9I1W: 60S ribosomal protein L2-like protein

High resolution structure of the thermophilic 60S ribosomal subunit of Chaetomium thermophilum. Determined by electron microscopy at 2.38 Å resolution. Released 17 Dec 2025.

Method
Electron microscopy
Resolution
2.38 Å
Organism
Thermochaetoides thermophila DSM 1495
Chains
51
Atoms
131,048
Mol. weight
2037.19 kDa
Ligands
SPD, SPM, ZN, MG
Released
17 Dec 2025

Explore 9I1W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I1W contains 324 α-helices and 310 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 La: 9 helices, 6 β-strands

ElementResiduesLengthSheet
α-helix7-115
α-helix15-184
α-helix42-476
α-helix65-684
β-strand72-74314
α-helix75-773
α-helix79-813
α-helix84-929
β-strand98-103615
α-helix105-1073
β-strand111-113314
β-strand124-127415
β-strand129-130214
α-helix132-14110
β-strand144-147415
Chain LA: 8 helices, 17 β-strands
ElementResiduesLengthSheet
α-helix6-94
α-helix30-323
α-helix34-385
β-strand40-49109
β-strand58-6479
β-strand71-7779
α-helix781
β-strand79110
β-strand83111
β-strand87-9159
β-strand101-10339
α-helix104-1063
β-strand112-11439
β-strand116112
β-strand126112
β-strand134-14079
β-strand145-14959
β-strand155-15959
β-strand163-16649
β-strand169110
α-helix174-1763
α-helix182-1898
α-helix201-2033
β-strand224-225213
β-strand237-238213
Chain Lb: 4 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix12-165
β-strand22191
α-helix23-264
α-helix37-5216
α-helix56-583
Chain LB: 15 helices, 17 β-strands
ElementResiduesLengthSheet
α-helix33-353
α-helix40-412
β-strand42-43216
β-strand45-591517
β-strand71-801017
β-strand84-951218
β-strand98-106918
α-helix112-1154
α-helix116-1183
α-helix131-1344
α-helix135-1384
α-helix143-15513
β-strand158-165818
α-helix167-1693
β-strand179-183518
β-strand184-185216
α-helix189-1979
β-strand200118
β-strand203-204218
α-helix206-2083
β-strand215-221717
β-strand224-228519
α-helix230-2334
α-helix236-2405
β-strand269-272419
β-strand275-2871317
α-helix3081
β-strand322-326517
β-strand336-341617
β-strand357-360417
α-helix374-3818
α-helix385-3873
Chain Lc: 4 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix13-2311
β-strand25-28423
α-helix30-3910
β-strand44-47423
α-helix53-6614
β-strand70-72323
α-helix77-837
β-strand92-97623
Chain LC: 21 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand6-11620
β-strand14-22920
α-helix23-242
α-helix25-284
α-helix33-4311
β-strand64-65221
β-strand76-77221
β-strand89121
α-helix116-12914
α-helix133-1386
β-strand151-153320
α-helix166-17611
α-helix179-1879
β-strand190-191222
α-helix195-1995
β-strand203-204222
β-strand210-213420
α-helix222-2276
β-strand233-236420
α-helix242-2454
α-helix247-2493
β-strand255-258420
α-helix259-27012
α-helix277-2804
α-helix287-2915
α-helix294-2974
α-helix300-3034
α-helix309-3113
α-helix323-3297
α-helix333-3386
α-helix344-3485
α-helix358-3625
Chain Ld: 4 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix9-113
β-strand16-22728
α-helix33-353
α-helix36-5217
β-strand57-59328
α-helix61-677
β-strand70129
β-strand74129
β-strand79-87928
β-strand97-103728
β-strand115-116228
Chain LD: 16 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix10-156
α-helix21-244
α-helix30-378
β-strand50-55624
β-strand60-68924
β-strand71-77724
α-helix81-866
α-helix95-11319
α-helix1341
β-strand135-137325
β-strand140-142325
α-helix143-1453
β-strand146126
β-strand148-150324
α-helix162-17211
β-strand175126
β-strand186-187227
β-strand192-193227
α-helix197-2026
α-helix205-21713
α-helix219-2257
α-helix227-2315
α-helix239-25012
α-helix267-27610
α-helix280-2834
α-helix284-30017

36 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
26S rRNA1RNA3337Thermochaetoides thermophila DSM 1495
5S RNA3RNA120Thermochaetoides thermophila DSM 1495
5.8S RNA4RNA156Thermochaetoides thermophila DSM 1495
E-site tRNA (5'-R(P*CP*CP*A)-3')9RNA3Thermochaetoides thermophila DSM 1495
60S ribosomal protein L2-like proteinLAprotein254Thermochaetoides thermophila DSM 1495G0S4P8 (AlphaFold model)
60S ribosomal protein L3-like proteinLBprotein392Thermochaetoides thermophila DSM 1495G0RXW1 (AlphaFold model)
60S ribosomal protein L4-like proteinLCprotein365Thermochaetoides thermophila DSM 1495G0SFC3 (AlphaFold model)
60S ribosomal protein l5-like proteinLDprotein304Thermochaetoides thermophila DSM 1495G0SEG2 (AlphaFold model)
60S ribosomal protein L6LEprotein200Thermochaetoides thermophila DSM 1495G0S0D6
60S ribosomal protein l7-like proteinLFprotein249Thermochaetoides thermophila DSM 1495G0SFL0
60S ribosomal protein L8LGprotein262Thermochaetoides thermophila DSM 1495G0SAJ9
60S ribosomal protein l9-like proteinLHprotein192Thermochaetoides thermophila DSM 1495G0S0E5

38 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>9I1W_1 26S rRNA (chains 1)
AGGUUGACCUCGGAUCAGGUAGGAGGACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGG
AAAAGAAACCAACAGGGAUUGCCCUAGUAACGGCGAGUGAAGCGGCAACAGCUCAAAUUU
GAAAGCUGGCUUCGGCCCGCGUUGUAAUUUGGAGAGGAUGCUUUGGGCGAGGCUCCUUCU
GAGUUCCCUGGAACGGGACGCCACAGAGGGUGAGAGCCCCGUAUAGUUGGAAGCCAAGCC
UGUGUAAAGCUCCUUCGACGAGUCGAGUAGUUUGGGAAUGCUGCUCAAAAUGGGAGGUAA
AUUUCUUCUAAAGCUAAAUACCGGCCAGAGACCGAUAGCGCACAAGUAGAGUGAUCGAAA
GAUGAAAAGCACUUUGAAAAGAGGGUUAAAUAGCACGUGAAAUUGUUGAAAGGGAAGCGC
UUGUGACCAGACUUGCGCCCGGCGGAUCAUCCGGUGUUCUCACCGGUGCACUCCGCCGGG
CUCAGGCCAGCAUCGGUUCUGGCGGGGGGAUAAAGGCCCAGGGAAUGUGGCUCCUCCGGG
AGUGUUAUAGCCCUGGGUGUAAUACCCUCGCCGGGACCGAGGACCGCGCUCUGCAAGGAU
GCUGGCGUAAUGGUCACCAGCGACCCGUCUUGAAACACGGACCAAGGAGUCAAGGUUUUG
CGCGAGUGUUUGGGUGUAAAACCCGCACGCGUAAUGAAAGUGAACGUAGGUGAGAGCUUC
GGCGCAUCAUCGACCGAUCCUGAUGUAUUCGGAUGGAUUUGAGUAGGAGCGUUAAGCCUU
GGACCCGAAAGAUGGUGAACUAUGCUUGGAUAGGGUGAAGCCAGAGGAAACUCUGGUGGA
GGCUCGCAGCGGUUCUGACGUGCAAAUCGAUCGUCAAAUCUGAGCAUGGGGGCGAAAGAC
UAAUCGAACCAUCUAGUAGCUGGUUACCGCCGAAGUUUCCCUCAGGAUAGCAGUGUCGAC
CUUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGGGACUCGGGGGCGAUUUUUAGCCUUCAU
CCAUUCUCAAACUUUAAAUAUGUAAGAAGCCCUUGUUACUUAACUGAACGUGGGCAUUCG
AAUGUAUCGACACUAGUGGGCCAUUUUUGGUAAGCAGAACUGGCGAUGCGGGAUGAACCG
AACGCGGGGUUAAGGUGCCGGAGUGGACGCUCAUCAGACACCACAAAAGGCGUUAGUACA
UCUUGACAGCAGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAAGGACUGUGUAACAACUC
ACCUGCCGAAUGUACUAGCCCUGAAAAUGGAUGGCGCUCAAGCGUCCCACCCAUACCCCG
CCCUCAGGGUAGAAACGAUGCCCUGAGGAGUAGGCGGCCGUGGAGGUCAGUGACGAAGCC
UAGGGCGUGAGCCCGGGUCGAACGGCCUCUAGUGCAGAUCUUGGUGGUAGUAGCAAAUAC
UUCAAUGAGAACUUGAAGGACCGAAGUGGGGAAAGGUUCCAUGUGAACAGCGGUUGGACA
UGGGUUAGUCGAUCCUAAGCCAUAGGGAAGUUCCGUUUCAAAGGGGCACUCGUGCCCCGU
GUGGCGAAAGGGAAGCCGGUUAAUAUUCCGGCACCUGGAUGUGGGUUUUGCGCGGCAACG
CAACUGAACGCGGAGACGACGGCGGGGGCCCCGGGCAGAGUUCUCUUUUCUUCUUAACGG
UCUAUCACCCUGGAAACAGUUUGUCUGGAGAUAGGGUUUAAUGGCCGGAAGAGCCCGACA
CUUCUGUCGGGUCCGGUGCGCUCUCGACGUCCCUUGAAAAUCCGCGGGAGGGAAUAAUUC
UCACGCCAGGUCGUACUCAUAACCGCAGCAGGUCCCCAAGGUGAACAGCCUCUGGUUGAU
AGAACAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGUAACUUCGGGAAAAGGAUUGG
CUCUAAGGGUUGGGCACGUUGGGCUUUGGGCGGACGCCCUGGGAGCAGAGGGCCUCUAGC
CGGGCAACCGGCCGGCGGCCCUCAGCACCCGGGGUUGAAGCCCUUAGCAGGCUUCGGCCG
UCCGGCGUGCGGUUAACAACCAACUUAGAACUGGUACGGACAGGGGGAAUCUGACUGUCU
AAUUAAAACAUAGCAUUGCGAUGGCCAGAAAGUGGUGUUGACGCAAUGUGAUUUCUGCCC
AGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAAC
UAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAXGGA
UUAACGAGAUUCCCACUGUCCCUAUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGG
CUUGGCAAAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUG
AAAAGACAUAGGAGGUGUAGAAUAGGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACUC
CUAUUGUUUUUUUACUUAUUCAAUGAAGCGGGGCUGGACUUGCGUCCAACUUCUGGAGUU
AAGGUCCUUCGCGGGCCGACCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGG
CGGCACAUCUGUUAAACCAUAACGCAGGUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAU
CUCCAGUAGAACAAAAGGGUAAAAGUCCCCUUGAUUUUGAUUUUCAGUGXGAAUACAAAC
CAUGAAAGUGUGGCCUAUCGAUCCUUUAGUCCCUCGAAAUUUGAGGCUAGAGGUGCCAGA
AAAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUU
UGAUCCUUCGAUGUCGGCUCUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUU
GUUCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUU
ACCCUACUGAUGAACUCGUCGCAAUGGUAAUUCAGCUUAGUACGAGAGGAACCGCUGAUU
CAGAUAAUUGGUUUUUGCGGUUGUCCGACCGGGCAGUGCCGCGAAGCUACCAUCUGCUGG
AUAAUGGCUGAACGCCUCUAAGUCAGAAUCCAUGCCAGAACGCGACGAUACUACCCGCAC
GUUGUAGACGUAUAAGAAUAGGCUCCGGCCUCGUAUCCUAGCAGGCGAUUCCUCCGCCGG
CCUCGAAGUGGCCGUCGGUAAUUCGCGUAUUGCAAUUUAGACACGCGCGGGAUCAAAUCC
UUUGCAGACGACUUAGAUGUGCGAAAGGGUCCUGUAAGCAGUAGAGUAGCCUUGUUGUUA
CGAUCUGCUGAGGGUAAGCCCUCCUUCGCCUAGAUUU
Sequence of entity 2 (3), FASTA
>9I1W_2 5S RNA (chains 3)
ACAUACGACCAUACCUAGUGGAAAACUCGGGAUCCCGUCCGCUCUCCCAUAGAUAGGCCA
CUAAGGGCGGGGUUAGUACUCAGGUCGGUGACGACUGGGGAAUCCCCCGUGUUGUAUGUU
Sequence of entity 3 (4), FASTA
>9I1W_3 5.8S RNA (chains 4)
AAACUUUCAACAACGGAUCUCUUGGUUCUGGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
AAGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCG
CCGGUAUUCCGGCGGGCAUGCCUGUUCGAGCGUCAU
Sequence of entity 4 (9), FASTA
>9I1W_4 E-site tRNA (5'-R(P*CP*CP*A)-3') (chains 9)
CCA
Sequence of entity 5 (LA), FASTA
>9I1W_5 60S ribosomal protein L2-like protein (chains LA)
MGRVIRNQRKGRGSVFTAHTRLRKAPAKFRPLDYAERHGYIRGIVKEIIHDPGRGAPLAR
VVFRSPYKYKQITETFIANEGMYTGQFIYAGKNAALTVGNILPLSSVPEGTVVSNVEEKP
GDRGALGRTSGNYVTVVGHNPDEGKTRIKLPSGAKKVVPSSSRGMIGIVAGGGRTDKPLL
KASRAKHKFAVKRNRWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRYAAQGQKAGLIAA
RRTGLLRGTQKTKE
Sequence of entity 6 (LB), FASTA
>9I1W_6 60S ribosomal protein L3-like protein (chains LB)
MSHRKYEAPRHGSLAFLPRKRAARHRGRVKSFPKDDPKKPVHLTAAMGYKAGMTTIVRDL
DRPGAKAHKKEVVEAVTIIDCPPMVVVGLVGYIETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYAKKYAENNGASITRELERIKKYCTVVRVLAHTQIRKTPLKQKKAHLM
EIQINGGSVADKVEFGRSLFEKPVTIDTIFEKDEMIDVIAVTKGHGFVGVTARWGTKKLP
RKTHKGLRKVACIGAWHPSHVQWTVARAGQMGYHHRTSVNHKIYRIGKGDDEANASTETD
LTKKKITPMGGFVRYGEVNNDYVMIKGSVPGVKKRIMTLRKSLFTHTSRKALEKVELKWI
DTSSEFGHGAFQTAAEKKQFMGTLKKDLQTSA
Sequence of entity 7 (LC), FASTA
>9I1W_7 60S ribosomal protein L4-like protein (chains LC)
MASRPTVTVFGADGKPTGATEVLPKVFSAPIRPDIVKHVHTGMAKNKRQPYAVSEKAGHQ
TSAESWGTGRAVARIPRVSGGGTHRAGQGAFGNMCRSGRMFAPTKIWRKWHVKINQGQKR
FATASALAASAVAPLLMARGHQVSTVPEVPLVVDSAAVAGDAVAKTAAAYKLLKAIGAGP
DVEKVKKSKKLRAGKGKMRGRRHRQRRGPLIVYSPEHDGKELVKGFRNIPGVETCPVDAL
NLLQLAPGGHLGRFIVWTSAAIKQLDAVYESKKGFFLPANIVSQADLSRLINSTEIQSVL
RAPKGEARTKRACVQKKNPLRNKQIMLRLNPYASTFAKEKLGEVKAEEGKPPKVPASFKE
LLHEA
Sequence of entity 8 (LD), FASTA
>9I1W_8 60S ribosomal protein l5-like protein (chains LD)
MAFHKLVKNSAYYSRFQTKFKRRRQGKTDYYARKRLITQAKNKYNAPKYRLVVRFTNRDI
ITQMVTSEINGDKIFAAAYSHELRAYGINHGLTNWAAAYATGLLLARRVLAKLGLDKTFT
GVEEPNGEYTLTEAAETEDGERRPFKAILDVGLARTSTGARVFGVMKGASDGGIFIPHSE
NRFPGYDIETEELDTEVLKKYIYGGHVAEYMETLADDDEERYKSQFVKYIEDDVEADSLE
ELYAEAHKQIRADPFRKYVSDAPKKSKEEWKAESLKYKKAKLSREERKARVEAKIKQLLA
EQDE
Sequence of entity 9 (LE), FASTA
>9I1W_9 60S ribosomal protein L6 (chains LE)
MSAAPTTKTFGKGTRTVPAPSEKAQKWYPAEDEAQPKKVRKAVRPWTPRKSLQPGTVLIL
LAGRFRGKRVVLLKCLDQGVLLVTGPFKINGVPLRRVNARYVIATSVKVDLTGVDQAKID
EVAQPKYFTAEKAKEKASEEAFFKQGEKPQKKPVSSTRAADQKAIDKALIANIKKVDMLA
SYLASSFSLRKGDKPHLMKF
Sequence of entity 10 (LF), FASTA
>9I1W_10 60S ribosomal protein l7-like protein (chains LF)
MSSTTVPTQNDILVPETLLKKRKSQEKARAERAAALEKRKQANKEKRQVIFKRAEKYVKE
YREQEREKIRLARIAKQQGSFHIPAEAKLVFVIRIKGINKIPPKPRKILQLLRLRQINNG
VFVKVTKATAEMIKIVEPWVAYGYPNLKSVRELIYKRGYGKVNGQRIPLTDNAIIEENLG
KYGIICIEDLIHEIFTVGPNFKQAANFLWPFKLSNPNGGFRPRKFKHFIEGGDLGNREEH
INALIRAMN
Sequence of entity 11 (LG), FASTA
>9I1W_11 60S ribosomal protein L8 (chains LG)
MPPKSGKKVAPAPFPQGKAGAKKAPKNPLLEKRPRNFGIGQDIQPKRNLSRMVKWPEYIR
LQRQKKILRMRLKVPPAIAQFQYTLDKNLAAQAFKLLNKYRPETKQEKKERLLREATAIK
EGKKKEDVSKKPYTVKYGLNHVVGLIENKKASLVLIANDVDPIELVVFLPALCRKMGIPY
AIIKGKARLGTLVHKKTAAVVAITEVRSEDKNELAKLISAVKEGYLEKVEDTRKRWGGGI
MGFKAQKREEKRKKSLETAIKV
Sequence of entity 12 (LH), FASTA
>9I1W_12 60S ribosomal protein l9-like protein (chains LH)
MRYIHSEETIPVPENLKVSIKSRLVTVEGPRGKLQKDLSHIAVNFSVVKKGVIGLEIHHG
SRKDVAALRTVRTIINNMIIGVTKGFKYKMRYVYAHFPINVNVEKNAETGCYEVEIRNFI
GEKIVRKVVMAPGVEVEISKAQKDELILSGNSLEAVSQSAADIQQICKVRNKDIRKFLDG
IYVSEKGNIVED

Ligands and cofactors

IDNameFormulaCopies
SPDSpermidineC7 H19 N32
SPMSpermineC10 H26 N42
ZNZinc ionZn5
MGMagnesium ionMg239

Water and common crystallization additives (K) are not listed.

Primary citation

Pseudouridine increases ribosome stability in a thermophilic eukaryote. Wild, K., Klein, M., Burkard, A. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf1368 · PubMed

Other PDB entries of the same protein (UniProt G0S4P8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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