3J6B: Yeast mitochondrial large ribosomal subunit

Structure of the yeast mitochondrial large ribosomal subunit. Determined by electron microscopy at 3.2 Å resolution. Released 9 Apr 2014.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae
Chains: 41
Atoms: 111,319
Mol. weight: 2040.16 kDa
Ligands: MG, ZN
Released: 9 Apr 2014

Explore 3J6B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J6B contains 347 α-helices and 291 β-strands across 39 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: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	57-59	3	1
β-strand	69-74	6	1
β-strand	77-82	6	1
β-strand	90-92	3	1

Chain 1: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	30-32	3
α-helix	37-44	8
α-helix	58-63	6
α-helix	66-67	2
α-helix	70-88	19
α-helix	98-109	12
α-helix	113-120	8
α-helix	137-149	13
α-helix	151-161	11
α-helix	165-168	4
β-strand	177-181	5	11
β-strand	191	1	11
α-helix	192-193	2
β-strand	197	1	12
β-strand	208-212	5	11
β-strand	223-234	12	12
β-strand	241-253	13	12
β-strand	260-261	2	11
α-helix	263-266	4
β-strand	271-273	3	12
α-helix	280-281	2
β-strand	282	1	13
β-strand	287-295	9	12
α-helix	322-329	8
β-strand	332-341	10	12
α-helix	347-354	8
β-strand	361	1	13
β-strand	362	1	86

Chain 2: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	37-49	13
α-helix	57-60	4
α-helix	63-108	46
α-helix	110-117	8
α-helix	130-132	3
β-strand	133	1	17

Chain 3: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	63-64	2	19
β-strand	70-71	2	19
α-helix	74-76	3
β-strand	78-80	3	74
β-strand	93-95	3	83
α-helix	99-101	3
β-strand	102-103	2	20
α-helix	115-127	13
β-strand	142-143	2	20

Chain 4: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	26
α-helix	10	1
β-strand	11	1	27
α-helix	12	1
β-strand	23-30	8	28
α-helix	35-37	3
α-helix	38-45	8
α-helix	48-55	8
β-strand	60-65	6	28
β-strand	71-76	6	28
β-strand	81-85	5	28
α-helix	91-103	13
α-helix	107-109	3
β-strand	118-119	2	66
α-helix	127-129	3

Chain 5: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	69-86	18
α-helix	89-94	6
α-helix	96-104	9
α-helix	113-119	7
β-strand	121	1	33
β-strand	139	1	34
α-helix	153-174	22
α-helix	180-191	12
α-helix	193-203	11
β-strand	207	1	35
α-helix	212-218	7
α-helix	222-227	6
β-strand	229	1	35
β-strand	230	1	33
β-strand	235	1	34
α-helix	239-241	3
β-strand	242-245	4	71
α-helix	248-250	3
α-helix	252-270	19
α-helix	278-283	6
α-helix	284-288	5
β-strand	291	1	27
α-helix	294-297	4
β-strand	298-300	3	26
α-helix	303-313	11
α-helix	317-319	3
β-strand	320-327	8	36
β-strand	335-342	8	36
β-strand	345-352	8	36
α-helix	355-371	17

Chain 6: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	39
β-strand	28-33	6	40
α-helix	34-35	2
β-strand	37	1	17
α-helix	38-42	5
α-helix	43-59	17
α-helix	60-63	4
α-helix	65-68	4
α-helix	74-82	9
β-strand	94	1	88
β-strand	96	1	41
β-strand	98	1	41
β-strand	102	1	42
β-strand	107	1	42
α-helix	142-144	3
α-helix	148-151	4
β-strand	166-169	4	40
β-strand	170	1	43
β-strand	178	1	43
β-strand	182	1	39
α-helix	191-203	13
β-strand	209-211	3	40
β-strand	217	1	40
β-strand	231-236	6	40
β-strand	255-257	3	40
α-helix	259-264	6
α-helix	268-273	6

Chain 7: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	52-54	3
β-strand	55	1	18
β-strand	66-68	3	47
β-strand	78-82	5	48
α-helix	83-86	4
β-strand	88-93	6	48
β-strand	96-98	3	47
α-helix	100-110	11
α-helix	116-118	3
β-strand	119-122	4	48
β-strand	127-130	4	48
α-helix	135-143	9

31 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
21S ribosomal RNA	A	RNA	3296	Saccharomyces cerevisiae
54S ribosomal protein RML2, mitochondrial	B	protein	393	Saccharomyces cerevisiae	P32611 (AlphaFold model)
54S ribosomal protein L9, mitochondrial	C	protein	269	Saccharomyces cerevisiae	P31334 (AlphaFold model)
54S ribosomal protein YmL6, mitochondrial	D	protein	286	Saccharomyces cerevisiae	P51998 (AlphaFold model)
54S ribosomal protein L7, mitochondrial	E	protein	292	Saccharomyces cerevisiae	P36519 (AlphaFold model)
54S ribosomal protein L6, mitochondrial	F	protein	214	Saccharomyces cerevisiae	P32904
54S ribosomal protein L50, mitochondrial	G	protein	139	Saccharomyces cerevisiae	P53724
54S ribosomal protein L23, mitochondrial	H	protein	163	Saccharomyces cerevisiae	Q12487
54S ribosomal protein L38, mitochondrial	I	protein	138	Saccharomyces cerevisiae	P35996
54S ribosomal protein L10, mitochondrial	J	protein	322	Saccharomyces cerevisiae	P36520
54S ribosomal protein L16, mitochondrial	K	protein	232	Saccharomyces cerevisiae	P38064
54S ribosomal protein L8, mitochondrial	L	protein	238	Saccharomyces cerevisiae	P22353

29 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>3J6B_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
CUUUUCACCUAAAACAUAAGGUUUAACUAUAAAAGUACGGCCCCUAAUUAAAUUAAUAAG
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

>3J6B_2 54S ribosomal protein RML2, mitochondrial (chains B)
MLVLGSLRSALSCSSTASLISKRNPCYPYGILCRTLSQSVKLWQENTSKDDSSLNITPRL
LKIIPNDTDIVTLEKQDELIKRRRKLSKEVTQMKRLKPVSPGLRWYRSPIYPYLYKGRPV
RALTVVRKKHGGRNNSGKITVRHQGGGHRNRTRLIDFNRWEGGAQTVQRIEYDPGRSSHI
ALLKHNTTGELSYIIACDGLRPGDVVESFRRGIPQTLLNEMGGKVDPAILSVKTTQRGNC
LPISMIPIGTIIHNVGITPVGPGKFCRSAGTYARVLAKLPEKKKAIVRLQSGEHRYVSLE
AVATIGVVSNIDHQNRSLGKAGRSRWLGIRPTVRGVAMNKCDHPHGGGRGKSKSNKLSMS
PWGQLAKGYKTRRGKNQNRMKVKDRPRGKDARL

Sequence of entity 3 (C), FASTA

>3J6B_3 54S ribosomal protein L9, mitochondrial (chains C)
MSKFLQGSIFSISKLHVRYSSTRPFLVAPSIANSITTEAPAINHSPELANARKWLPKRCG
LITRKKGMMPYFDKSTGERSAATILEVNNVEVIMHRTSEVNGYFACQVGYGSRHLSKVSR
QMLGHFASKVVNPKEHVAEFRVKDEKGLIPPGTLLKPSFFKEGQYVDVRSVSKGKGFTGV
MKRYGFKGLRASHGTSIMHRHGGSYGQNQDPGRVLPGRKMPGHMGNEHVTIQNVKVLKVD
DENNVIWVKGSVAGPKNSFVKIQDAIKKT

Sequence of entity 4 (D), FASTA

>3J6B_4 54S ribosomal protein YmL6, mitochondrial (chains D)
MTIKRNLVKTLQSIRYQATTATAHAESTLNPLPNAAIPPKYALVTVRSFPSLEPLTFVPV
PTSTVAAPLRRDILWRAVVYENDNRRVGASNPPGRSENGFSRRKLMPQKGSGRARVGDAN
SPTRHNGGRALARTAPNDYTTELPSKVYSMAFNNALSHQYKSGKLFVIGGEKVDLISPTP
ELDLNRLDLVNTNTVEGKEIFEGEVIFRKFLEEFQLKGKRLLFITDKTREGLIKSSDPYK
QKVDVIQKELVEVNDILRAQAVFIELEALEYLAMAHQKEILHSVSN

Sequence of entity 5 (E), FASTA

>3J6B_5 54S ribosomal protein L7, mitochondrial (chains E)
MQRFSLVTHRSFSHSCVKPKSACSLVKPVHHLVKIDKSKLSPRFPELKYDKSDIRSPGFK
PKDTHADRLNDHYLNTLQSDLLLINYSHNAAVVKGLKQRAWSGDSPYHLNRPPKNPRGSK
AQLPDIHPIKWSNIPGLESVVINCFVREARENQLLAITAALQLQQITGCKPHPIFSKNDV
PTWKLRKGHQMGAKVELKGKEMSQFLSTLTEIVLPRIREYKGISNQSGNRFGGISFGLTA
EDIKFFPEIDANQDSWPKTFGMHININTSAQLDYQARTLLSGFQFPFFGEEK

Sequence of entity 6 (F), FASTA

>3J6B_6 54S ribosomal protein L6, mitochondrial (chains F)
MSFIQRRLLSQTLFLRSQVGSLPLYISPEVQVSINALSMPRIIRKGRTSMNISQNITVKG
PKGELSVEVPDFLHLDKDEKHGKINVTVQNSEDKHQRSMWGTVRSLINNHIIGVTEGHLA
VLRFVGTGYRAQLENDGKFVNVKVGASIKQGLDVPEGIVVKTPAPTSLIIEGCNKQQVLL
FAAKLRKFHPPEPYKGKGIYVNDETIKLKDKKIK

Sequence of entity 7 (G), FASTA

>3J6B_7 54S ribosomal protein L50, mitochondrial (chains G)
MLHCTQVCLSALTKRTHRVKVQVLKDFPRFQLYKGQVANVKPSLMRNYLHNFNGAKYILS
EEHDINTELLKQYQTLEAKLEEDHQQLSKRHETEVQKNMELRKESVFGHKKEEKPKEEKK
GLLDSGITIEEVKIPGLDI

Sequence of entity 8 (H), FASTA

>3J6B_8 54S ribosomal protein L23, mitochondrial (chains H)
MSQKIGHSGLAFARLWHHVDVARDKRTLGRLASAIAITLIGRHKPVYHPSQDCGDYVVVT
NCQKIRVTGKKFEQKTYWSHSGRPGQLKLQTMNKVVADKGFGEILKKAVSGMLPKNKLRK
QRLDRLKVFDGSENPYKQNITAFAHEQSSIPEPLKESIFNQLK

Sequence of entity 9 (I), FASTA

>3J6B_9 54S ribosomal protein L38, mitochondrial (chains I)
MIFLKSVIKVIDNSGAQLAECIKVIRKGSPKSPAMVGDRIVCVIQKAKPLTQNITGTANT
NRVKKGDICHAIVVRSKQRNMCRKDGSTVAFGDTACVLINKNTGEPLGTRIMANDGCVDR
TLKDKGYNKICSLASRVI

Sequence of entity 10 (J), FASTA

>3J6B_10 54S ribosomal protein L10, mitochondrial (chains J)
MKAERQTGLRNSFTTVIGRKLINTFVPSMMLTSVAGNDIFFRGLFKSPVLAFQSYRYVSI
LGQLKPSDGSTKSFKRLGRGPSSGLGKTSGRGQKGQKARGKVKSWFEGGQTPIYKLFPKI
GFTNVGAKPLKELNLKRIQWFHDKNRLHLQPGEVLDMNKMRKLGLVTGPIKYGVKILASG
KFHYNLPIALEASRASAKAIAAIEKAGGKFTARYYTPLGLRAHLNPQWFLEKRGRVPLQA
RPTKRRDIDFYSKEEKRGYLVMEKDKLLQDIKEAQNKGSRHFLKQNVKKSSLEIELEELS
PEKDWVPVVSNSKVMNIKALDH

Sequence of entity 11 (K), FASTA

>3J6B_11 54S ribosomal protein L16, mitochondrial (chains K)
MFPYLTRMNLSIKMGGLTLKESSPNAFLNNTTIARRFKHEYAPRFKIVQKKQKGRVPVRT
GGSIKGSTLQFGKYGLRLKSEGIRISAQQLKEADNAIMRYVRPLNNGHLWRRLCTNVAVC
IKGNETRMGKGKGGFDHWMVRVPTGKILFEINGDDLHEKVAREAFRKAGTKLPGVYEFVS
LDSLVRVGLHSFKNPKDDPVKNFYDENAKKPSKKYLNILKSQEPQYKLFRGR

Sequence of entity 12 (L), FASTA

>3J6B_12 54S ribosomal protein L8, mitochondrial (chains L)
MTVGIARKLSRDKAHRDALLKNLACQLFQHESIVSTHAKCKEASRVAERIITWTKRAITT
SNSVAQAELKSQIQSQLFLAGDNRKLMKRLFSEIAPRYLERPGGYTRVLRLEPRANDSAP
QSVLELVDSPVMSESHTVNRGNLKMWLLVKSVINDDANQLPHNPLTLQNLHKVAKFKAEA
QLHGEIMLIKQVLLKEMSLPYDEALENERTQALLKEVYSSSLPKKTKKPSSYVMVPRP

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	110
ZN	Zinc ion	Zn	2

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

Primary citation

Structure of the yeast mitochondrial large ribosomal subunit. Amunts, A., Brown, A., Bai, X.C. et al. Science (2014) 343:1485-1489. DOI 10.1126/science.1249410 · PubMed

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

9HM0 3.0 Å, Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome
8UXA 3.2 Å, Glucose treated mitochondrial ribosome of saccharomyces cerevisiae class I
9HLZ 3.2 Å, Translational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast…
5MRC 3.25 Å, Structure of the yeast mitochondrial ribosome - Class A
8UX4 3.3 Å, Mitochondrial ribosome of saccharomyces cerevisiae class II from YEP with Dextrose culture
5MRE 3.75 Å, Structure of the yeast mitochondrial ribosome - Class B
5MRF 4.97 Å, Structure of the yeast mitochondrial ribosome - Class C

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