8D8K: PDB entry 8D8K

Yeast mitochondrial small subunit assembly intermediate (State 2). Determined by electron microscopy at 3.13 Å resolution. Released 21 Dec 2022.

Method: Electron microscopy
Resolution: 3.13 Å
Organism: Saccharomyces cerevisiae
Chains: 35
Atoms: 88,977
Mol. weight: 1603.33 kDa
Ligands: ATP, MG, SF4
Released: 21 Dec 2022

Explore 8D8K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D8K contains 396 α-helices and 218 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: 20 helices, 16 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	98-112	15
α-helix	125-134	10
α-helix	136-154	19
β-strand	163-168	6	2
α-helix	173-181	9
β-strand	190-195	6	2
α-helix	200-210	11
β-strand	258-260	3	2
β-strand	269-275	7	2
α-helix	288-297	10
β-strand	300-310	11	2
α-helix	314-328	15
α-helix	330-332	3
β-strand	342	1	2
β-strand	367-369	3	2
α-helix	386-390	5
β-strand	402-407	6	1
α-helix	408-409	2
α-helix	410-415	6
β-strand	446-451	6	1
β-strand	452-458	7	2
α-helix	459-460	2
α-helix	463-474	12
α-helix	491-493	3
β-strand	496-497	2	3
β-strand	502-504	3	3
β-strand	507-513	7	3
β-strand	519-525	7	3
α-helix	530-537	8
β-strand	551-554	4	3

Chain 2: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	31-35	5
α-helix	41-48	8
α-helix	53-55	3
α-helix	56-59	4
α-helix	63-66	4
α-helix	71-77	7
α-helix	81-95	15
α-helix	104-106	3
α-helix	114-127	14

Chain 3: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	54
α-helix	11-13	3
α-helix	17-22	6
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	77-96	20
α-helix	117-126	10
α-helix	132-145	14
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	228-235	8
α-helix	240-249	10
α-helix	253-259	7

Chain 4: 18 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	65
β-strand	32	1	65
α-helix	34-37	4
α-helix	38-43	6
α-helix	44-55	12
α-helix	58-60	3
α-helix	64-71	8
α-helix	78-95	18
β-strand	97	1	66
α-helix	103-104	2
α-helix	109-111	3
α-helix	114-117	4
α-helix	119-120	2
α-helix	130-133	4
α-helix	136-146	11
α-helix	149-162	14
β-strand	167-174	8	67
β-strand	196-202	7	67
α-helix	215-229	15
α-helix	245-257	13
β-strand	267-274	8	67
α-helix	277-280	4
α-helix	289-298	10
β-strand	300	1	66
α-helix	302-308	7

Chain 5: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	42-56	15
α-helix	62-66	5
α-helix	68-70	3
α-helix	71-76	6
α-helix	92-94	3
α-helix	96-98	3
α-helix	99-105	7
α-helix	116-124	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
α-helix	181-185	5
α-helix	186-198	13
α-helix	204-217	14
α-helix	227-239	13
α-helix	264-287	24
α-helix	295-307	13
α-helix	314-326	13

Chain 6: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	53-62	10
α-helix	64-66	3
β-strand	74	1	4
α-helix	90-93	4
β-strand	98	1	4
β-strand	99	1	5
β-strand	106	1	5
β-strand	108-109	2	6
β-strand	115-116	2	6
α-helix	123-126	4
α-helix	130-133	4
α-helix	145-147	3
β-strand	148	1	7
α-helix	149-150	2
α-helix	151-158	8
α-helix	159-163	5
α-helix	168-174	7
α-helix	179-197	19
α-helix	203-214	12
α-helix	217	1
β-strand	218	1	7
α-helix	219	1
β-strand	294-296	3	8
α-helix	297-298	2
β-strand	299-300	2	29
β-strand	306-311	6	8
α-helix	319-320	2
β-strand	321	1	42
β-strand	334-336	3	9
β-strand	342-344	3	9

Chain A: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	11-14	4
α-helix	16-17	2
α-helix	34-35	2
β-strand	36-37	2	41
α-helix	40-44	5
α-helix	53-55	3
β-strand	62-63	2	41
β-strand	64-67	4	52
β-strand	76-78	3	52
α-helix	82-93	12
β-strand	215-216	2	53
β-strand	221-222	2	53
β-strand	226-231	6	33
β-strand	244-247	4	33
β-strand	250-255	6	33
α-helix	260-261	2
α-helix	262-267	6
α-helix	268-273	6
β-strand	276-285	10	33
β-strand	291-297	7	33

Chain B: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	134-136	3
α-helix	140-142	3
α-helix	143-156	14
β-strand	163-164	2	54
α-helix	170-175	6
α-helix	177-179	3
α-helix	180-182	3
α-helix	185-190	6
β-strand	195-198	4	40
α-helix	199-201	3
α-helix	204-209	6
β-strand	210-214	5	40
β-strand	217-220	4	40
α-helix	222-241	20
β-strand	246-249	4	55
α-helix	256-265	10
β-strand	269-271	3	55
α-helix	283-286	4
β-strand	292-295	4	56
β-strand	301	1	56
α-helix	304-307	4
α-helix	308-312	5
β-strand	319-322	4	55
α-helix	325-327	3
α-helix	329-338	10
β-strand	342-346	5	55
α-helix	352-354	3
β-strand	357-360	4	55
α-helix	366-391	26

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)
Mitochondrial group I intron splicing factor CCM1	d	protein	864	Saccharomyces cerevisiae	P48237 (AlphaFold model)
37S ribosomal protein SWS2, mitochondrial	M	protein	143	Saccharomyces cerevisiae	P53937
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

23 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8D8K_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

>8D8K_2 37S ribosomal protein MRP13, mitochondrial (chains 5)
MGTITVVINEGPILLIRALHRATTNKKMFRSTVWRRFASTGEIAKAKLDEFLIYHKTDAK
LKPFIYRPKNAQILLTKDIRDPKTREPLQPRPPVKPLSKQTLNDFIYSVEPNSTELLDWF
KEWTGTSIRKRAIWTYISPIHVQKMLTASFFKIGKYAHMVGLLYGIEHKFLKAQNPSVFD
IEHFFNTNIMCALHRNRLKDYKDAEIAQRKLQVAWKKVLNRKNNTGLANILVATLGRQIG
FTPELTGLQPVDISLPDIPNSSSGAELKDLLSKYEGIYLIARTLLDIDQHNAQYLELQEF
IRQYQNALSESSDPYDTHLKALGLLETPPPQESTEKEEK

Sequence of entity 3 (C), FASTA

>8D8K_3 Ribosomal protein VAR1, mitochondrial (chains C)
MKLKLLNMILSMMNKTNNNNNIIINNTLDSLMNKKLLLKNMLLDMNNKKMNNMKRMLNNN
NMNPAGANPVVHRIGPAGNINNKLQHLNNMNNWNTQIYNYNKNMEIMNTMNDKLINKLLY
KMMTLKLNNMNINKIIMSKTINQHSLNKLNIKFYYYNNDINNNNNNNNNNYYMNMMNKLM
NIMNNNMNNNLCNILSYYYKKKVTIEPIKLSYIYLNSDIFSKYISLNDMDKYNNGILTNY
QRMLNNIMPKLNDHNISMNYINNINNINNNKYNNMINLLNNNNNINNNNNYNNNNNNYIG
NINNIYNNMTIDNIPMDILMYKYLVGWSIKFKGRLSNNNGRTSTTNLLNGTFNNKKYLWS
NINNNYKLNYIPSNHNLYNNSNINKNGKYNIKVKLNFI

Sequence of entity 4 (d), FASTA

>8D8K_4 Mitochondrial group I intron splicing factor CCM1 (chains d)
MYMARCGPKNNVLCFPFQLSFLFSKRLINKRFKYTLQTEDEKNMMGSLSKNKIITPEDVE
FKLAQLREFSNTLKERIHNTKSVNSDGHQSNSIAPISEDSRNVNVTKTSSVPNEEKSKNL
SDLIHSSFLEKMDHLVPKVIRERVADDDILAKNLFDRSHSNWAPVIDRLYVSEKRFMDID
SREFSVWLNGTVKYLPFHSILHLDEMLLEQINGDVVKFNTHMYECIFNNLGNLKPTNFNQ
DGTNDKVILKMKELLERYDKALKITEERINKKEGFPSKVPKMTQAILNNCLKYSTKCSSF
HDMDYFITKFRDDYGITPNKQNLTTVIQFYSRKEMTKQAWNTFDTMKFLSTKHFPDICTY
NTMLRICEKERNFPKALDLFQEIQDHNIKPTTNTYIMMARVLASSSSNAVVSEGKSDSLR
LLGWKYLHELEDKNLYRHKKDDLNLFLAMMALAAFDGDIELSRALYYLFIAKKYKTLCAN
WKGNILVDQDTIWKSTLMPEMLNYLMLAYARFDPRNLPVLSGYEKGIELRRKFLREFDSS
MRLDDTDKLVKFKLPFLPISDLNSEAQVLAESNAIWSFNMENGGTRNTLTSSNEAALEDI
KKYRQLLDSFAQEAEDFNEFKFKVMYEVTKMQRESINVNVFNKISLHTYLSIPINLKQQK
EFLRRLTFFTFQQHEFEAVIKRLYEGYRNIPSSHTRDQNSISTEAISVSKPETTEDLNLI
MHDIWYITCLRHKIMMDTTLYELVMKAAIEFQNEDLAKKVWNDRGKFRTTVPFLKMDQRI
RIAKDQKFAHLMVEFFTKQGKYSDAIAIILSSKNRFNWTYSMVRNLHKALEEIEDRNSVE
ILLDVVNKKSHAKALKWEEQELNM

Sequence of entity 5 (M), FASTA

>8D8K_5 37S ribosomal protein SWS2, mitochondrial (chains M)
MVVHILGKGFKGKEVIKIALASKFYGIGKTTAEKICSKLGFYPWMRMHQLSEPQIMSIAS
ELSTMTIEGDARAIVKDNIALKRKIGSYSGMRHTLHLPVRGQHTRNNAKTARKLNKIDRR
GIHTFSQAKVQHNPSLWSCIFGK

Sequence of entity 6 (N), FASTA

>8D8K_6 37S ribosomal protein MRP2, mitochondrial (chains N)
MGNFRFPIKTKLPPGFINARILRDNFKRQQFKENEILVKSLKFIARNMNLPTKLRLEAQL
KLNALPNYMRSTQIKNRCVDSGHARFVLSDFRLCRYQFRENALKGNLPGVKKGIW

Sequence of entity 7 (O), FASTA

>8D8K_7 37S ribosomal protein S28, mitochondrial (chains O)
MSIVGRNAILNLRISLCPLFMGKRSFVSSPVSNSAKAVKFLKAQRRKQKNEAKQATLKAS
TDKVDPVLGRADTPFITRIMAELKEPLVLSKGYNIEEVDKFLAAIESAKRERAELSGLNT
EVVGIEDIEKLEDRREAILRILSMRNSENKNAIKMAVELARKEFERFPGDTGSSEVQAAC
MTVRIQNMANHIKEHRKDFANTRNLRILVQQRQAILRYLKRDNPEKYYWTIQKLGLNDAA
ITDEFNMDRRYMQDYEFFGDKILIRDSKKVANQKRKEIRKQKRATF

Sequence of entity 8 (P), FASTA

>8D8K_8 37S ribosomal protein S16, mitochondrial (chains P)
MTCGLVRIRLARFGRKNSPVYNIVVANSRKARDAKPIEVLGTYVPVPSPVTKRELKRGVV
PIKDVKLDFDRTKYWIGVGAQPSETVTKLLRKAGILNDAWATSKNSNVNRKVVFERMETL
E

Sequence of entity 9 (Q), FASTA

>8D8K_9 37S ribosomal protein S17, mitochondrial (chains Q)
MARQNFLGLVVSQGKMQKTVKVRVETKVFNKKINKELFHRRDYLVHDEGEISREGDLVRI
EATRPLSKRKFFAIAEIIRNKGQQFALYESEAQLSVAKEEAQKAKEFLDKRSVRENKLNE
KTTLLRDIRTIQDALSSGSTPKELLEIKQRYGIQDFSQETVRQLLQLDISGLEVNLEKQR
SLIDRIQTRLSELLSNDLKCDQFLKDHGVEDPLTLKKNIKKNLLRKHVMMDMQQPSQ

Sequence of entity 10 (R), FASTA

>8D8K_10 37S ribosomal protein RSM18, mitochondrial (chains R)
MQPIIKGAVSSTFKRALYNFGIKEKKSVNIEMGRTQQTKKIDQSLSKKLPKGTIYDPFDF
SMGRIHLDRKYQANKNSNRNDIMKSGANPLEFYARPRILSRYVTSTGRIQHRDITGLSAK
NQRRLSKAIRRCQAIGLM

Sequence of entity 11 (S), FASTA

>8D8K_11 37S ribosomal protein S19, mitochondrial (chains S)
MQPAARLLSRSVWKGPNIVPLPIREAMTKGTPIRTNARAATILPQFVGLKFQIHNGKEYV
PIEISEDMVGHKLGEFAPTRKRFSYTQTKNK

Sequence of entity 12 (T), FASTA

>8D8K_12 37S ribosomal protein MRP21, mitochondrial (chains T)
MLKSTLRLSRISLRRGFTTIDCLRQQNSDIDKIILNPIKLAQGSNSDRGQTSKSKTDNAD
ILSMEIPVDMMQSAGRINKRELLSEAEIARSSVENAQMRFNSGKSIIVNKNNPAESFKRL
NRIMFENNIPGDKRSQRFYMKPGKVAELKRSQRHRKEFMMGFKRLIEIVKDAKRKGY

Ligands and cofactors

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

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.
8D8L 2.6 Å, Yeast mitochondrial small subunit assembly intermediate (State 3)
8D8J 3.8 Å, Yeast mitochondrial small subunit assembly intermediate (State 1)

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