | 78 | 1 | 24 |
| β-strand | 90 | 1 | 24 |
| β-strand | 93 | 1 | 23 |
| β-strand | 109 | 1 | 23 |
Chain D: 16 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-24 | 4 | |
| α-helix | 33-35 | 3 | |
| β-strand | 50-53 | 4 | 41 |
| β-strand | 62-65 | 4 | 41 |
| β-strand | 74-78 | 5 | 41 |
| α-helix | 83-86 | 4 | |
| α-helix | 95-111 | 17 | |
| α-helix | 134-135 | 2 | |
| α-helix | 140-142 | 3 | |
| β-strand | 145-147 | 3 | 41 |
| α-helix | 162-167 | 6 | |
| α-helix | 192-195 | 4 | |
| α-helix | 196-198 | 3 | |
| α-helix | 202-208 | 7 | |
| α-helix | 225-228 | 4 | |
| α-helix | 235-241 | 7 | |
| α-helix | 243-247 | 5 | |
| α-helix | 269-271 | 3 | |
| α-helix | 283-286 | 4 | |
| α-helix | 289-293 | 5 | |
Chain e: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-19 | 2 | |
| α-helix | 55-57 | 3 | |
| α-helix | 58-60 | 3 | |
| α-helix | 61-63 | 3 | |
| β-strand | 74-75 | 2 | 40 |
| α-helix | 80-85 | 6 | |
| β-strand | 93-95 | 3 | 40 |
| α-helix | 102-109 | 8 | |
| α-helix | 112-115 | 4 | |
| α-helix | 117 | 1 | |
| β-strand | 118-119 | 2 | 40 |
37 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 L30 | c | protein | 105 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P14120 (AlphaFold model) |
| 60S ribosomal protein L3 | B | protein | 387 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P14126 (AlphaFold model) |
| 60S ribosomal protein L31-A | d | protein | 113 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0C2H8 (AlphaFold model) |
| 60S ribosomal protein L4-A | C | protein | 362 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P10664 |
| 60S ribosomal protein L32 | e | protein | 130 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P38061 |
| 60S ribosomal protein L5 | D | protein | 297 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P26321 |
| 60S ribosomal protein L33-A | f | protein | 107 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P05744 |
| 60S ribosomal protein L6-A | E | protein | 176 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q02326 |
| 60S ribosomal protein L34-A | g | protein | 121 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P87262 |
| 60S ribosomal protein L7-A | F | protein | 244 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P05737 |
| 60S ribosomal protein L35-A | h | protein | 120 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX84 |
36 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>5JCS_1 60S ribosomal protein L2-A (chains A)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD
Sequence of entity 2 (c), FASTA
>5JCS_2 60S ribosomal protein L30 (chains c)
MAPVKSQESINQKLALVIKSGKYTLGYKSTVKSLRQGKSKLIIIAANTPVLRKSELEYYA
MLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA
Sequence of entity 3 (B), FASTA
>5JCS_3 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 4 (d), FASTA
>5JCS_4 60S ribosomal protein L31-A (chains d)
MAGLKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIW
KRGVKGVEYRLRLRISRKRNEEEDAKNPLFSYVEPVLVASAKGLQTVVVEEDA
Sequence of entity 5 (C), FASTA
>5JCS_5 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Sequence of entity 6 (e), FASTA
>5JCS_6 60S ribosomal protein L32 (chains e)
MASLPHPKIVKKHTKKFKRHHSDRYHRVAENWRKQKGIDSVVRRRFRGNISQPKIGYGSN
KKTKFLSPSGHKTFLVANVKDLETLTMHTKTYAAEIAHNISAKNRVVILARAKALGIKVT
NPKGRLALEA
Sequence of entity 7 (D), FASTA
>5JCS_7 60S ribosomal protein L5 (chains D)
MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI
ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK
GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF
PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY
TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ
Sequence of entity 8 (f), FASTA
>5JCS_8 60S ribosomal protein L33-A (chains f)
MAESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVR
GSKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI
Sequence of entity 9 (E), FASTA
>5JCS_9 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Sequence of entity 10 (g), FASTA
>5JCS_10 60S ribosomal protein L34-A (chains g)
MAQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSALQGISTLRPR
QYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIVKKVVKEQTEAAKKSEKKAK
K
Sequence of entity 11 (F), FASTA
>5JCS_11 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN
Sequence of entity 12 (h), FASTA
>5JCS_12 60S ribosomal protein L35-A (chains h)
MAGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPSLPKIKTVRKSIACVLTVINE
QQREAVRQLYKGKKYQPKDLRAKKTRALRRALTKFEASQVTEKQRKKQIAFPQRKYAIKA
Primary citation
Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling. Barrio-Garcia, C., Thoms, M., Flemming, D. et al. Nat Struct Mol Biol (2016) 23:37-44. DOI 10.1038/nsmb.3132 · 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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