9OJM: Human mitochondrial 28S PIC with tRNA and mtIF2

Human mitochondrial 28S PIC with tRNA and mtIF2. Determined by electron microscopy at 2.5 Å resolution. Released 18 Mar 2026.

Method: Electron microscopy
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 34
Atoms: 74,356
Mol. weight: 1069.94 kDa
Ligands: ATP, GDP, FES, ZN
Released: 18 Mar 2026

Explore 9OJM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OJM contains 356 α-helices and 209 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, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	10-25	16
α-helix	27-29	3
α-helix	30-33	4
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
β-strand	62	1	2
α-helix	64-68	5
α-helix	72-75	4
β-strand	79-82	4	2
α-helix	83-88	6
β-strand	94-102	9	2
β-strand	112-120	9	2
β-strand	123-124	2	2
β-strand	129-130	2	2
β-strand	139-141	3	2
α-helix	144-146	3
α-helix	147-151	5
α-helix	155-157	3
β-strand	163-165	3	3
α-helix	166-167	2
α-helix	168-181	14
α-helix	187-189	3
β-strand	190-192	3	3

Chain 1: 21 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	47-55	9
α-helix	56-59	4
α-helix	66-69	4
β-strand	86	1	5
α-helix	89-91	3
α-helix	96-98	3
α-helix	103-107	5
α-helix	112-114	3
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	6
β-strand	162	1	7
α-helix	166-169	4
β-strand	171-176	6	6
α-helix	177-179	3
α-helix	184-194	11
α-helix	195-197	3
β-strand	198-199	2	6
β-strand	204-209	6	6
α-helix	215-234	20
α-helix	238-242	5
α-helix	257-273	17
α-helix	280-284	5
α-helix	287-301	15
α-helix	306-320	15

Chain 2: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	3-5	3
α-helix	18-19	2
α-helix	37-41	5
α-helix	46-58	13
α-helix	63-65	3
α-helix	67-93	27
α-helix	101-110	10

Chain 3: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	131-149	19
α-helix	151-179	29
α-helix	185-186	2

Chain 4: 43 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
β-strand	61-64	4	13
α-helix	69-75	7
α-helix	100-123	24
α-helix	125-128	4
β-strand	134	1	7
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	332-341	10
α-helix	343-348	6
α-helix	350-363	14
α-helix	365-367	3
α-helix	369-379	11
α-helix	385-387	3
α-helix	389-400	12
α-helix	412-414	3
α-helix	415-426	12
α-helix	429-440	12
β-strand	441	1	14
α-helix	444-447	4
α-helix	451-467	17
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	542-560	19
α-helix	563-566	4
α-helix	568-569	2
α-helix	573-586	14
α-helix	589-595	7
α-helix	597-602	6
α-helix	605-607	3
α-helix	608-621	14
α-helix	624-637	14
α-helix	641-652	12
α-helix	654-656	3
α-helix	657-669	13

Chain 7: 21 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	160-162	3
α-helix	170-172	3
β-strand	177-178	2	23
β-strand	182-187	6	24
α-helix	193-201	9
α-helix	210-212	3
β-strand	218-223	6	24
β-strand	229-234	6	24
α-helix	242-251	10
β-strand	254-260	7	24
α-helix	267-279	13
β-strand	283-288	6	24
α-helix	297-304	8
α-helix	305-307	3
β-strand	311	1	25
α-helix	312-314	3
β-strand	318	1	25
β-strand	319-322	4	24
β-strand	324	1	26
β-strand	329	1	26
α-helix	331-345	15
β-strand	348-349	2	23
β-strand	356-365	10	27
β-strand	369-378	10	27
β-strand	381	1	28
β-strand	386-389	4	27
β-strand	392-400	9	27
β-strand	406	1	27
β-strand	410	1	28
β-strand	415-421	7	27
α-helix	424-426	3
β-strand	430-433	4	27
α-helix	437-479	43
α-helix	486-496	11
α-helix	502-506	5
α-helix	509-512	4
β-strand	515-522	8	29
α-helix	525-535	11
β-strand	545-553	9	29
α-helix	558-567	10
β-strand	570-574	5	29
α-helix	580-589	10
β-strand	592-596	5	29
α-helix	599-613	15
α-helix	615-616	2
β-strand	617-636	20	30
β-strand	639-650	12	30
β-strand	652-654	3	31
β-strand	658-663	6	30
β-strand	666-671	6	30
β-strand	673-677	5	30
β-strand	682	1	30
β-strand	685-687	3	31
β-strand	691-696	6	30
α-helix	701-703	3
β-strand	708-717	10	30

Chain B: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	54-58	5
α-helix	59-63	5
α-helix	65-68	4
α-helix	81-86	6
β-strand	91-94	4	32
α-helix	95-97	3
α-helix	100-105	6
β-strand	106-110	5	32
β-strand	113-116	4	32
α-helix	118-137	20
β-strand	142-145	4	33
α-helix	152-162	11
β-strand	165-167	3	33
α-helix	179-182	4
β-strand	192-195	4	33
β-strand	199	1	34
β-strand	205	1	34
α-helix	206	1
α-helix	207-215	9
β-strand	219-223	5	33
β-strand	234-237	4	33
α-helix	243-276	34

Chain C: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	50-51	2	35
α-helix	59-61	3
β-strand	62	1	36
β-strand	66	1	36
β-strand	70-71	2	37
α-helix	82-99	18
β-strand	104	1	37
β-strand	109-113	5	37
β-strand	116-124	9	37
α-helix	129-147	19
β-strand	151-158	8	37
α-helix	161-163	3
β-strand	165-166	2	35

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
Small ribosomal subunit protein mS34	0	protein	215	Homo sapiens	P82930 (AlphaFold model)
Small ribosomal subunit protein mS35	1	protein	278	Homo sapiens	P82673 (AlphaFold model)
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1	2	protein	118	Homo sapiens	Q96BP2 (AlphaFold model)
Small ribosomal subunit protein mS38	3	protein	71	Homo sapiens	Q9NWT8 (AlphaFold model)
Small ribosomal subunit protein mS39	4	protein	616	Homo sapiens	Q96EY7
RNA (71-mer)	5	RNA	71	Homo sapiens
mRNA (5'-r(papupgpu)-3')	6	RNA	4	Homo sapiens
Translation initiation factor IF-2, mitochondrial	7	protein	571	Homo sapiens	P46199
12S mitochondrial RNA	A	RNA	955	Homo sapiens
Small ribosomal subunit protein uS2m	B	protein	225	Homo sapiens	Q9Y399
28S ribosomal protein S24, mitochondrial	C	protein	132	Homo sapiens	Q96EL2
28S ribosomal protein S5, mitochondrial	D	protein	343	Homo sapiens	P82675

22 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>9OJM_1 Small ribosomal subunit protein mS34 (chains 0)
KKVRPRLIAELARRVRALREQLNRPRDSQLYAVDYETLTRPFSGRRLPVRAWADVRRESR
LLQLLGRLPLFGLGRLVTRKSWLWQHDEPCYWRLTRVRPDYTAQNLDHGKAWGILTFKGK
TESEAREIEHVMYHDWRLVPKHEEEAFTAFTPAPEDSLASVPYPPLLRAMIIAERQKNGD
TSTEEPMLNVQRIRMEPWDYPAKQEDKGRAKGTPV

Sequence of entity 2 (1), FASTA

>9OJM_2 Small ribosomal subunit protein mS35 (chains 1)
RPPRRKALPPRTEKMAVDQDWPSVYPVAAPFKPSAVPLPVRMGYPVKKGVPMAKEGNLEL
LKIPNFLHLTPVAIKKHCEALKDFCTEWPAALDSDEKCEKHFPIEIDSTDYVSSGPSVRN
PRARVVVLRVKLSSLNLDDHAKKKLIKLVGERYCKTTDVLTIKTDRCPLRRQNYDYAVYL
LTVLYHESWNTEEWEKSKTEADMEEYIWENSSSERNILETLLQMKAAEKNMEINKEELLG
TKEIEEYKKSVVSLKNEEENENSISQYKESVKRLLNVT

Sequence of entity 3 (2), FASTA

>9OJM_3 Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 (chains 2)
MATPSLRGRLARFGNPRKPVLKPNKPLILANRVGERRREKGEATCITEMSVMMACWKQNE
FRDDACRKEIQGFLDCAARAQEARKMRSIQETLGESGSLLPNKLNKLLQRFPNKPYLS

Sequence of entity 4 (3), FASTA

>9OJM_4 Small ribosomal subunit protein mS38 (chains 3)
KNVLKIRRRKMNHHKYRKLVKKTRFLRRKVQEGRLRRKQIKFEKDLRRIWLKAGLKEAPE
GWQTPKIYLRG

Sequence of entity 5 (4), FASTA

>9OJM_5 Small ribosomal subunit protein mS39 (chains 4)
EEVVIPKKKTWDKVAVLQALASTVNRDTTAVPYVFQDDPYLMPASSLESRSFLLAKKSGE
NVAKFIINSYPKYFQKDIAEPHIPCLMPEYFEPQIKDISEAALKERIELRKVKASVDMFD
QLLQAGTTVSLETTNSLLDLLCYYGDQEPSTDYHFQQTGQSEALEEENDETSRRKAGHQF
GVTWRAKNNAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTF
NALIEATVCAINEKFEEKWSKILELLRHMVAQKVKPNLQTFNTILKCLRRFHVFARSPAL
QVLREMKAIGIEPSLATYHHIIRLFDQPGDPLKRSSFIIYDIMNELMGKRFSPKDPDDDK
FFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYSKFFDLICLMEQIDVT
LKWYEDLIPSAYFPHSQTMIHLLQALDVANRLEVIPKIWKDSKEYGHTFRSDLREEILML
MARDKHPPELQVAFADCAADIKSAYESQPIRQTAQDWPATSLNCIAILFLRAGRTQEAWK
MLGLFRKHNKIPRSELLNELMDSAKVSNSPSQAIEVVELASAFSLPICEGLTQRVMSDFA
INQEQKEALSNLTALT

Sequence of entity 6 (5), FASTA

>9OJM_6 RNA (71-MER) (chains 5)
AGUAAGGUCAGCUAAAUAAGCUAUCGGGCCCAUACCCCGAAAAUGUUGGUUAUACCCUUC
CCGUACUACCA

Sequence of entity 7 (6), FASTA

>9OJM_7 mRNA (5'-R(P*AP*UP*GP*U)-3') (chains 6)
AUGU

Sequence of entity 8 (7), FASTA

>9OJM_8 Translation initiation factor IF-2, mitochondrial (chains 7)
DKVRKNKDAVRRPQADPALLTPRSPVVTIMGHVDHGKTTLLDKFRKTQVAAVETGGITQH
IGAFLVSLPSGEKITFLDTPGHAAFSAMRARGAQVTDIVVLVVAADDGVMKQTVESIQHA
KDAQVPIILAVNKCDKAEADPEKVKKELLAYDVVCEDYGGDVQAVPVSALTGDNLMALAE
ATVALAEMLELKADPNGPVEGTVIESFTDKGRGLVTTAIIQRGTLRKGSVLVAGKCWAKV
RLMFDENGKTIDEAYPSMPVGITGWRDLPSAGEEILEVESEPRAREVVDWRKYEQEQEKG
QEDLKIIEEKRKEHKEAHQKAREKYGHLLWKKRSILRFLERKEQIPLKPKEKRERDSNVL
SVIIKGDVDGSVEAILNIIDTYDASHECELELVHFGVGDVSANDVNLAETFDGVIYGFNV
NAGNVIQQSAAKKGVKIKLHKIIYRLVEDLQEELSSRLPCAVEEHPVGEASILATFSVTE
GKKKVPVAGCRVQKGQLEKQKKFKLTRNGHVIWKGSLTSLKHHKDDISIVKTGMDCGLSL
DEDNMEFQVGDRIVCYEEKQIQAKTSWDPGF

Sequence of entity 9 (A), FASTA

>9OJM_9 12S mitochondrial RNA (chains A)
AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCC
CGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGC
AGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAA
CCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCG
UGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUU
UUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUG
ACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCA
AACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAA
CUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAU
AUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUG
CUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAG
UACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACA
UUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUA
GCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCC
CGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAU
AGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAACC

Sequence of entity 10 (B), FASTA

>9OJM_10 Small ribosomal subunit protein uS2m (chains B)
EDSTDFNDKILNEPLKHSDFFNVKELFSVRSLFDARVHLGHKAGCRHRFMEPYIFGSRLD
HDIIDLEQTATHLQLALNFTAHMAYRKGIILFISRNRQFSYLIENMARDCGEYAHTRYFR
GGMLTNARLLFGPTVRLPDLIIFLHTLNNIFEPHVAVRDAAKMNIPTVGIVDTNCNPCLI
TYPVPGNDDSPLAVHLYCRLFQTAITRAKEKRQQVEALYRLQGQK

Sequence of entity 11 (C), FASTA

>9OJM_11 28S ribosomal protein S24, mitochondrial (chains C)
KNRAARVRVSKGDKPVTYEEAHAPHYIAHRKGWLSLHTGNLDGEDHAAERTVEDVFLRKF
MWGTFPGCLADQLVLKRRGNQLEICAVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHL
QTVPSKVVYKYL

Sequence of entity 12 (D), FASTA

>9OJM_12 28S ribosomal protein S5, mitochondrial (chains D)
SFFTKLTADELWKGALAETGAGAKKGRGKRTKKKKRKDLNRGQIIGEGRYGFLWPGLNVP
LMKNGAVQTIAQRSKEEQEKVEADMIQQREEWDRKKKMKVKRERGWSGNSWGGISLGPPD
PGPCGETYEDFDTRILEVRNVFTMTAKEGRKKSIRVLVAVGNGKGAAGFSIGKATDRMDA
FRKAKNRAVHHLHYIERYEDHTIFHDISLRFKRTHIKMKKQPKGYGLRCHRAIITICRLI
GIKDMYAKVSGSINMLSLTQGLFRGLSRQETHQQLADKKGLHVVEIREECGPLPIVVASP
RGPLRKDPEPEDEVPDVKLDWEDVKTAQGMKRSVWSNLKRAAT

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
ZN	Zinc ion	Zn	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	72

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

Primary citation

Mechanisms of human mitochondrial leaderless mRNA translation initiation. Shen, S., Xu, Y., Kober, D.L. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-71535-4 · 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
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)
7PNX 2.76 Å, Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in…

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