9H4N: RPL13 (eL13)-mutant 80S ribosome from mouse

RPL13 (eL13)-mutant 80S ribosome from mouse. Determined by electron microscopy at 2.46 Å resolution. Released 5 Nov 2025.

Method
Electron microscopy
Resolution
2.46 Å
Organism
Mus musculus
Chains
76
Atoms
204,064
Mol. weight
3015.96 kDa
Ligands
ZN, MG
Released
5 Nov 2025

Explore 9H4N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9H4N contains 490 α-helices and 470 β-strands across 69 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 A1: 14 helices, 11 β-strands

ElementResiduesLengthSheet
α-helix50-9950
β-strand103-10531
α-helix106-1094
β-strand111-11662
α-helix125-1339
β-strand141-14662
α-helix149-1579
α-helix159-1613
β-strand162-16542
α-helix169-17911
β-strand181-18443
β-strand187-19043
α-helix194-2018
α-helix202-2043
α-helix209-2179
α-helix223-2297
β-strand23013
α-helix231-2322
β-strand233-23422
α-helix237-2382
β-strand24814
α-helix249-2513
β-strand25514
β-strand256-25722
α-helix262-2698
Chain a2: 7 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand20-24556
β-strand30-34556
α-helix35-395
α-helix41-422
β-strand43157
α-helix441
β-strand52157
α-helix531
α-helix61-666
α-helix69-724
α-helix84-11431
Chain A3: 9 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand12-13244
α-helix15-173
β-strand20-21244
β-strand25145
α-helix26-294
α-helix30-323
α-helix38-4710
β-strand55145
α-helix61-7212
α-helix75-773
α-helix81-833
β-strand86146
β-strand96146
α-helix101-11717
α-helix120-1278
Chain B1: 15 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix45-473
β-strand56111
α-helix59-7315
β-strand75-76212
α-helix78-814
α-helix89-10012
α-helix103-1053
α-helix107-12115
β-strand137-138213
α-helix140-1489
β-strand154-158513
α-helix164-1663
α-helix170-1767
β-strand181-184413
α-helix188-1936
β-strand201-204413
α-helix209-2113
α-helix212-22211
α-helix223-2275
α-helix231-2344
β-strand238-239212
α-helix244-25815
Chain b2: 7 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix6-94
α-helix14-3623
α-helix41-7232
α-helix89-935
α-helix95-962
α-helix97-1004
α-helix105-1139
β-strand119-121341
Chain B3: 7 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix11-2515
α-helix52-6615
β-strand70150
α-helix72-787
β-strand81-83351
α-helix89-902
β-strand91-93351
α-helix94-963
α-helix98-10912
β-strand113-115350
β-strand121-123350
α-helix125-14319
Chain C1: 8 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand3-11916
α-helix12-132
β-strand17-21517
β-strand24-29617
β-strand32-37617
β-strand44-48516
β-strand54-62916
α-helix64-674
α-helix69-8517
β-strand88-95818
β-strand102-106519
β-strand111-115519
α-helix117-1193
α-helix122-1232
β-strand124-127419
α-helix128-1292
β-strand133-136418
β-strand143-148618
α-helix151-16414
α-helix172-1754
β-strand178-185818
Chain c2: 8 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix181
β-strand19140
α-helix20-212
α-helix23-253
α-helix26-294
α-helix35-4814
α-helix52-6211
α-helix66-7712
α-helix80-10223

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Large ribosomal subunit protein uL30A1protein222Mus musculusP14148 (AlphaFold model)
Large ribosomal subunit protein eL8B1protein232Mus musculusP12970 (AlphaFold model)
Large ribosomal subunit protein uL6C1protein190Mus musculusP51410 (AlphaFold model)
Large ribosomal subunit protein uL16-likeD1protein213Mus musculusP86048 (AlphaFold model)
Large ribosomal subunit protein uL5E1protein174Mus musculusQ9CXW4
Large ribosomal subunit protein eL13F1protein203Mus musculusP47963
60S ribosomal protein L14G1protein139Mus musculusQ9CR57
60S ribosomal protein L15H1protein203Mus musculusQ9CZM2
28S ribosomal RNAA2RNA3609Mus musculus
5S ribosomal RNAB2RNA120Mus musculus
5.8S ribosomal RNAC2RNA156Mus musculus
Large ribosomal subunit protein uL2D2protein251Mus musculusP62918

64 more molecules are not listed.

Sequence of entity 1 (A1), FASTA
>9H4N_1 Large ribosomal subunit protein uL30 (chains A1)
ELKVKRLRKKFALKTLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYVPAE
PKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYPN
LKSVNELIYKRGYGKINKKRIALTDNSLIARSLGKFGIICMEDLIHEIYTVGKRFKEANN
FLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN
Sequence of entity 2 (B1), FASTA
>9H4N_2 Large ribosomal subunit protein eL8 (chains B1)
VNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQAL
DRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTTLV
ENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGHLVHRKTCTTVAFTQV
NSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAK
Sequence of entity 3 (C1), FASTA
>9H4N_3 Large ribosomal subunit protein uL6 (chains C1)
MKTILSNQTVDIPENVEITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRTGVACSVSQAQKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQA
Sequence of entity 4 (D1), FASTA
>9H4N_4 Large ribosomal subunit protein uL16-like (chains D1)
GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLS
SEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGK
PQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEF
EDKVAAKRLIPDGCGVKYIPERGPLDKWRALHS
Sequence of entity 5 (E1), FASTA
>9H4N_5 Large ribosomal subunit protein uL5 (chains E1)
QDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGI
RRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPS
IGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILP
Sequence of entity 6 (F1), FASTA
>9H4N_6 Large ribosomal subunit protein eL13 (chains F1)
APSRNGMILKPHFHKDWQQRVDTWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVRC
PTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYR
SKLILFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVYKKEKARVITEEEKNFKAFAS
LRMARANARLFGIRAKRAKEAAE
Sequence of entity 7 (G1), FASTA
>9H4N_7 60S ribosomal protein L14 (chains G1)
VFRRYVEVGRVAYISFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDFI
LKFPHSARQKYVRKAWEKADINTKWAATRWAKKIDARERKAKMTDFDRFKVMKAKKMRNR
IIKTEVKKLQRAAILKASP
Sequence of entity 8 (H1), FASTA
>9H4N_8 60S ribosomal protein L15 (chains H1)
GAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVI
YRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWV
GEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGHKFH
HTIGGSRRAAWRRRNTLQLHRYR
Sequence of entity 9 (A2), FASTA
>9H4N_9 28S ribosomal RNA (chains A2)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAA
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCGCGCGUCGCGGCGUGGGAAAUGUGGCGUACGGAAGACCCACUCCCCGGCGC
CGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCG
GUAGCGGCCCCCGGCGCGCCGGGCUCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCA
GCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAA
CAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGGGAGAGUUCAAGAGGGCGUGAAA
CCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGC
GUCCGGCCGUGCCGGUGGGCGGAUCUUGGGACCGCCCCCGGCCGGCGACCGGCCGCCGCC
GGGCGCACUUCCACCGUGGCGGUGCGCCGCGACCGGCUCCGGGACGGCCGGGAAGGCCCG
GUGGGGAAGGUGGCUCGGGGGGGGCUCACCCCGAGUGUUACAGCCCUCCGGCCGCGCUUU
UCGCCGAAUCCCGGGGCCGAGGAAGACCGUCGCCGCGCUCUCCCUCUCCCGGGUGGGGGC
CGGGCCGCCCCUCCCACGGCGCGACCGCUCCGGGGCGGACUGUCCCCAGUGCGCCCCGGG
CGUCGUCGCGCCGUCGGGUCCCGGGGGCGUCGGUCACGCGUGACGAAGCCGAGCGCACGG
GGUCGGCGGCGAUGUCGGCUACCCACCCGACCCGUCUUGAAACCCGGACCAAGGAGUCUA
ACGCGUGCGCGAGUCAGGGGCUCGUCCGAAAGCCGCCGUGGCGCAAUGAAGGUGAAGGGC
CCCGCCCGGGGGCCCGAGGUGGGAUCCCGAGGCCUCUCCAGUCCGCCGAGGGCGCACCAC
CGGCCCGUCUCGCCCGCCGCGCCGGGGAGGUGGAGCACGAGCGUACGCGUUAGGACCCGA
AAGAUGGUGAACUAUGCUUGGGCAGGGCGAAGCCAGAGGAAACUCUGGUGGAGGUCCGUA
GCGGUCCUGACGUGCAAAUCGGUCGUCCGACCUGGGUAUAGGGGCGAAAGACUAAUCGAA
CCAUCUAGUAGCUGGUUCCCUCCGAAGUUUCCCUCAGGAUAGCUGGCGCUCUCGCUACGC
AGUUUUAUCCGGUAAAGCGAAUGAUUAGAGGUCUUGGGGCAUCUCAACCUAUUCUCAAAC
UUUAAAUGGGUAAGAAGCCCGGCUCGCUGGCGUGGAGCCGGGCGUGGAAUGCGAGUGCCU
AGUGGGCCACUUUUGGGAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAA
GCGCCCGAUGCCGACGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGG
ACCUGCCGAAUCAACUAGCCCUGAAAAUGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGG
CCGUCGCCGGCAGUCGGAACGGAACGGGACGGGAGCGUCGGGCCCCGCGGAGCCUACGCC
GCGACGAGUAGGAGGGCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGA
GCCGCCGCAGGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGC
CGAAGUGGAGAAGGGUUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAG
AUGGGCGAGUGCCGUUCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAA
AGGGAGUCGGGUUCAGAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCC
AGUGCGGUAACGCGACCGAUCCCGGAGAAGCCGGCGGGAGCCUCGGGGAGAGUUCUCUUU
UCUUUGUGAAGGGCAGGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUU
GGAAAGCGUCGCGGUUCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGG
GGAGAGGGUGUAAAUCUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGA
ACAGCCUCUGGCAUGUUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAAC
UUCGGGAUAAGGAUUGGCUCUAAGGGCUGGGCGGCCGGCGCCUAGCAGCCGACUUAGAAC
UGGUGCGGACCAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUCGCGAAGGCCCGCGG
CGGGUGUUGACGCGAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCA
AUGAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCG
UCAUCUAAUUAGUGACGCGCAUGAAUGGAUGAACGAGAUUCCCACUGUCCCUACCUACUA
UCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGGAAAGAAGAGCCU
GUUGAGCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGAGAGGUGUAGAAUAAGUGGGA
GGCCCGGCCGCCGGUGAAAUACCACUACUCUCAUCGUUUUUUCACUGACCCGGUGAGGCG
GGGGGGCGAGCCCGGCUCUCGCUUCUGGCGCCAAGCGUCCGUCCCGGCGGGCGGGCGCGA
CCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACCGGGGCGGUACACCUGUCAAACGG
UAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGG
CAAAAGCUCGCUUGAUCUUGAUUUUCAGGACGAAUACAGACCGUGAAAGCGGGGCCUCAC
GAUCCUUCUGACCUUUUUGGUUUUAAGCAGGAGAUGUCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCU
CUUCCUAUCAUUGUGAAGCAGAAUUUACCAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUGUGUU
GUUGCCAUGGUAAUCCUGCCCAGUACGAGAGGAACCGCAGGUUCAGACAUUUGGUGUAUG
UGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGGAUUAUGACUGAACGCCU
CUAAGUCAGAAUCCCGCCCAGGCGGAACGAUACGGCAGCGCCGAGGAGCCUCGGUUGGCC
CCGGAUAGCCGGGCCCCGUCCGUCCCGGCGUCGGGACCGGGGUCCGGUGCGGAGAGCCGU
UCGUCUUGGGAAACGGGGUGCGGCCGGAAAGGGGGCCGCCCUCUCGCCCGUCACGUUGAC
GCACGUUCGUGUGGAACCUGGCGCUAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGG
UUUCGUACGUAGCAGAGCAGCUCCCUCGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACA
AGGGUUUGU
Sequence of entity 10 (B2), FASTA
>9H4N_10 5S ribosomal RNA (chains B2)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
Sequence of entity 11 (C2), FASTA
>9H4N_11 5.8S ribosomal RNA (chains C2)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU
Sequence of entity 12 (D2), FASTA
>9H4N_12 Large ribosomal subunit protein uL2 (chains D2)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGRLRGTKTV

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn6
MGMagnesium ionMg1

Primary citation

Analysis of Rpl13 variant consequences on bone development using a mouse model of spondyloepimetaphyseal dysplasia (Isidor-Toutain type). Orgebin, E., Astier, A., Rinaldi, D. et al. To be published.

Other PDB entries of the same protein (UniProt P14148 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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