8OM3: Small subunit of yeast mitochondrial ribosome

Name: PDB 8OM3: Small subunit of yeast mitochondrial ribosome in complex with IF3/Aim23.
Published: 2024-01-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Small subunit of yeast mitochondrial ribosome in complex with IF3/Aim23. Determined by electron microscopy at 2.87 Å resolution. Released 10 Jan 2024.

Method: Electron microscopy
Resolution: 2.87 Å
Organism: Saccharomyces cerevisiae
Chains: 35
Atoms: 91,387
Mol. weight: 1513.71 kDa
Ligands: MG, LMT, ATP
Released: 10 Jan 2024

Explore 8OM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OM3 contains 441 α-helices and 239 β-strands across 34 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 1: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	80-107	28

Chain 2: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	32-34	3
α-helix	41-48	8
α-helix	52-55	4
α-helix	56-59	4
α-helix	63-66	4
α-helix	71-76	6
α-helix	81-95	15
α-helix	104-106	3
α-helix	114-116	3
α-helix	117-124	8

Chain 3: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	7
α-helix	11-14	4
α-helix	17-23	7
β-strand	25	1	16
β-strand	29	1	16
α-helix	31-34	4
α-helix	35-40	6
α-helix	41-53	13
α-helix	57-60	4
α-helix	63-70	8
α-helix	74-76	3
α-helix	77-95	19
α-helix	117-126	10
α-helix	132-146	15
β-strand	151-157	7	17
β-strand	163-169	7	17
α-helix	177-179	3
α-helix	191-206	16
β-strand	219-225	7	17
α-helix	228-231	4
α-helix	240-249	10
α-helix	253-258	6

Chain 4: 18 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	34-37	4
α-helix	38-42	5
α-helix	43-53	11
α-helix	64-70	7
α-helix	78-95	18
β-strand	97	1	26
α-helix	103-104	2
α-helix	109-111	3
α-helix	113-117	5
α-helix	119-120	2
α-helix	131-133	3
α-helix	136-146	11
α-helix	149-162	14
β-strand	167-173	7	4
β-strand	174	1	27
β-strand	175	1	4
β-strand	192-202	11	4
α-helix	215-234	20
α-helix	242-255	14
β-strand	267	1	27
β-strand	271-274	4	4
α-helix	277-284	8
α-helix	289-297	9
β-strand	300	1	26
α-helix	302-308	7
β-strand	311-312	2	4

Chain 5: 25 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	40-56	17
α-helix	62-66	5
α-helix	68-70	3
α-helix	71-77	7
α-helix	79	1
β-strand	80	1	32
α-helix	81	1
β-strand	87	1	32
α-helix	88	1
α-helix	92-94	3
α-helix	96-98	3
α-helix	99-106	8
α-helix	115-123	9
α-helix	131-136	6
α-helix	139-148	10
α-helix	149-153	5
α-helix	156-172	17
α-helix	176-178	3
β-strand	180	1	33
α-helix	181-185	5
α-helix	186-198	13
α-helix	206-216	11
β-strand	220	1	33
α-helix	227-239	13
α-helix	265-273	9
α-helix	275-287	13
α-helix	289-293	5
α-helix	296-307	12
α-helix	314-326	13

Chain 6: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	53-62	10
β-strand	74	1	35
α-helix	90-93	4
β-strand	98	1	35
β-strand	99	1	36
β-strand	106	1	36
β-strand	108-109	2	37
β-strand	115-116	2	37
α-helix	123-125	3
α-helix	130-133	4
α-helix	145-147	3
β-strand	148	1	38
α-helix	149-150	2
α-helix	151-159	9
α-helix	160-164	5
α-helix	168-175	8
α-helix	179-197	19
α-helix	203-213	11
α-helix	217	1
β-strand	218	1	38
α-helix	219	1
α-helix	228-229	2
β-strand	232-234	3	20
β-strand	244-247	4	31
α-helix	255-262	8
α-helix	267-275	9
β-strand	293-296	4	39
β-strand	299-300	2	67
β-strand	306-311	6	39
β-strand	314	1	40
β-strand	317	1	40
α-helix	319-320	2
β-strand	321	1	73
α-helix	323-325	3
β-strand	334-336	3	41
β-strand	342-344	3	41

Chain 8: 30 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	35-37	3
β-strand	39-44	6	43
β-strand	47-52	6	43
α-helix	55-57	3
β-strand	61	1	44
α-helix	63-78	16
β-strand	84-89	6	43
β-strand	95-97	3	45
β-strand	100	1	44
α-helix	102-110	9
α-helix	114-133	20
β-strand	138-142	5	43
β-strand	145-147	3	45
α-helix	149-154	6
β-strand	159-162	4	43
β-strand	167-169	3	45
α-helix	183-190	8
α-helix	199-207	9
β-strand	211-212	2	45
α-helix	214-219	6
β-strand	224-225	2	43
α-helix	228-230	3
α-helix	231-240	10
α-helix	252-265	14
α-helix	268-270	3
α-helix	279-288	10
α-helix	297-305	9
α-helix	311-324	14
α-helix	329-342	14
α-helix	347-362	16
α-helix	371-375	5
α-helix	376-380	5
α-helix	386-389	4
α-helix	397-403	7
α-helix	414-416	3
α-helix	429-432	4
α-helix	434-436	3
α-helix	437-448	12
α-helix	454-456	3
α-helix	458-466	9
α-helix	470-472	3
α-helix	478-489	12
β-strand	490-493	4	46
β-strand	496-499	4	46

Chain A: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
α-helix	11-14	4
α-helix	16-17	2
β-strand	36-37	2	1
α-helix	40-44	5
α-helix	53-55	3
β-strand	62-63	2	1
β-strand	64-65	2	2
β-strand	77-78	2	2
α-helix	83-92	10
β-strand	98	1	3
α-helix	103-105	3
α-helix	116-119	4
α-helix	120-123	4
α-helix	126-129	4
α-helix	141-151	11
α-helix	154-164	11
α-helix	166-171	6
α-helix	176-188	13
α-helix	209-210	2
β-strand	213	1	4
β-strand	215	1	5
β-strand	222	1	5
β-strand	226-231	6	3
α-helix	236-237	2
β-strand	243-247	5	3
β-strand	250-255	6	3
α-helix	263-267	5
α-helix	268-273	6
β-strand	276-285	10	3
β-strand	291-298	8	3

26 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
37S ribosomal protein MRP51, mitochondrial	A	protein	344	Saccharomyces cerevisiae	Q02950 (AlphaFold model)
37S ribosomal protein MRP4, mitochondrial	B	protein	394	Saccharomyces cerevisiae	P32902 (AlphaFold model)
Ribosomal protein VAR1, mitochondrial	C	protein	398	Saccharomyces cerevisiae	P02381 (AlphaFold model)
37S ribosomal protein NAM9, mitochondrial	D	protein	486	Saccharomyces cerevisiae	P27929 (AlphaFold model)
37S ribosomal protein S5, mitochondrial	E	protein	307	Saccharomyces cerevisiae	P33759
37S ribosomal protein MRP17, mitochondrial	F	protein	131	Saccharomyces cerevisiae	P28778
37S ribosomal protein S7, mitochondrial	G	protein	247	Saccharomyces cerevisiae	P47150
37S ribosomal protein S8, mitochondrial	H	protein	155	Saccharomyces cerevisiae	Q03799
37S ribosomal protein S9, mitochondrial	I	protein	278	Saccharomyces cerevisiae	P38120
37S ribosomal protein S10, mitochondrial	J	protein	203	Saccharomyces cerevisiae	Q03201
37S ribosomal protein S18, mitochondrial	K	protein	217	Saccharomyces cerevisiae	P42847
37S ribosomal protein S12, mitochondrial	L	protein	153	Saccharomyces cerevisiae	P53732

23 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8OM3_1 37S ribosomal protein MRP51, mitochondrial (chains A)
MTLAELLGRSRIAQVANNHKPLTYTGKKFHPTHQIIETKPSTLYRQEWGLKSAIPSKIKS
RYLVYNDLDTLERITTFEPRGGTQWNRLRFQEMGVPIVSNIGRQNPFFKYISRPEDESHA
KLSLFKEMKGDTDISPAAMKKRLKKITALIRSFQDEFKEWLVENHPDELKLNSNKLEDYV
VKFLNKKLETKTNKKFNTEIIGTGGLSYSLPGKLKNSPNGVIQRTVVPGRILNVVKENND
NKWLAAIGGFVADVVFFQSPPSSFNSMGDFIRMKTFLFEILEASMEKNGSVSMHARLLEP
QNDKTREFFNKRPIYKPLTSRRARRPSVGNIQEANNLLNIIKGN

Sequence of entity 2 (B), FASTA

>8OM3_2 37S ribosomal protein MRP4, mitochondrial (chains B)
MQRHVFARNFRRLSLLRNPSLTKRFQSSASGAANTPNNNDEVMLLQQKLLYDEIRSELKS
LSQVPEDEILPELKKSLEQDKLSDKEQQLEAELSDFFRNYALLNKLFDSKTLDGQSSTTT
AAATPTKPYPNLIPSANDKPYSSQELFLRQLNHSMRTAKLGATISKVYYPHKDIFYPPLP
ENITVESLMSAGVHLGQSTSLWRSSTQSYIYGEYKGIHIIDLNQTLSYLKRAAKVVEGVS
ESGGIILFLGTRQGQKRGLEEAAKKTHGYYVSTRWIPGTLTNSTEISGIWEKQEIDSNDN
PTERALSPNETSKQVKPDLLVVLNPTENRNALLEAIKSRVPTIAIIDTDSEPSLVTYPIP
GNDDSLRSVNFLLGVLARAGQRGLQNRLARNNEK

Sequence of entity 3 (C), FASTA

>8OM3_3 Ribosomal protein VAR1, mitochondrial (chains C)
MKLKLLNMILSMMNKTNNNNNIIINNTLDSLMNKKLLLKNMLLDMNNKKMNNMKRMLNNN
NMNPAGANPVVHRIGPAGNINNKLQHLNNMNNWNTQIYNYNKNMEIMNTMNDKLINKLLY
KMMTLKLNNMNINKIIMSKTINQHSLNKLNIKFYYYNNDINNNNNNNNNNYYMNMMNKLM
NIMNNNMNNNLCNILSYYYKKKVTIEPIKLSYIYLNSDIFSKYISLNDMDKYNNGILTNY
QRMLNNIMPKLNDHNISMNYINNINNINNNKYNNMINLLNNNNNINNNNNYNNNNNNYIG
NINNIYNNMTIDNIPMDILMYKYLVGWSIKFKGRLSNNNGRTSTTNLLNGTFNNKKYLWS
NINNNYKLNYIPSNHNLYNNSNINKNGKYNIKVKLNFI

Sequence of entity 4 (D), FASTA

>8OM3_4 37S ribosomal protein NAM9, mitochondrial (chains D)
MPRKANLLKSLARGRVRTSFNKYNLFNLYKKGGVDLKSKSLYQQKWTAKQETRAYHGEHL
TEKRWQTVFKPKLDSVAQLDASLRGGEIKETPFLLQTFAVLEKRLDFALFRAMFASSVRQ
ARQFILHGNVRVNGVKIKHPSYTLKPGDMFSVKPDKVLEALGAKKPSFQEALKIDKTQIV
LWNKYVKEAKTEPKEVWEKKLENFEKMSDSNPKKLQFQEFLRQYNKNLESQQYNALKGCT
QEGILRKLLNVEKEIGKSNNEPLSIDELKQGLPEIQDSQLLESLNNAYQEFFKSGEIRRE
IISKCQPDELISLATEMMNPNETTKKELSDGAKSALRSGKRIIAESVKLWTKNITDHFKT
RMSDISDGSLTFDPKWAKNLKYHDPIKLSELEGDEPKARKLINLPWQKNYVYGRQDPKKP
FFTPWKPRPFLSPFAILPHHLEISFKTCHAVYLRDPVARPGQSEVISPFDVPVHERAYMY
YLRNGK

Sequence of entity 5 (E), FASTA

>8OM3_5 37S ribosomal protein S5, mitochondrial (chains E)
MFKRQLSTSVRYLQHYDESLLSRYYPESLLKSIKLAQQTIPEDTKFRVSRNVEFAPPYLD
DFTKIHPFWDYKPGMPHLHAQEENNNFSIFRWDQVQQPLPGEGNILPPGVSLPNDGGRKS
KSADVAAGLHKQTGVDPDYITRKLTMKPLVMKRVSNQTGKGKIASFYALVVVGDKNGMVG
LGEGKSREEMSKAIFKAHWDAVRNLKEIPRYENRTIYGDIDFRYHGVKLHLRSAKPGFGL
RVNHVIFEICECAGIKDLSGKVYKSRNDMNIAKGTIEAFTKAQKTLDEVALGRGKKLVDV
RKVYYSS

Sequence of entity 6 (F), FASTA

>8OM3_6 37S ribosomal protein MRP17, mitochondrial (chains F)
MLYELIGLVRITNSNAPKLEAKELSSTIGKLIIQNRGVVRDIVPMGIRYLPKIMKKDQEK
HFRAYHFLMLFDSSAAVQSEILRTLKKDPRVIRSSIVKVDLDKQLDRASSLHRSLGKKSI
LELVNEDYQSI

Sequence of entity 7 (G), FASTA

>8OM3_7 37S ribosomal protein S7, mitochondrial (chains G)
MLHCARRYMLVRPRLLWQSGTCVARFQSSVRTPASEPSAEKGVDEWLEAINELREEFSAK
EYLPETSLAPPGQSKVDLLQGSQAGSKIKPTAEQLAQWEALKSVPIPPRKNATLDHITNM
IMRHGKKEKAQTILSRALYLVYCQTRQDPIQALEKSLDELAPLMMTKTFNTGVAKASVIP
VPLNKRQRNRIAWNWIVQSANQRVSSDFAVRLGEELTAIAKGTSSAFEKRDQIHKTAIAH
RAYIQLK

Sequence of entity 8 (H), FASTA

>8OM3_8 37S ribosomal protein S8, mitochondrial (chains H)
XSLVKLANTCAHLQNCSKVRVALTSIPYTKLQLQFAYNLYQQGFLSSLQKGSTMGPDKDF
VEVTPDNISTRRLWVGLKYRDNKPVLSSCKLISKPNSRIHLPMEDMKKLCSGVTIRNIKP
LQPGELILVRAHNNIMDINEAISKKLDGEVLCRVK

Sequence of entity 9 (I), FASTA

>8OM3_9 37S ribosomal protein S9, mitochondrial (chains I)
MFSRLSLFRRAALAPAPMRMSFRTIYQKTEDELPRRIVPKLATFYSANPNHEDRINRLER
LLRKYIKLPSQNNNEAQQTKAPWISFDEYALIGGGTKLKPTQYTQLLYMLNKLHNIDPQL
TNDEITSELSQYYKKSSMLSNNIKIKTLDEFGRSIAVGKRKSSTAKVFVVRGTGEILVNG
RQLNDYFLKMKDRESIMYPLQVIESVGKYNIFATTSGGGPTGQAESIMHAIAKALVVFNP
LLKSRLHKAGVLTRDYRHVERKKPGKKKARKMPTWVKR

Sequence of entity 10 (J), FASTA

>8OM3_10 37S ribosomal protein S10, mitochondrial (chains J)
MLRNTIALRSFIRTQSTRPYPVNVEAVYYAPLKLPIKYGDLVADIQLRSYDNENLDFYSD
FILRTGYYLGIPLTGPKPLPTRRERWTVIKSPFVHAKSKENFERHTHKRLIRAWDTNPEV
LQMLIAYITKHSMAGVGMKCNFFQRSEISLDLGSDANGLEKSLSNIDELYSLRNDDKAQT
SAVGQKVLELLDSPDFKKHLEKK

Sequence of entity 11 (K), FASTA

>8OM3_11 37S ribosomal protein S18, mitochondrial (chains K)
MLLQPVWKGCRWTQFVRPIRRWNSTGTNRGVPFSFKDISNQEDITNISYPSSSDSVLTKS
NGSSEVYKPKEEVVKYILHGKFTKNNTHLTFSSVVEDKNFHKNKGLTYNDTMLYYLNLPQ
KVKISLSTGCLGFRKAARGEYEAAFQTSGRMFELIKEKNMLNKDIEVVMDDFGKGRAAFI
SALVGKEGASVVKKVVKISDATKLKFGGVRSPKMRRL

Sequence of entity 12 (L), FASTA

>8OM3_12 37S ribosomal protein S12, mitochondrial (chains L)
MLSRFMSNTWCTPLRQAQRLFSSTTTMQATLNQIKRGSGPPRRKKISTAPQLDQCPQRKG
VVLRVMVLKPKKPNSAQRKACRVRLTNGNVVSAYIPGEGHDAQEHSIVYVRGGRCQDLPG
VKYHVIRGAGDLSGVVNRISSRSKYGAKKPSKS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	96
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

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

Primary citation

METTL17 is an Fe-S cluster checkpoint for mitochondrial translation. Ast, T., Itoh, Y., Sadre, S. et al. Mol Cell (2024) 84:359. DOI 10.1016/j.molcel.2023.12.016 · PubMed

Other PDB entries of the same protein (UniProt Q02950 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8OM4 2.32 Å, Small subunit of yeast mitochondrial ribosome.
8OM2 2.57 Å, Small subunit of yeast mitochondrial ribosome in complex with METTL17/Rsm22.
8D8L 2.6 Å, Yeast mitochondrial small subunit assembly intermediate (State 3)
9HM0 3.0 Å, Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome
8D8K 3.13 Å, Yeast mitochondrial small subunit assembly intermediate (State 2)
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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