9HFM: 28S ribosomal protein S34, mitochondrial
Translation-initiation state of human mitochondrial ribosome small subunit (State D). Determined by electron microscopy at 3.0 Å resolution. Released 23 Apr 2025.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organism
- Homo sapiens
- Chains
- 32
- Atoms
- 66,106
- Mol. weight
- 1176.1 kDa
- Ligands
- MG, ZN, FES, ATP
- Released
- 23 Apr 2025
Explore 9HFM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9HFM contains 331 α-helices and 179 β-strands across 31 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: 16 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-8 | 4 | |
| α-helix | 10-25 | 16 | |
| α-helix | 30-33 | 4 | |
| β-strand | 37 | 1 | 1 |
| β-strand | 42-43 | 2 | 1 |
| β-strand | 48-49 | 2 | 1 |
| α-helix | 50-51 | 2 | |
| α-helix | 52-54 | 3 | |
| α-helix | 55-60 | 6 | |
| α-helix | 64-68 | 5 | |
| α-helix | 72-75 | 4 | |
| β-strand | 80-81 | 2 | 2 |
| α-helix | 83-88 | 6 | |
| β-strand | 94-95 | 2 | 2 |
| β-strand | 99-102 | 4 | 3 |
| β-strand | 112-116 | 5 | 3 |
| β-strand | 118-120 | 3 | 2 |
| β-strand | 123-124 | 2 | 2 |
| β-strand | 129-130 | 2 | 3 |
| α-helix | 131 | 1 | |
| β-strand | 140-141 | 2 | 2 |
| α-helix | 142-143 | 2 | |
| α-helix | 147-151 | 5 | |
| α-helix | 155-157 | 3 | |
| β-strand | 163-165 | 3 | 4 |
| α-helix | 166-167 | 2 | |
| α-helix | 168-181 | 14 | |
| α-helix | 187-189 | 3 | |
| β-strand | 190-192 | 3 | 4 |
Chain 1: 21 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-55 | 6 | |
| α-helix | 56-59 | 4 | |
| α-helix | 66-69 | 4 | |
| β-strand | 86 | 1 | 6 |
| β-strand | 87 | 1 | 7 |
| α-helix | 89-91 | 3 | |
| β-strand | 97 | 1 | 7 |
| α-helix | 103-107 | 5 | |
| α-helix | 116-126 | 11 | |
| α-helix | 127-129 | 3 | |
| α-helix | 132-134 | 3 | |
| α-helix | 140-146 | 7 | |
| β-strand | 149-157 | 9 | 8 |
| β-strand | 162 | 1 | 9 |
| α-helix | 166-169 | 4 | |
| β-strand | 171-176 | 6 | 8 |
| α-helix | 177-179 | 3 | |
| α-helix | 184-194 | 11 | |
| α-helix | 195-197 | 3 | |
| β-strand | 198-199 | 2 | 8 |
| β-strand | 204-209 | 6 | 8 |
| α-helix | 215-234 | 20 | |
| α-helix | 238-241 | 4 | |
| α-helix | 245-247 | 3 | |
| α-helix | 257-273 | 17 | |
| α-helix | 280-284 | 5 | |
| α-helix | 287-301 | 15 | |
| α-helix | 303-304 | 2 | |
| α-helix | 306-320 | 15 | |
Chain 2: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 18-19 | 2 | |
| α-helix | 34-37 | 4 | |
| α-helix | 46-59 | 14 | |
| α-helix | 63-65 | 3 | |
| α-helix | 67-91 | 25 | |
| α-helix | 101-110 | 10 | |
Chain 3: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 131-149 | 19 | |
| α-helix | 151-180 | 30 | |
Chain 4: 40 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 59-60 | 2 | |
| β-strand | 61-64 | 4 | 20 |
| α-helix | 69-75 | 7 | |
| α-helix | 100-123 | 24 | |
| α-helix | 125-128 | 4 | |
| β-strand | 134 | 1 | 9 |
| α-helix | 138-140 | 3 | |
| α-helix | 154-163 | 10 | |
| α-helix | 166-179 | 14 | |
| α-helix | 185-198 | 14 | |
| α-helix | 202-204 | 3 | |
| α-helix | 243-250 | 8 | |
| α-helix | 256-268 | 13 | |
| α-helix | 272-284 | 13 | |
| α-helix | 291-304 | 14 | |
| α-helix | 309-326 | 18 | |
| α-helix | 328-330 | 3 | |
| α-helix | 332-342 | 11 | |
| α-helix | 343-345 | 3 | |
| α-helix | 347-363 | 17 | |
| α-helix | 369-379 | 11 | |
| α-helix | 389-400 | 12 | |
| α-helix | 412-414 | 3 | |
| α-helix | 415-426 | 12 | |
| α-helix | 429-440 | 12 | |
| α-helix | 444-447 | 4 | |
| α-helix | 451-468 | 18 | |
| α-helix | 471-481 | 11 | |
| α-helix | 487-489 | 3 | |
| α-helix | 490-503 | 14 | |
| α-helix | 509-519 | 11 | |
| α-helix | 525-536 | 12 | |
| α-helix | 542-561 | 20 | |
| α-helix | 563-566 | 4 | |
| α-helix | 568-569 | 2 | |
| α-helix | 573-586 | 14 | |
| α-helix | 589-602 | 14 | |
| α-helix | 604-607 | 4 | |
| α-helix | 608-621 | 14 | |
| α-helix | 624-637 | 14 | |
| α-helix | 641-652 | 12 | |
| α-helix | 657-669 | 13 | |
Chain 8: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 158-164 | 7 | 21 |
| α-helix | 169-184 | 16 | |
| β-strand | 188-194 | 7 | 21 |
| α-helix | 203-215 | 13 | |
| β-strand | 221-230 | 10 | 21 |
| β-strand | 235-242 | 8 | 21 |
| α-helix | 243-244 | 2 | |
| α-helix | 245-253 | 9 | |
Chain B: 11 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 56-62 | 7 | |
| α-helix | 66-68 | 3 | |
| α-helix | 76-78 | 3 | |
| α-helix | 81-86 | 6 | |
| β-strand | 91-94 | 4 | 22 |
| α-helix | 95-97 | 3 | |
| α-helix | 100-105 | 6 | |
| β-strand | 106-109 | 4 | 22 |
| β-strand | 113-116 | 4 | 22 |
| α-helix | 118-137 | 20 | |
| β-strand | 142-146 | 5 | 23 |
| α-helix | 152-162 | 11 | |
| β-strand | 165-167 | 3 | 23 |
| α-helix | 179-183 | 5 | |
| β-strand | 192-197 | 6 | 23 |
| β-strand | 199 | 1 | 24 |
| β-strand | 205 | 1 | 24 |
| α-helix | 207-215 | 9 | |
| β-strand | 219-223 | 5 | 23 |
| β-strand | 234-237 | 4 | 23 |
| α-helix | 243-273 | 31 | |
Chain C: 5 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 50-51 | 2 | 25 |
| α-helix | 53-56 | 4 | |
| α-helix | 59-61 | 3 | |
| β-strand | 62 | 1 | 26 |
| β-strand | 66 | 1 | 26 |
| β-strand | 70-71 | 2 | 27 |
| α-helix | 73-75 | 3 | |
| α-helix | 82-99 | 18 | |
| β-strand | 104 | 1 | 27 |
| β-strand | 109-113 | 5 | 27 |
| β-strand | 116-124 | 9 | 27 |
| α-helix | 129-147 | 19 | |
| β-strand | 151-158 | 8 | 27 |
| β-strand | 165-166 | 2 | 25 |
23 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 |
|---|
| 28S ribosomal protein S34, mitochondrial | 0 | protein | 218 | Homo sapiens | P82930 (AlphaFold model) |
| 28S ribosomal protein S35, mitochondrial | 1 | protein | 323 | Homo sapiens | P82673 (AlphaFold model) |
| Small ribosomal subunit protein mS37 | 2 | protein | 118 | Homo sapiens | Q96BP2 (AlphaFold model) |
| Aurora kinase A-interacting protein | 3 | protein | 199 | Homo sapiens | Q9NWT8 (AlphaFold model) |
| Pentatricopeptide repeat domain-containing protein 3, mitochondrial | 4 | protein | 689 | Homo sapiens | Q96EY7 |
| Translation initiation factor IF-3, mitochondrial | 8 | protein | 278 | Homo sapiens | Q9H2K0 |
| 12S mitochondrial rRNA | A | RNA | 955 | Homo sapiens | |
| 28S ribosomal protein S2, mitochondrial | B | protein | 296 | Homo sapiens | Q9Y399 |
| 28S ribosomal protein S24, mitochondrial | C | protein | 167 | Homo sapiens | Q96EL2 |
| 28S ribosomal protein S5, mitochondrial | D | protein | 430 | Homo sapiens | P82675 |
| 28S ribosomal protein S6, mitochondrial | E | protein | 125 | Homo sapiens | P82932 |
| 28S ribosomal protein S7, mitochondrial | F | protein | 242 | Homo sapiens | Q9Y2R9 |
20 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>9HFM_1 28S ribosomal protein S34, mitochondrial (chains 0)
MARKKVRPRLIAELARRVRALREQLNRPRDSQLYAVDYETLTRPFSGRRLPVRAWADVRR
ESRLLQLLGRLPLFGLGRLVTRKSWLWQHDEPCYWRLTRVRPDYTAQNLDHGKAWGILTF
KGKTESEAREIEHVMYHDWRLVPKHEEEAFTAFTPAPEDSLASVPYPPLLRAMIIAERQK
NGDTSTEEPMLNVQRIRMEPWDYPAKQEDKGRAKGTPV
Sequence of entity 2 (1), FASTA
>9HFM_2 28S ribosomal protein S35, mitochondrial (chains 1)
MAAAALPAWLSLQSRARTLRAFSTAVYSATPVPTPSLPERTPGNERPPRRKALPPRTEKM
AVDQDWPSVYPVAAPFKPSAVPLPVRMGYPVKKGVPMAKEGNLELLKIPNFLHLTPVAIK
KHCEALKDFCTEWPAALDSDEKCEKHFPIEIDSTDYVSSGPSVRNPRARVVVLRVKLSSL
NLDDHAKKKLIKLVGERYCKTTDVLTIKTDRCPLRRQNYDYAVYLLTVLYHESWNTEEWE
KSKTEADMEEYIWENSSSERNILETLLQMKAAEKNMEINKEELLGTKEIEEYKKSVVSLK
NEEENENSISQYKESVKRLLNVT
Sequence of entity 3 (2), FASTA
>9HFM_3 Small ribosomal subunit protein mS37 (chains 2)
XATPSLRGRLARFGNPRKPVLKPNKPLILANRVGERRREKGEATCITEMSVMMACWKQNE
FRDDACRKEIQGFLDCAARAQEARKMRSIQETLGESGSLLPNKLNKLLQRFPNKPYLS
Sequence of entity 4 (3), FASTA
>9HFM_4 Aurora kinase A-interacting protein (chains 3)
MLLGRLTSQLLRAVPWAGGRPPWPVSGVLGSRVCGPLYSTSPAGPGRAASLPRKGAQLEL
EEMLVPRKMSVSPLESWLTARCFLPRLDTGTAGTVAPPQSYQCPPSQIGEGAEQGDEGVA
DAPQIQCKNVLKIRRRKMNHHKYRKLVKKTRFLRRKVQEGRLRRKQIKFEKDLRRIWLKA
GLKEAPEGWQTPKIYLRGK
Sequence of entity 5 (4), FASTA
>9HFM_5 Pentatricopeptide repeat domain-containing protein 3, mitochondrial (chains 4)
MAVVSAVRWLGLRSRLGQPLTGRRAGLCEQARSCRFYSGSATLSKVEGTDVTGIEEVVIP
KKKTWDKVAVLQALASTVNRDTTAVPYVFQDDPYLMPASSLESRSFLLAKKSGENVAKFI
INSYPKYFQKDIAEPHIPCLMPEYFEPQIKDISEAALKERIELRKVKASVDMFDQLLQAG
TTVSLETTNSLLDLLCYYGDQEPSTDYHFQQTGQSEALEEENDETSRRKAGHQFGVTWRA
KNNAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTFNALIEA
TVCAINEKFEEKWSKILELLRHMVAQKVKPNLQTFNTILKCLRRFHVFARSPALQVLREM
KAIGIEPSLATYHHIIRLFDQPGDPLKRSSFIIYDIMNELMGKRFSPKDPDDDKFFQSAM
SICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYSKFFDLICLMEQIDVTLKWYED
LIPSAYFPHSQTMIHLLQALDVANRLEVIPKIWKDSKEYGHTFRSDLREEILMLMARDKH
PPELQVAFADCAADIKSAYESQPIRQTAQDWPATSLNCIAILFLRAGRTQEAWKMLGLFR
KHNKIPRSELLNELMDSAKVSNSPSQAIEVVELASAFSLPICEGLTQRVMSDFAINQEQK
EALSNLTALTSDSDTDSSSDSDSDTSEGK
Sequence of entity 6 (8), FASTA
>9HFM_6 Translation initiation factor IF-3, mitochondrial (chains 8)
MAALFLKRLTLQTVKSENSCIRCFGKHILQKTAPAQLSPIASAPRLSFLIHAKAFSTAED
TQNEGKKTKKNKTAFSNVGRKISQRVIHLFDEKGNDLGNMHRANVIRLMDERDLRLVQRN
TSTEPAEYQLMTGLQILQERQRLREMEKANPKTGPTLRKELILSSNIGQHDLDTKTKQIQ
QWIKKKHLVQITIKKGKNVDVSENEMEEIFHQILQTMPGIATFSSRPQAVQGGKALMCVL
RALSKNEEKAYKETQETQERDTLNKDHGNDKESNVLHQ
Sequence of entity 7 (A), FASTA
>9HFM_7 12S mitochondrial rRNA (chains A)
AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCC
CGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGC
AGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAA
CCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCG
UGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUU
UUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUG
ACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCA
AACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAA
CUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAU
AUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUG
CUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAG
UACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACA
UUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUA
GCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCC
CGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAU
AGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAACC
Sequence of entity 8 (B), FASTA
>9HFM_8 28S ribosomal protein S2, mitochondrial (chains B)
MATSSAALPRILGAGARAPSRWLGFLGKATPRPARPSRRTLGSATALMIRESEDSTDFND
KILNEPLKHSDFFNVKELFSVRSLFDARVHLGHKAGCRHRFMEPYIFGSRLDHDIIDLEQ
TATHLQLALNFTAHMAYRKGIILFISRNRQFSYLIENMARDCGEYAHTRYFRGGMLTNAR
LLFGPTVRLPDLIIFLHTLNNIFEPHVAVRDAAKMNIPTVGIVDTNCNPCLITYPVPGND
DSPLAVHLYCRLFQTAITRAKEKRQQVEALYRLQGQKEPGDQGPAHPPGADMSHSL
Sequence of entity 9 (C), FASTA
>9HFM_9 28S ribosomal protein S24, mitochondrial (chains C)
MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNRAARVRVSKGDKPVTYEEAHAPH
YIAHRKGWLSLHTGNLDGEDHAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEIC
AVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHLQTVPSKVVYKYL
Sequence of entity 10 (D), FASTA
>9HFM_10 28S ribosomal protein S5, mitochondrial (chains D)
MATAVRAVGCLPVLCSGTAGHLLGRQCSLNTLPAASILAWKSVLGNGHLSSLGTRDTHPY
ASLSRALQTQCCISSPSHLMSQQYRPYSFFTKLTADELWKGALAETGAGAKKGRGKRTKK
KKRKDLNRGQIIGEGRYGFLWPGLNVPLMKNGAVQTIAQRSKEEQEKVEADMIQQREEWD
RKKKMKVKRERGWSGNSWGGISLGPPDPGPCGETYEDFDTRILEVRNVFTMTAKEGRKKS
IRVLVAVGNGKGAAGFSIGKATDRMDAFRKAKNRAVHHLHYIERYEDHTIFHDISLRFKR
THIKMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSINMLSLTQGLFRGLSRQETHQ
QLADKKGLHVVEIREECGPLPIVVASPRGPLRKDPEPEDEVPDVKLDWEDVKTAQGMKRS
VWSNLKRAAT
Sequence of entity 11 (E), FASTA
>9HFM_11 28S ribosomal protein S6, mitochondrial (chains E)
MPRYELALILKAMQRPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNR
GGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKHPLTQELKECEGIVPVPLAEKLYST
KKRKK
Sequence of entity 12 (F), FASTA
>9HFM_12 28S ribosomal protein S7, mitochondrial (chains F)
MAAPAVKVARGWSGLALGVRRAVLQLPGLTQVRWSRYSPEFKDPLIDKEYYRKPVEELTE
EEKYVRELKKTQLIKAAPAGKTSSVFEDPVISKFTNMMMIGGNKVLARSLMIQTLEAVKR
KQFEKYHAASAEEQATIERNPYTIFHQALKNCEPMIGLVPILKGGRFYQVPVPLPDRRRR
FLAMKWMITECRDKKHQRTLMPEKLSHKLLEAFHNQGPVIKRKHDLHKMAEANRALAHYR
WW
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 44 |
| ZN | Zinc ion | Zn | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 1 |
Water and common crystallization additives (K) are not listed.
Primary citation
Coupling of ribosome biogenesis and translation initiation in human mitochondria. Heinrichs, M., Finke, A.F., Aibara, S. et al. Nat Commun (2025) 16:3641-3641. DOI 10.1038/s41467-025-58827-x · PubMed
Other PDB entries of the same protein (UniProt P82930 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7QI4 2.21 Å, Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)
- 8CSS 2.36 Å, Human mitochondrial small subunit assembly intermediate (State D)
- 7P2E 2.4 Å, Human mitochondrial ribosome small subunit in complex with IF3, GMPPMP and streptomycin
- 8RRI 2.4 Å, Human mitochondrial ribosome in complex with antibiotic tigecycline
- 9OLF 2.46 Å, Membrane-associated human mitoribosome in complex with TACO1
- 9OJM 2.5 Å, Human mitochondrial 28S PIC with tRNA and mtIF2
- 8CSQ 2.54 Å, Human mitochondrial small subunit assembly intermediate (State B)
- 8CSR 2.54 Å, Human mitochondrial small subunit assembly intermediate (State C)
- 6ZM6 2.59 Å, Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA
- 7QI5 2.63 Å, Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A…
- 9RU6 2.64 Å, Human mitoribosome bound to TACO1 (Translational activator of COX1), mRNA, A/A-, P/P-…
- 8CSP 2.66 Å, Human mitochondrial small subunit assembly intermediate (State A)
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