5MRE: Yeast mitochondrial ribosome - Class B

Structure of the yeast mitochondrial ribosome - Class B. Determined by electron microscopy at 3.75 Å resolution. Released 15 Feb 2017.

Method
Electron microscopy
Resolution
3.75 Å
Organism
Saccharomyces cerevisiae
Chains
78
Atoms
201,462
Mol. weight
3325.59 kDa
Ligands
GDP, ZN, MG
Released
15 Feb 2017

Explore 5MRE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MRE contains 744 α-helices and 554 β-strands across 75 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 0: 1 helix, 4 β-strands

ElementResiduesLengthSheet
β-strand57-5931
β-strand69-7461
β-strand77-8261
α-helix86-883
β-strand90-9231
Chain 1: 18 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix21-233
α-helix30-323
α-helix37-437
α-helix58-636
α-helix66-672
α-helix70-9425
α-helix98-10912
α-helix113-1208
α-helix137-14913
α-helix151-16212
α-helix165-1684
β-strand176-181614
β-strand191114
α-helix192-1932
β-strand196115
α-helix206-2072
β-strand208-213614
β-strand223-229715
β-strand233-235316
β-strand240-242316
β-strand245-253915
β-strand260-261214
α-helix268-2703
β-strand271-273315
α-helix280-2812
β-strand282117
β-strand287-295915
α-helix296-2994
α-helix322-3298
β-strand332-3411015
α-helix347-3548
β-strand361117
β-strand3621139
Chain 11: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix80-9920
α-helix101-1088
Chain 2: 4 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix37-4913
α-helix63-10846
α-helix110-1167
α-helix130-1323
β-strand133122
Chain 22: 7 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix31-355
α-helix41-488
α-helix63-686
α-helix71-777
α-helix81-9515
α-helix104-1063
α-helix117-12711
Chain 3: 5 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand63-64227
β-strand70-71227
α-helix74-763
β-strand78-803113
β-strand93-953125
α-helix99-1013
β-strand102-103228
α-helix111-1133
α-helix115-12814
α-helix134-1374
β-strand143-144228
Chain 33: 15 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand9-102116
α-helix17-237
β-strand24-252135
β-strand29-302135
α-helix31-344
α-helix35-406
α-helix41-5212
α-helix57-604
α-helix63-708
α-helix77-9620
α-helix113-1164
α-helix117-12610
α-helix132-14514
β-strand152-1576136
β-strand163-1686136
α-helix177-1793
α-helix191-20616
β-strand219-2257136
α-helix228-2358
α-helix240-24910
α-helix253-2586
Chain 4: 6 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand3-5339
β-strand11140
β-strand23-30841
α-helix35-373
α-helix38-458
α-helix48-558
β-strand60-65641
β-strand71-76641
β-strand83-85341
α-helix91-10313
α-helix107-1093
β-strand119198
α-helix123-1242

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
21S ribosomal RNAARNA3296Saccharomyces cerevisiae
uL2mBprotein393Saccharomyces cerevisiaeP32611 (AlphaFold model)
uL3mCprotein249Saccharomyces cerevisiaeP31334 (AlphaFold model)
uL4mDprotein252Saccharomyces cerevisiaeP51998 (AlphaFold model)
uL5mEprotein274Saccharomyces cerevisiaeP36519 (AlphaFold model)
uL6mFprotein196Saccharomyces cerevisiaeP32904
bL9mGprotein74Saccharomyces cerevisiaeP53724
uL13mHprotein160Saccharomyces cerevisiaeQ12487
uL14mIprotein138Saccharomyces cerevisiaeP35996
uL15mJprotein220Saccharomyces cerevisiaeP36520
uL16mKprotein195Saccharomyces cerevisiaeP38064
bL17mLprotein237Saccharomyces cerevisiaeP22353

66 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>5MRE_1 21S ribosomal RNA (chains A)
GUAAAAAGUAGAAUAAUAGAUUUGAAAUAUUUAUUAUAUAGAUUUAAAGAGAUAAUCAUG
GAGUAUAAUAAUUAAAUUUAAUAAAUUUAAUAUAACUAUUAAUAGAAUUAGGUUACUAAU
AAAUUAAUAACAAUUAAUUUUAAAACCUAAAGGUAAACCUUUAUAUUAAUAAUGUUAUUU
UUUAUUAUUUUUAUAAUAAGAAUAAUUAUUAAUAAUAAUAAACUAAGUGAACUGAAACAU
CUAAGUAACUUAAGGAUAAGAAAUCAACAGAGAUAUUAUGAGUAUUGGUGAGAGAAAAUA
AUAAAGGUCUAAUAAGUAUUAUGUGAAAAAAAUGUAAGAAAAUAGGAUAACAAAUUCUAA
GACUAAAUACUAUUAAUAAGUAUAGUAAGUACCGUAAGGGAAAGUAUGAAAAUGAUUAUU
UUAUAAGCAAUCAUGAAUAUAUUAUAUUAUAUUAAUGAUGUACCUUUUGUAUAAUGGGUC
AGCAAGUAAUUAAUAUUAGUAAAACAAUAAGUUAUAAAUAAAUAGAAUAAUAUAUAUAUA
UAAAAAAAUAUAUUAAAAUAUUUAAUUAAUAUUAAUUGACCCGAAAGCAAACGAUCUAAC
UAUGAUAAGAUGGAUAAACGAUCGAACAGGUUGAUGUUGCAAUAUCAUCUGAUUAAUUGU
GGUUAGUAGUGAAAGACAAAUCUGGUUUGCAGAUAGCUGGUUUUCUAUGAAAUAUAUGUA
AGUAUAGCCUUUAUAAAUAAUAAUUAUUAUAUAAUAUUAUAUUAAUAUUAUAUAAAGAAU
GGUACAGCAAUUAAUAUAUAUUAGGGAACUAUUAAAGUUUUAUUAAUAAUAUUAAAUCUC
GAAAUAUUUAAUUAUAUAUAAUAAAGAGUCAGAUUAUGUGCGAUAAGGUAAAUAAUCUAA
AGGGAAACAGCCCAGAUUAAGAUAUAAAGUUCCUAAUAAAUAAUAAGUGAAAUAAAUAUU
AAAAUAUUAUAAUAUAAUCAGUUAAUGGGUUUGACAAUAACCAUUUUUUAAUGAACAUGU
AACAAUGCACUGAUUUAUAAUAAAUAAAAAAAAAUAAUAUUUAAAAUCAAAUAUAUAUAU
AUUUGUUAAUAGAUAAUAUACGGAUCUUAAUAAUAAGAAUUAUUUAAUUCCUAAUAUGGA
AUAUUAUAUUUUUAUAAUAAAAAUAUAAAUACUGAAUAUCUAAAUAUUAUUAUUACUUUU
UUUUUAAUAAUAAUAAUAUGGUAAUAGAACAUUUAAUGAUAAUAUAUAUUAGUUAUUAAU
UAAUAUAUGUAUUAAUUAAAUAGAGAAUGCUGACAUGAGUAACGAAAAAAAGGUAUAAAC
CUUUUCACCUAAAACAUAAGGUUUAACUAUAAAAGUACGGCCCCUAAUUAAAUUAAUAAA
AAUAUAAAUAUAUUUAAGAUGGGAUAAUCUAUAUUAAUAAAAAUUUAUCUUAAAAUAUAU
AUAUUAUUAAUAAUUAUAUUAAUUAAUUAAUAAUAUAUAUAAUUAUAUUAUAUAUUAUAU
AUUUUUUAUAUAAUAUAAACUAAUAAAGAUCAGGAAAUAAUUAAUGUAUACCGUAAUGUA
GACCGACUCAGGUAUGUAAGUAGAGAAUAUGAAGGUGAAUUAGAUAAUUAAAGGGAAGGA
ACUCGGCAAAGAUAGCUCAUAAGUUAGUCAAUAAAGAGUAAUAAGAACAAAGUUGUACAA
CUGUUUACUAAAAACACCGCACUUUGCAGAAACGAUAAGUUUAAGUAUAAGGUGUGAACU
CUGCUCCAUGCUUAAUAUAUAAAUAAAAUUAUUUAACGAUAAUUUAAUUAAAUUUAGGUA
AAUAGCAGCCUUAUUAUGAGGGUUAUAAUGUAGCGAAAUUCCUUGGCCUAUAAUUGAGGU
CCCGCAUGAAUGACGUAAUGAUACAACAACUGUCUCCCCUUUAAGCUAAGUGAAAUUGAA
AUCGUAGUGAAGAUGCUAUGUACCUUCAGCAAGACGGAAAGACCCUAUGCAGCUUUACUG
UAAUUAGAUAGAUCGAAUUAUUGUUUAUUAUAUUCAGCAUAUUAAGUAAUCCUAUUAUUA
GGUAAUCGUUUAGAUAUUAAUGAGAUACUUAUUAUAAUAUAAUGAUAAUUCUAAUCUUAU
AAAUAAUUAUUAUUAUUAUUAUUAAUAAUAAUAAUAUGCUUUCAAGCAUAGUGAUAAAAC
AUAUUUAUAUGAUAAUCACUUUACUUAAUAGAUAUAAUUCUUAAGUAAUAUAUAAUAUAU
AUUUUAUAUAUAUUAUAUAUAAUAUAAGAGACAAUCUCUAAUUGGUAGUUUUGAUGGGGC
GUCAUUAUCAGCAAAAGUAUCUGAAUAAGUCCAUAAAUAAAUAUAUAAAAUUAUUGAAUA
AAAAAAAAAUAAUAUAUAUUAUAUAUAUUAAUUAUAAAUUGAAAUAUGUUUAUAUAAAUU
UAUAUUUAUUGAAUAUAUUUUAGUAAUAGAUAAAAAUAUGUACAGUAAAAUUGUAAGGAA
AACAAUAAUAACUUUCUCCUCUCUCGGUGGGGGUUCACACCUAUUUUUAAUAGGUGUGAA
CCCCUCUUCGGGGUUCCGGUUCCCUUUCGGGUCCCGGAACUUAAAUAAAAAUGGAAAGAA
UUAAAUUAAUAUAAUGGUAUAACUGUGCGAUAAUUGUAACACAAACGAGUGAAACAAGUA
CGUAAGUAUGGCAUAAUGAACAAAUAACACUGAUUGUAAAGGUUAUUGAUAACGAAUAAA
AGUUACGCUAGGGAUAACAGGGUAAUAUAGCGAAAGAGUAGAUAUUGUAAGCUAUGUUUG
CCACCUCGAUGUCGACUCAACAUUUCCUCUUGGUUGUAAAAGCUAAGAAGGGUUUGACUG
UUCGUCAAUUAAAAUGUUACGUGAGUUGGGUUAAAUACGAUGUGAAUCAGUAUGGUUCCU
AUCUGCUGAAGGAAAUAUUAUCAAAUUAAAUCUCAUUAUUAGUACGCAAGGACCAUAAUG
AAUCAACCCAUGGUGUAUCUAUUGAUAAUAAUAUAAUAUAUUUAAUAAAAAUAAUACUUU
AUUAAUAUAUUAUCUAUAUUAGUUUAUAUUUUAAUUAUAUAUUAUCAUAGUAGAUAAGCU
AAGUUGAUAAUAAAUAAAUAUUGAAUACAUAUUAAAUAUGAAGUUGUUUUAAUAAGAUAA
UUAAUCUGAUAAUUUUAUACUAAAAUUAAUAAUUAUAGGUUUUAUAUAUUAUUUAUAAAU
AAAUAUAUUAUAAUAAUAAUAAUUAUUAUUAUUAAUAAAAAAUAUUAAUUAUAAUAUUAA
UAAAAUACUAAUUUAUCAGUUAUCUAUAUAAUAUCUAAUCUAUUAUUCUAUAUACU
Sequence of entity 2 (B), FASTA
>5MRE_2 uL2m (chains B)
MLVLGSLRSALSCSSTASLISKRNPCYPYGILCRTLSQSVKLWQENTSKDDSSLNITPRL
LKIIPNDTDIVTLEKQDELIKRRRKLSKEVTQMKRLKPVSPGLRWYRSPIYPYLYKGRPV
RALTVVRKKHGGRNNSGKITVRHQGGGHRNRTRLIDFNRWEGGAQTVQRIEYDPGRSSHI
ALLKHNTTGELSYIIACDGLRPGDVVESFRRGIPQTLLNEMGGKVDPAILSVKTTQRGNC
LPISMIPIGTIIHNVGITPVGPGKFCRSAGTYARVLAKLPEKKKAIVRLQSGEHRYVSLE
AVATIGVVSNIDHQNRSLGKAGRSRWLGIRPTVRGVAMNKCDHPHGGGRGKSKSNKLSMS
PWGQLAKGYKTRRGKNQNRMKVKDRPRGKDARL
Sequence of entity 3 (C), FASTA
>5MRE_3 uL3m (chains C)
STRPFLVAPSIANSITTEAPAINHSPELANARKWLPKRCGLITRKKGMMPYFDKSTGERS
AATILEVNNVEVIMHRTSEVNGYFACQVGYGSRHLSKVSRQMLGHFASKVVNPKEHVAEF
RVKDEKGLIPPGTLLKPSFFKEGQYVDVRSVSKGKGFTGVMKRYGFKGLRASHGTSIMHR
HGGSYGQNQDPGRVLPGRKMPGHMGNEHVTIQNVKVLKVDDENNVIWVKGSVAGPKNSFV
KIQDAIKKT
Sequence of entity 4 (D), FASTA
>5MRE_4 uL4m (chains D)
LNPLPNAAIPPKYALVTVRSFPSLEPLTFVPVPTSTVAAPLRRDILWRAVVYENDNRRVG
ASNPPGRSENGFSRRKLMPQKGSGRARVGDANSPTRHNGGRALARTAPNDYTTELPSKVY
SMAFNNALSHQYKSGKLFVIGGEKVDLISPTPELDLNRLDLVNTNTVEGKEIFEGEVIFR
KFLEEFQLKGKRLLFITDKTREGLIKSSDPYKQKVDVIQKELVEVNDILRAQAVFIELEA
LEYLAMAHQKEI
Sequence of entity 5 (E), FASTA
>5MRE_5 uL5m (chains E)
PKSACSLVKPVHHLVKIDKSKLSPRFPELKYDKSDIRSPGFKPKDTHADRLNDHYLNTLQ
SDLLLINYSHNAAVVKGLKQRAWSGDSPYHLNRPPKNPRGSKAQLPDIHPIKWSNIPGLE
SVVINCFVREARENQLLAITAALQLQQITGCKPHPIFSKNDVPTWKLRKGHQMGAKVELK
GKEMSQFLSTLTEIVLPRIREYKGISNQSGNRFGGISFGLTAEDIKFFPEIDANQDSWPK
TFGMHININTSAQLDYQARTLLSGFQFPFFGEEK
Sequence of entity 6 (F), FASTA
>5MRE_6 uL6m (chains F)
SQVGSLPLYISPEVQVSINALSMPRIIRKGRTSMNISQNITVKGPKGELSVEVPDFLHLD
KDEKHGKINVTVQNSEDKHQRSMWGTVRSLINNHIIGVTEGHLAVLRFVGTGYRAQLEND
GKFVNVKVGASIKQGLDVPEGIVVKTPAPTSLIIEGCNKQQVLLFAAKLRKFHPPEPYKG
KGIYVNDETIKLKDKK
Sequence of entity 7 (G), FASTA
>5MRE_7 bL9m (chains G)
SALTKRTHRVKVQVLKDFPRFQLYKGQVANVKPSLMRNYLHNFNGAKYILSEEHDINTEL
LKQYQTLEAKLEED
Sequence of entity 8 (H), FASTA
>5MRE_8 uL13m (chains H)
SQKIGHSGLAFARLWHHVDVARDKRTLGRLASAIAITLIGRHKPVYHPSQDCGDYVVVTN
CQKIRVTGKKFEQKTYWSHSGRPGQLKLQTMNKVVADKGFGEILKKAVSGMLPKNKLRKQ
RLDRLKVFDGSENPYKQNITAFAHEQSSIPEPLKESIFNQ
Sequence of entity 9 (I), FASTA
>5MRE_9 uL14m (chains I)
MIFLKSVIKVIDNSGAQLAECIKVIRKGSPKSPAMVGDRIVCVIQKAKPLTQNITGTANT
NRVKKGDICHAIVVRSKQRNMCRKDGSTVAFGDTACVLINKNTGEPLGTRIMANDGCVDR
TLKDKGYNKICSLASRVI
Sequence of entity 10 (J), FASTA
>5MRE_10 uL15m (chains J)
VSILGQLKPSDGSTKSFKRLGRGPSSGLGKTSGRGQKGQKARGKVKSWFEGGQTPIYKLF
PKIGFTNVGAKPLKELNLKRIQWFHDKNRLHLQPGEVLDMNKMRKLGLVTGPIKYGVKIL
ASGKFHYNLPIALEASRASAKAIAAIEKAGGKFTARYYTPLGLRAHLNPQWFLEKRGRVP
LQARPTKRRDIDFYSKEEKRGYLVMEKDKLLQDIKEAQNK
Sequence of entity 11 (K), FASTA
>5MRE_11 uL16m (chains K)
KHEYAPRFKIVQKKQKGRVPVRTGGSIKGSTLQFGKYGLRLKSEGIRISAQQLKEADNAI
MRYVRPLNNGHLWRRLCTNVAVCIKGNETRMGKGKGGFDHWMVRVPTGKILFEINGDDLH
EKVAREAFRKAGTKLPGVYEFVSLDSLVRVGLHSFKNPKDDPVKNFYDENAKKPSKKYLN
ILKSQEPQYKLFRGR
Sequence of entity 12 (L), FASTA
>5MRE_12 bL17m (chains L)
TVGIARKLSRDKAHRDALLKNLACQLFQHESIVSTHAKCKEASRVAERIITWTKRAITTS
NSVAQAELKSQIQSQLFLAGDNRKLMKRLFSEIAPRYLERPGGYTRVLRLEPRANDSAPQ
SVLELVDSPVMSESHTVNRGNLKMWLLVKSVINDDANQLPHNPLTLQNLHKVAKFKAEAQ
LHGEIMLIKQVLLKEMSLPYDEALENERTQALLKEVYSSSLPKKTKKPSSYVMVPRP

Ligands and cofactors

IDNameFormulaCopies
GDPGuanosine-5'-diphosphateC10 H15 N5 O11 P21
ZNZinc ionZn2
MGMagnesium ionMg299

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

Primary citation

The structure of the yeast mitochondrial ribosome. Desai, N., Brown, A., Amunts, A. et al. Science (2017) 355:528-531. DOI 10.1126/science.aal2415 · PubMed

Other PDB entries of the same protein (UniProt P32611 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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