8D8J: PDB entry 8D8J
Yeast mitochondrial small subunit assembly intermediate (State 1). Determined by electron microscopy at 3.8 Å resolution. Released 21 Dec 2022.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 16
- Atoms
- 51,386
- Mol. weight
- 1085.45 kDa
- Ligands
- SF4, MG
- Released
- 21 Dec 2022
Explore 8D8J in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8D8J contains 187 α-helices and 108 β-strands across 15 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: 22 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 66-71 | 6 | |
| 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 | 125-154 | 30 | |
| β-strand | 163-168 | 6 | 2 |
| α-helix | 173-182 | 10 | |
| β-strand | 190-195 | 6 | 2 |
| α-helix | 199-210 | 12 | |
| 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 | 367-369 | 3 | 2 |
| α-helix | 386-390 | 5 | |
| β-strand | 402-407 | 6 | 1 |
| α-helix | 410-415 | 6 | |
| β-strand | 446-451 | 6 | 1 |
| β-strand | 453-458 | 6 | 2 |
| α-helix | 459-461 | 3 | |
| α-helix | 465-475 | 11 | |
| α-helix | 481-482 | 2 | |
| α-helix | 491-493 | 3 | |
| α-helix | 494-495 | 2 | |
| 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 | 531-537 | 7 | |
| β-strand | 544 | 1 | 3 |
| β-strand | 551-554 | 4 | 3 |
| α-helix | 560-598 | 39 | |
| α-helix | 606-627 | 22 | |
Chain 2: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-35 | 4 | |
| 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 | 114-126 | 13 | |
Chain 5: 19 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-56 | 15 | |
| α-helix | 62-66 | 5 | |
| α-helix | 71-76 | 6 | |
| α-helix | 92-94 | 3 | |
| α-helix | 96-98 | 3 | |
| α-helix | 99-103 | 5 | |
| 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 | 228-239 | 12 | |
| α-helix | 264-287 | 24 | |
| α-helix | 295-307 | 13 | |
| α-helix | 314-326 | 13 | |
Chain 6: 16 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-62 | 10 | |
| α-helix | 64-66 | 3 | |
| β-strand | 74 | 1 | 24 |
| α-helix | 90-93 | 4 | |
| β-strand | 98-99 | 2 | 24 |
| β-strand | 106-107 | 2 | 24 |
| β-strand | 108 | 1 | 25 |
| β-strand | 116 | 1 | 25 |
| α-helix | 123-126 | 4 | |
| α-helix | 132-134 | 3 | |
| α-helix | 145-147 | 3 | |
| β-strand | 148 | 1 | 26 |
| α-helix | 149-150 | 2 | |
| α-helix | 151-158 | 8 | |
| α-helix | 159-164 | 6 | |
| α-helix | 168-175 | 8 | |
| α-helix | 179-198 | 20 | |
| α-helix | 203-213 | 11 | |
| α-helix | 217 | 1 | |
| β-strand | 218 | 1 | 26 |
| α-helix | 219-220 | 2 | |
| β-strand | 294-296 | 3 | 7 |
| α-helix | 297-298 | 2 | |
| β-strand | 299-300 | 2 | 8 |
| β-strand | 306-311 | 6 | 7 |
| α-helix | 319-320 | 2 | |
| β-strand | 321 | 1 | 11 |
| β-strand | 335-336 | 2 | 27 |
| β-strand | 342-343 | 2 | 27 |
Chain d: 40 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 149 | 1 | |
| α-helix | 150-154 | 5 | |
| α-helix | 163-171 | 9 | |
| α-helix | 181-191 | 11 | |
| α-helix | 197-210 | 14 | |
| α-helix | 220-232 | 13 | |
| α-helix | 234-235 | 2 | |
| α-helix | 246-269 | 24 | |
| α-helix | 284-297 | 14 | |
| α-helix | 300-314 | 15 | |
| α-helix | 320-332 | 13 | |
| α-helix | 336-349 | 14 | |
| α-helix | 357-370 | 14 | |
| α-helix | 373-385 | 13 | |
| α-helix | 388-390 | 3 | |
| α-helix | 392-405 | 14 | |
| α-helix | 409-412 | 4 | |
| α-helix | 416-432 | 17 | |
| α-helix | 441-455 | 15 | |
| α-helix | 459-479 | 21 | |
| α-helix | 489-496 | 8 | |
| α-helix | 499-510 | 12 | |
| α-helix | 519-522 | 4 | |
| α-helix | 524-542 | 19 | |
| α-helix | 565-580 | 16 | |
| α-helix | 582-584 | 3 | |
| α-helix | 593-613 | 21 | |
| α-helix | 617-635 | 19 | |
| α-helix | 643-656 | 14 | |
| α-helix | 659-669 | 11 | |
| β-strand | 670-671 | 2 | 4 |
| α-helix | 673-688 | 16 | |
| α-helix | 719-729 | 11 | |
| α-helix | 730-732 | 3 | |
| β-strand | 734-735 | 2 | 4 |
| α-helix | 738-751 | 14 | |
| α-helix | 754-767 | 14 | |
| α-helix | 771-775 | 5 | |
| α-helix | 778-798 | 21 | |
| α-helix | 802-811 | 10 | |
| α-helix | 820-833 | 14 | |
| α-helix | 836-847 | 12 | |
Chain D: 19 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| β-strand | 19 | 1 | 14 |
| α-helix | 22-31 | 10 | |
| α-helix | 41-55 | 15 | |
| α-helix | 62-68 | 7 | |
| β-strand | 75 | 1 | 15 |
| α-helix | 93-103 | 11 | |
| β-strand | 104 | 1 | 16 |
| α-helix | 105-111 | 7 | |
| β-strand | 117 | 1 | 14 |
| α-helix | 118-126 | 9 | |
| β-strand | 130-132 | 3 | 17 |
| β-strand | 135-136 | 2 | 17 |
| α-helix | 142 | 1 | |
| β-strand | 143 | 1 | 16 |
| α-helix | 144-145 | 2 | |
| β-strand | 149-152 | 4 | 17 |
| α-helix | 154-160 | 7 | |
| β-strand | 162 | 1 | 18 |
| α-helix | 163-167 | 5 | |
| α-helix | 168-191 | 24 | |
| α-helix | 193-204 | 12 | |
| α-helix | 375-379 | 5 | |
| α-helix | 384-386 | 3 | |
| α-helix | 388-391 | 4 | |
| α-helix | 395-401 | 7 | |
| β-strand | 403 | 1 | 19 |
| β-strand | 408 | 1 | 19 |
| β-strand | 427 | 1 | 18 |
| α-helix | 428 | 1 | |
| β-strand | 441-444 | 4 | 17 |
| β-strand | 449-452 | 4 | 17 |
| β-strand | 458 | 1 | 15 |
| β-strand | 459 | 1 | 20 |
| β-strand | 462 | 1 | 20 |
| α-helix | 471-483 | 13 | |
Chain E: 7 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 140-143 | 4 | |
| β-strand | 145-157 | 13 | 21 |
| β-strand | 162-173 | 12 | 21 |
| β-strand | 178-186 | 9 | 21 |
| α-helix | 190-203 | 14 | |
| β-strand | 206-207 | 2 | 21 |
| β-strand | 211 | 1 | 22 |
| β-strand | 215 | 1 | 22 |
| β-strand | 220-224 | 5 | 23 |
| β-strand | 227-232 | 6 | 23 |
| β-strand | 240-241 | 2 | 23 |
| α-helix | 244-253 | 10 | |
| β-strand | 257 | 1 | 22 |
| β-strand | 258-264 | 7 | 23 |
| α-helix | 268-280 | 13 | |
| α-helix | 286-292 | 7 | |
| α-helix | 297-300 | 4 | |
| α-helix | 302-304 | 3 | |
Chain F: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-10 | 9 | 13 |
| α-helix | 19-34 | 16 | |
| β-strand | 38-43 | 6 | 13 |
| β-strand | 47-55 | 9 | 13 |
| β-strand | 60-72 | 13 | 13 |
| α-helix | 75-87 | 13 | |
| β-strand | 91-93 | 3 | 13 |
| β-strand | 96-99 | 4 | 13 |
| α-helix | 110-115 | 6 | |
| α-helix | 120-123 | 4 | |
7 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) |
| Mitochondrial group I intron splicing factor CCM1 | d | protein | 864 | Saccharomyces cerevisiae | P48237 (AlphaFold model) |
| 37S ribosomal protein S28, mitochondrial | O | protein | 286 | Saccharomyces cerevisiae | P21771 (AlphaFold model) |
| 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 PET123, mitochondrial | V | protein | 318 | Saccharomyces cerevisiae | P17558 |
| Protein FYV4, mitochondrial | 2 | protein | 130 | Saccharomyces cerevisiae | P38783 |
| 37S ribosomal protein NAM9, mitochondrial | D | protein | 486 | Saccharomyces cerevisiae | P27929 |
| 37S ribosomal protein S5, mitochondrial | E | protein | 307 | Saccharomyces cerevisiae | P33759 |
| 37S ribosomal protein MRP17, mitochondrial | F | protein | 131 | Saccharomyces cerevisiae | P28778 |
4 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>8D8J_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
>8D8J_2 37S ribosomal protein MRP13, mitochondrial (chains 5)
MGTITVVINEGPILLIRALHRATTNKKMFRSTVWRRFASTGEIAKAKLDEFLIYHKTDAK
LKPFIYRPKNAQILLTKDIRDPKTREPLQPRPPVKPLSKQTLNDFIYSVEPNSTELLDWF
KEWTGTSIRKRAIWTYISPIHVQKMLTASFFKIGKYAHMVGLLYGIEHKFLKAQNPSVFD
IEHFFNTNIMCALHRNRLKDYKDAEIAQRKLQVAWKKVLNRKNNTGLANILVATLGRQIG
FTPELTGLQPVDISLPDIPNSSSGAELKDLLSKYEGIYLIARTLLDIDQHNAQYLELQEF
IRQYQNALSESSDPYDTHLKALGLLETPPPQESTEKEEK
Sequence of entity 3 (d), FASTA
>8D8J_3 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 4 (O), FASTA
>8D8J_4 37S ribosomal protein S28, mitochondrial (chains O)
MSIVGRNAILNLRISLCPLFMGKRSFVSSPVSNSAKAVKFLKAQRRKQKNEAKQATLKAS
TDKVDPVLGRADTPFITRIMAELKEPLVLSKGYNIEEVDKFLAAIESAKRERAELSGLNT
EVVGIEDIEKLEDRREAILRILSMRNSENKNAIKMAVELARKEFERFPGDTGSSEVQAAC
MTVRIQNMANHIKEHRKDFANTRNLRILVQQRQAILRYLKRDNPEKYYWTIQKLGLNDAA
ITDEFNMDRRYMQDYEFFGDKILIRDSKKVANQKRKEIRKQKRATF
Sequence of entity 5 (P), FASTA
>8D8J_5 37S ribosomal protein S16, mitochondrial (chains P)
MTCGLVRIRLARFGRKNSPVYNIVVANSRKARDAKPIEVLGTYVPVPSPVTKRELKRGVV
PIKDVKLDFDRTKYWIGVGAQPSETVTKLLRKAGILNDAWATSKNSNVNRKVVFERMETL
E
Sequence of entity 6 (Q), FASTA
>8D8J_6 37S ribosomal protein S17, mitochondrial (chains Q)
MARQNFLGLVVSQGKMQKTVKVRVETKVFNKKINKELFHRRDYLVHDEGEISREGDLVRI
EATRPLSKRKFFAIAEIIRNKGQQFALYESEAQLSVAKEEAQKAKEFLDKRSVRENKLNE
KTTLLRDIRTIQDALSSGSTPKELLEIKQRYGIQDFSQETVRQLLQLDISGLEVNLEKQR
SLIDRIQTRLSELLSNDLKCDQFLKDHGVEDPLTLKKNIKKNLLRKHVMMDMQQPSQ
Sequence of entity 7 (R), FASTA
>8D8J_7 37S ribosomal protein RSM18, mitochondrial (chains R)
MQPIIKGAVSSTFKRALYNFGIKEKKSVNIEMGRTQQTKKIDQSLSKKLPKGTIYDPFDF
SMGRIHLDRKYQANKNSNRNDIMKSGANPLEFYARPRILSRYVTSTGRIQHRDITGLSAK
NQRRLSKAIRRCQAIGLM
Sequence of entity 8 (V), FASTA
>8D8J_8 37S ribosomal protein PET123, mitochondrial (chains V)
MGKGAAKYGFKSGVFPTTRSILKSPTTKQTDIINKVKSPKPKGVLGIGYAKGVKHPKGSH
RLSPKVNFIDVDNLIAKTVAEPQSIKSSNGSAQKVRLQKAELRRKFLIEAFRKEEARLLH
KHEYLQKRTKELEKAKELELEKLNKEKSSDLTIMTLDKMMSQPLLRNRSPEESELLKLKR
NYNRSLLNFQAHKKKLNELLNLYHVANEFIVTESQLLKKIDKVFNDETEEFTDAYDVTSN
FTQFGNRKLLLSGNTTLQTQINNAIMGSLSNEKFFDISLVDSYLNKDLKNISNKIDSKLN
PTSNGAGNNGNNNNTTNL
Sequence of entity 9 (2), FASTA
>8D8J_9 Protein FYV4, mitochondrial (chains 2)
MIPSRISHKFPLFLRSSLAAPKAAYRFSSTIPKPSDQVPDVDAFLNKIGRNCNELKDTFE
NNWNNLFQWDSKILKEKGVNIQQRKYILKQVHNYRNNRPIHEIKLGKKSFFGGERKRKAF
TAKWKAENKQ
Sequence of entity 10 (D), FASTA
>8D8J_10 37S ribosomal protein NAM9, mitochondrial (chains D)
MPRKANLLKSLARGRVRTSFNKYNLFNLYKKGGVDLKSKSLYQQKWTAKQETRAYHGEHL
TEKRWQTVFKPKLDSVAQLDASLRGGEIKETPFLLQTFAVLEKRLDFALFRAMFASSVRQ
ARQFILHGNVRVNGVKIKHPSYTLKPGDMFSVKPDKVLEALGAKKPSFQEALKIDKTQIV
LWNKYVKEAKTEPKEVWEKKLENFEKMSDSNPKKLQFQEFLRQYNKNLESQQYNALKGCT
QEGILRKLLNVEKEIGKSNNEPLSIDELKQGLPEIQDSQLLESLNNAYQEFFKSGEIRRE
IISKCQPDELISLATEMMNPNETTKKELSDGAKSALRSGKRIIAESVKLWTKNITDHFKT
RMSDISDGSLTFDPKWAKNLKYHDPIKLSELEGDEPKARKLINLPWQKNYVYGRQDPKKP
FFTPWKPRPFLSPFAILPHHLEISFKTCHAVYLRDPVARPGQSEVISPFDVPVHERAYMY
YLRNGK
Sequence of entity 11 (E), FASTA
>8D8J_11 37S ribosomal protein S5, mitochondrial (chains E)
MFKRQLSTSVRYLQHYDESLLSRYYPESLLKSIKLAQQTIPEDTKFRVSRNVEFAPPYLD
DFTKIHPFWDYKPGMPHLHAQEENNNFSIFRWDQVQQPLPGEGNILPPGVSLPNDGGRKS
KSADVAAGLHKQTGVDPDYITRKLTMKPLVMKRVSNQTGKGKIASFYALVVVGDKNGMVG
LGEGKSREEMSKAIFKAHWDAVRNLKEIPRYENRTIYGDIDFRYHGVKLHLRSAKPGFGL
RVNHVIFEICECAGIKDLSGKVYKSRNDMNIAKGTIEAFTKAQKTLDEVALGRGKKLVDV
RKVYYSS
Sequence of entity 12 (F), FASTA
>8D8J_12 37S ribosomal protein MRP17, mitochondrial (chains F)
MLYELIGLVRITNSNAPKLEAKELSSTIGKLIIQNRGVVRDIVPMGIRYLPKIMKKDQEK
HFRAYHFLMLFDSSAAVQSEILRTLKKDPRVIRSSIVKVDLDKQLDRASSLHRSLGKKSI
LELVNEDYQSI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SF4 | Iron/sulfur cluster | Fe4 S4 | 1 |
| MG | Magnesium ion | Mg | 29 |
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)
- 8D8K 3.13 Å, Yeast mitochondrial small subunit assembly intermediate (State 2)
Browse structure collections
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