8D8L: PDB entry 8D8L

Yeast mitochondrial small subunit assembly intermediate (State 3). Determined by electron microscopy at 2.6 Å resolution. Released 14 Dec 2022.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Saccharomyces cerevisiae
Chains: 35
Atoms: 87,007
Mol. weight: 1558.11 kDa
Ligands: SF4, ATP, MG
Released: 14 Dec 2022

Explore 8D8L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D8L contains 408 α-helices and 237 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 0: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	66-71	6
α-helix	72-74	3
α-helix	77	1
β-strand	78	1	1
α-helix	82-87	6
α-helix	88-92	5
α-helix	98-110	13
α-helix	125-134	10
α-helix	136-153	18
α-helix	155-158	4
β-strand	163-168	6	2
α-helix	174-182	9
β-strand	190-195	6	2
α-helix	200-210	11
β-strand	257-260	4	2
β-strand	269-275	7	2
α-helix	285-297	13
β-strand	300-309	10	2
α-helix	314-328	15
α-helix	330-332	3
β-strand	342	1	2
β-strand	367-371	5	2
α-helix	386-390	5
β-strand	402-407	6	1
α-helix	408-409	2
α-helix	410-415	6
α-helix	418-421	4
β-strand	446-451	6	1
β-strand	453-458	6	2
α-helix	463-475	13
β-strand	496-497	2	3
α-helix	500-501	2
β-strand	502-504	3	3
β-strand	507-513	7	3
β-strand	519-525	7	3
α-helix	530-536	7
β-strand	544	1	3
β-strand	551-554	4	3
α-helix	556-558	3
α-helix	575-589	15

Chain 2: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	33-35	3
α-helix	41-48	8
α-helix	52-56	5
α-helix	63-68	6
α-helix	71-77	7
α-helix	81-95	15
α-helix	101-106	6
α-helix	114-116	3
α-helix	117-127	11

Chain 3: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	53
α-helix	11-14	4
α-helix	17-23	7
β-strand	25	1	56
β-strand	29	1	56
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	77-94	18
α-helix	117-126	10
α-helix	132-146	15
β-strand	151-157	7	57
β-strand	163-169	7	57
α-helix	177-179	3
α-helix	191-206	16
β-strand	219-225	7	57
α-helix	228-231	4
α-helix	240-249	10
α-helix	253-258	6

Chain 4: 18 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	34-37	4
α-helix	38-42	5
α-helix	43-55	13
α-helix	58-61	4
α-helix	64-70	7
α-helix	78-95	18
β-strand	97	1	65
α-helix	103-104	2
α-helix	109-111	3
α-helix	113-117	5
α-helix	118-120	3
α-helix	131-133	3
α-helix	136-146	11
α-helix	149-161	13
β-strand	167-174	8	66
β-strand	196-202	7	66
α-helix	215-229	15
α-helix	245-257	13
β-strand	267-274	8	66
α-helix	277-284	8
α-helix	289-299	11
β-strand	300	1	65
α-helix	302-307	6

Chain 5: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	42-56	15
α-helix	62-66	5
α-helix	71-75	5
α-helix	99-103	5
α-helix	104-107	4
α-helix	116-124	9
α-helix	131-136	6
α-helix	139-148	10
α-helix	149-153	5
α-helix	156-170	15
α-helix	171-173	3
α-helix	181-185	5
α-helix	186-199	14
α-helix	204-216	13
α-helix	227-239	13
α-helix	264-287	24
α-helix	290-292	3
α-helix	296-307	12
α-helix	314-326	13

Chain 6: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	53-62	10
α-helix	64-66	3
β-strand	74	1	72
β-strand	98	1	72
β-strand	99	1	73
β-strand	106	1	73
β-strand	108-109	2	74
β-strand	115-116	2	74
α-helix	132-134	3
α-helix	147	1
β-strand	148	1	75
α-helix	149-150	2
α-helix	151-162	12
α-helix	168-175	8
α-helix	179-197	19
α-helix	203-213	11
α-helix	217	1
β-strand	218	1	75
α-helix	219	1
α-helix	228-229	2
β-strand	232-234	3	60
α-helix	237-240	4
β-strand	244-248	5	70
α-helix	255-261	7
α-helix	267-275	9
β-strand	294-296	3	26
α-helix	297-299	3
β-strand	300	1	27
β-strand	306-311	6	26
α-helix	319-320	2
β-strand	321	1	41
α-helix	323-325	3
β-strand	334-336	3	76
β-strand	342-344	3	76

Chain 8: 27 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	39-44	6	14
β-strand	47-52	6	14
β-strand	61	1	15
α-helix	63-78	16
β-strand	84-89	6	14
β-strand	95-98	4	16
β-strand	100	1	15
α-helix	102-110	9
α-helix	114-132	19
β-strand	138-142	5	14
β-strand	145-147	3	16
α-helix	149-155	7
β-strand	159-162	4	14
β-strand	167-169	3	16
α-helix	173-175	3
α-helix	183-190	8
α-helix	199-207	9
β-strand	211-212	2	16
α-helix	213-218	6
β-strand	224-225	2	14
α-helix	228-230	3
α-helix	231-240	10
α-helix	252-263	12
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	347-363	17
α-helix	371-379	9
α-helix	386-387	2
α-helix	397-401	5
α-helix	414-416	3
α-helix	434-436	3
α-helix	437-446	10
α-helix	458-463	6
α-helix	464-468	5
α-helix	470-472	3
α-helix	478-489	12

Chain A: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
α-helix	11-14	4
α-helix	16-17	2
α-helix	34-35	2
β-strand	36-37	2	40
α-helix	40-44	5
α-helix	53-55	3
β-strand	62-63	2	40
β-strand	64-67	4	51
β-strand	76-78	3	51
α-helix	83-93	11
α-helix	200-201	2
β-strand	215	1	52
β-strand	222	1	52
β-strand	226-233	8	30
β-strand	243-247	5	30
β-strand	250-255	6	30
α-helix	262-267	6
α-helix	268-273	6
β-strand	276-285	10	30
β-strand	291-297	7	30

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
Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial	0	protein	628	Saccharomyces cerevisiae	P36056 (AlphaFold model)
37S ribosomal protein MRP13, mitochondrial	5	protein	339	Saccharomyces cerevisiae	P12686 (AlphaFold model)
Ribosomal protein VAR1, mitochondrial	C	protein	398	Saccharomyces cerevisiae	P02381 (AlphaFold model)
37S ribosomal protein SWS2, mitochondrial	M	protein	143	Saccharomyces cerevisiae	P53937 (AlphaFold model)
37S ribosomal protein MRP2, mitochondrial	N	protein	115	Saccharomyces cerevisiae	P10663
37S ribosomal protein S28, mitochondrial	O	protein	286	Saccharomyces cerevisiae	P21771
37S ribosomal protein S16, mitochondrial	P	protein	121	Saccharomyces cerevisiae	Q02608
37S ribosomal protein S17, mitochondrial	Q	protein	237	Saccharomyces cerevisiae	Q03246
37S ribosomal protein RSM18, mitochondrial	R	protein	138	Saccharomyces cerevisiae	P40033
37S ribosomal protein S19, mitochondrial	S	protein	91	Saccharomyces cerevisiae	P53733
37S ribosomal protein MRP21, mitochondrial	T	protein	177	Saccharomyces cerevisiae	P38175
37S ribosomal protein S25, mitochondrial	U	protein	264	Saccharomyces cerevisiae	P40496

23 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8D8L_1 Probable S-adenosyl-L-methionine-dependent RNA methyltransferase RSM22, mitochondrial (chains 0)
MMKRCFSILPQNVRFSSKFTSLNLPKLDLADFIDSNKRGINVLPSYRDETASTTQATNSK
ELRLLSKTLQGQSYRDQLELNPDVSKAINNNIMAVHIPNNLRRVATNYYKEIQEPNSLHR
PCRTKMEVDAHIASIFLQNYGSIFQSLKELQKRVGPDNFKPQRILDVGYGPATGIVALND
ILGPNYRPDLKDAVILGNAEMQERAKIILSRQLNEVVDTVEENVSTEKEQETDRRNKNFQ
EDEHIGEVMTKKINIMTNLRSSIPASKEYDLIILTHQLLHDGNQFPIQVDENIEHYLNIL
APGGHIVIIERGNPMGFEIIARARQITLRPENFPDEFGKIPRPWSRGVTVRGKKDAELGN
ISSNYFLKVIAPCPHQRKCPLQVGNPNFYTHKEGKDLKFCNFQKSIKRPKFSIELKKGKL
LATSWDGSQGNASRLKGTGRRNGRDYEILNYSYLIFERSHKDENTLKEIKKLRNENVNGK
YDIGSLGDDTQNSWPRIINDPVKRKGHVMMDLCAPSGELEKWTVSRSFSKQIYHDARKSK
KGDLWASAAKTQIKGLGDLNVKKFHKLEKERIKQLKKEERQKARKAMESYNELEDSLQFD
DHQFSNFEVMKKLSTFHGNDFLQHVNRK

Sequence of entity 2 (5), FASTA

>8D8L_2 37S ribosomal protein MRP13, mitochondrial (chains 5)
MGTITVVINEGPILLIRALHRATTNKKMFRSTVWRRFASTGEIAKAKLDEFLIYHKTDAK
LKPFIYRPKNAQILLTKDIRDPKTREPLQPRPPVKPLSKQTLNDFIYSVEPNSTELLDWF
KEWTGTSIRKRAIWTYISPIHVQKMLTASFFKIGKYAHMVGLLYGIEHKFLKAQNPSVFD
IEHFFNTNIMCALHRNRLKDYKDAEIAQRKLQVAWKKVLNRKNNTGLANILVATLGRQIG
FTPELTGLQPVDISLPDIPNSSSGAELKDLLSKYEGIYLIARTLLDIDQHNAQYLELQEF
IRQYQNALSESSDPYDTHLKALGLLETPPPQESTEKEEK

Sequence of entity 3 (C), FASTA

>8D8L_3 Ribosomal protein VAR1, mitochondrial (chains C)
MKLKLLNMILSMMNKTNNNNNIIINNTLDSLMNKKLLLKNMLLDMNNKKMNNMKRMLNNN
NMNPAGANPVVHRIGPAGNINNKLQHLNNMNNWNTQIYNYNKNMEIMNTMNDKLINKLLY
KMMTLKLNNMNINKIIMSKTINQHSLNKLNIKFYYYNNDINNNNNNNNNNYYMNMMNKLM
NIMNNNMNNNLCNILSYYYKKKVTIEPIKLSYIYLNSDIFSKYISLNDMDKYNNGILTNY
QRMLNNIMPKLNDHNISMNYINNINNINNNKYNNMINLLNNNNNINNNNNYNNNNNNYIG
NINNIYNNMTIDNIPMDILMYKYLVGWSIKFKGRLSNNNGRTSTTNLLNGTFNNKKYLWS
NINNNYKLNYIPSNHNLYNNSNINKNGKYNIKVKLNFI

Sequence of entity 4 (M), FASTA

>8D8L_4 37S ribosomal protein SWS2, mitochondrial (chains M)
MVVHILGKGFKGKEVIKIALASKFYGIGKTTAEKICSKLGFYPWMRMHQLSEPQIMSIAS
ELSTMTIEGDARAIVKDNIALKRKIGSYSGMRHTLHLPVRGQHTRNNAKTARKLNKIDRR
GIHTFSQAKVQHNPSLWSCIFGK

Sequence of entity 5 (N), FASTA

>8D8L_5 37S ribosomal protein MRP2, mitochondrial (chains N)
MGNFRFPIKTKLPPGFINARILRDNFKRQQFKENEILVKSLKFIARNMNLPTKLRLEAQL
KLNALPNYMRSTQIKNRCVDSGHARFVLSDFRLCRYQFRENALKGNLPGVKKGIW

Sequence of entity 6 (O), FASTA

>8D8L_6 37S ribosomal protein S28, mitochondrial (chains O)
MSIVGRNAILNLRISLCPLFMGKRSFVSSPVSNSAKAVKFLKAQRRKQKNEAKQATLKAS
TDKVDPVLGRADTPFITRIMAELKEPLVLSKGYNIEEVDKFLAAIESAKRERAELSGLNT
EVVGIEDIEKLEDRREAILRILSMRNSENKNAIKMAVELARKEFERFPGDTGSSEVQAAC
MTVRIQNMANHIKEHRKDFANTRNLRILVQQRQAILRYLKRDNPEKYYWTIQKLGLNDAA
ITDEFNMDRRYMQDYEFFGDKILIRDSKKVANQKRKEIRKQKRATF

Sequence of entity 7 (P), FASTA

>8D8L_7 37S ribosomal protein S16, mitochondrial (chains P)
MTCGLVRIRLARFGRKNSPVYNIVVANSRKARDAKPIEVLGTYVPVPSPVTKRELKRGVV
PIKDVKLDFDRTKYWIGVGAQPSETVTKLLRKAGILNDAWATSKNSNVNRKVVFERMETL
E

Sequence of entity 8 (Q), FASTA

>8D8L_8 37S ribosomal protein S17, mitochondrial (chains Q)
MARQNFLGLVVSQGKMQKTVKVRVETKVFNKKINKELFHRRDYLVHDEGEISREGDLVRI
EATRPLSKRKFFAIAEIIRNKGQQFALYESEAQLSVAKEEAQKAKEFLDKRSVRENKLNE
KTTLLRDIRTIQDALSSGSTPKELLEIKQRYGIQDFSQETVRQLLQLDISGLEVNLEKQR
SLIDRIQTRLSELLSNDLKCDQFLKDHGVEDPLTLKKNIKKNLLRKHVMMDMQQPSQ

Sequence of entity 9 (R), FASTA

>8D8L_9 37S ribosomal protein RSM18, mitochondrial (chains R)
MQPIIKGAVSSTFKRALYNFGIKEKKSVNIEMGRTQQTKKIDQSLSKKLPKGTIYDPFDF
SMGRIHLDRKYQANKNSNRNDIMKSGANPLEFYARPRILSRYVTSTGRIQHRDITGLSAK
NQRRLSKAIRRCQAIGLM

Sequence of entity 10 (S), FASTA

>8D8L_10 37S ribosomal protein S19, mitochondrial (chains S)
MQPAARLLSRSVWKGPNIVPLPIREAMTKGTPIRTNARAATILPQFVGLKFQIHNGKEYV
PIEISEDMVGHKLGEFAPTRKRFSYTQTKNK

Sequence of entity 11 (T), FASTA

>8D8L_11 37S ribosomal protein MRP21, mitochondrial (chains T)
MLKSTLRLSRISLRRGFTTIDCLRQQNSDIDKIILNPIKLAQGSNSDRGQTSKSKTDNAD
ILSMEIPVDMMQSAGRINKRELLSEAEIARSSVENAQMRFNSGKSIIVNKNNPAESFKRL
NRIMFENNIPGDKRSQRFYMKPGKVAELKRSQRHRKEFMMGFKRLIEIVKDAKRKGY

Sequence of entity 12 (U), FASTA

>8D8L_12 37S ribosomal protein S25, mitochondrial (chains U)
MKIQTNAVNVLQRTSAYLKSGLLKETPAWYNVVASIPPSTKFTREPRFKNPSNGHIIGKL
VDVTEQPHANNKGLYKTRPNSSDKRVGVKRLYRPPKLTYVEDRLRSLFYKQHPWELSRPK
ILVENEIGDENYDWSHMLQIGRPLDGESVIQRTMYLIKTKQYGDMVEAYDHARYEFYALR
MQEETEQQVALEEAEMFGSLFGVSAIEHGIQKEQEVLDVWEKKVVEETELMAARTSNPAG
SWKDDTTLNTAQEEESTTSENLHF

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
MG	Magnesium ion	Mg	72

Primary citation

Principles of mitoribosomal small subunit assembly in eukaryotes. Harper, N.J., Burnside, C., Klinge, S. Nature (2023) 614:175-181. DOI 10.1038/s41586-022-05621-0 · PubMed

Other PDB entries of the same protein (UniProt P36056 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8OM2 2.57 Å, Small subunit of yeast mitochondrial ribosome in complex with METTL17/Rsm22.
8D8K 3.13 Å, Yeast mitochondrial small subunit assembly intermediate (State 2)
8D8J 3.8 Å, Yeast mitochondrial small subunit assembly intermediate (State 1)

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