9H54: 28S ribosomal protein S2, mitochondrial

Name: PDB 9H54: Assembly intermediate of human mitochondrial ribosome small subunit in complex with NOA1 and partial RBFA (state N2)
Published: 2026-05-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Assembly intermediate of human mitochondrial ribosome small subunit in complex with NOA1 and partial RBFA (state N2). Determined by electron microscopy at 3.0 Å resolution. Released 6 May 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 31
Atoms: 65,094
Mol. weight: 1226.09 kDa
Ligands: MG, ZN, FES, ATP
Released: 6 May 2026

Explore 9H54 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9H54 contains 358 α-helices and 201 β-strands across 30 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: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	10-25	16
α-helix	27-29	3
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
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
α-helix	131	1
β-strand	139-141	3	2
α-helix	142-143	2
α-helix	144-146	3
α-helix	147-150	4
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
α-helix	207-209	3

Chain 1: 20 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	47-50	4
α-helix	52-55	4
α-helix	56-59	4
α-helix	66-69	4
β-strand	86	1	29
α-helix	89-91	3
α-helix	96-98	3
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	7
β-strand	162	1	8
α-helix	166-169	4
β-strand	171-176	6	7
α-helix	184-194	11
α-helix	195-197	3
β-strand	198-199	2	7
β-strand	204-209	6	7
α-helix	215-234	20
α-helix	239-242	4
α-helix	257-272	16
α-helix	280-283	4
α-helix	287-301	15
α-helix	306-319	14

Chain 4: 39 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	58-60	3
β-strand	61-64	4	34
α-helix	69-76	8
α-helix	100-123	24
α-helix	125-128	4
β-strand	134	1	8
α-helix	138-140	3
α-helix	154-162	9
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	309-325	17
α-helix	328-330	3
α-helix	332-342	11
α-helix	347-363	17
α-helix	365-367	3
α-helix	369-379	11
α-helix	389-400	12
α-helix	410-414	5
α-helix	415-425	11
α-helix	429-439	11
β-strand	441	1	33
α-helix	444-447	4
α-helix	451-468	18
α-helix	471-481	11
α-helix	487-489	3
α-helix	490-502	13
α-helix	509-518	10
α-helix	525-537	13
α-helix	542-560	19
α-helix	568-569	2
α-helix	573-586	14
α-helix	589-601	13
α-helix	605-607	3
α-helix	608-621	14
α-helix	624-637	14
α-helix	640-652	13
α-helix	657-669	13

Chain 9: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	75-77	3
α-helix	80-82	3
α-helix	88-93	6
α-helix	180-190	11
β-strand	195-196	2	20
α-helix	198-204	7
α-helix	206-209	4
β-strand	215-222	8	21
α-helix	234-238	5
β-strand	242-248	7	21
α-helix	260-274	15
β-strand	278-279	2	21
β-strand	309-315	7	21
α-helix	324-333	10
β-strand	340-345	6	21
β-strand	346	1	20
α-helix	351-359	9
β-strand	364	1	22
α-helix	371-373	3
β-strand	376-379	4	21
α-helix	380	1
β-strand	386-391	6	21
β-strand	392	1	22
β-strand	493-496	4	21
α-helix	497-498	2
β-strand	499-500	2	20
α-helix	506-509	4
α-helix	512-518	7
α-helix	523-526	4
β-strand	527-531	5	23
β-strand	535-539	5	24
β-strand	543-548	6	24
β-strand	554-560	7	23
β-strand	566-570	5	24
α-helix	571-581	11
α-helix	593-599	7
α-helix	601-602	2
β-strand	603-609	7	24
α-helix	610-613	4
β-strand	621-625	5	23
β-strand	629-634	6	23
α-helix	635-636	2
β-strand	642-648	7	24
β-strand	654-656	3	23
α-helix	668-669	2
β-strand	670	1	25
α-helix	671	1
β-strand	676	1	23
β-strand	677	1	25
α-helix	678-679	2

Chain a: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	272-279	8
α-helix	376-379	4

Chain B: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	55-58	4
α-helix	59-64	6
α-helix	66-68	3
α-helix	75-78	4
α-helix	81-86	6
β-strand	91-94	4	4
α-helix	95-97	3
α-helix	100-105	6
β-strand	106-110	5	4
β-strand	113-116	4	4
α-helix	118-137	20
β-strand	142-145	4	5
α-helix	149-151	3
α-helix	152-162	11
β-strand	165-167	3	5
α-helix	179-183	5
α-helix	187-190	4
β-strand	192-195	4	5
β-strand	199	1	6
β-strand	205	1	6
α-helix	207-214	8
β-strand	219-223	5	5
β-strand	234-237	4	5
α-helix	243-276	34

Chain C: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	9
α-helix	53-56	4
α-helix	59-61	3
β-strand	62	1	10
β-strand	66	1	10
β-strand	70-71	2	11
α-helix	82-99	18
β-strand	104	1	11
β-strand	109-113	5	11
β-strand	116-123	8	11
α-helix	129-147	19
β-strand	151-157	7	11
α-helix	161-163	3
β-strand	165-166	2	9

Chain D: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	89-91	3
α-helix	95-103	9
α-helix	108-111	4
α-helix	130-131	2
β-strand	139-140	2	12
β-strand	142	1	13
β-strand	146	1	13
β-strand	149-150	2	14
β-strand	153-154	2	14
β-strand	158-159	2	12
α-helix	162-184	23
α-helix	187-191	5
β-strand	202	1	15
α-helix	206-208	3
β-strand	209	1	16
β-strand	213	1	16
β-strand	219-232	14	15
β-strand	236-248	13	15
β-strand	253-261	9	15
α-helix	264-275	12
β-strand	280-281	2	15
β-strand	285	1	17
β-strand	289	1	17
β-strand	294-298	5	18
β-strand	301-307	7	18
β-strand	314-315	2	18
α-helix	318-327	10
β-strand	332-338	7	18
α-helix	342-354	13
α-helix	356-358	3
α-helix	359-366	8
β-strand	369-373	5	19
α-helix	375-377	3
β-strand	382-385	4	19
α-helix	390-392	3
α-helix	395-397	3
α-helix	408-414	7

22 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
12S mitochondrial rRNA	A	RNA	955	Homo sapiens
28S ribosomal protein S2, mitochondrial	B	protein	296	Homo sapiens	Q9Y399 (AlphaFold model)
28S ribosomal protein S24, mitochondrial	C	protein	167	Homo sapiens	Q96EL2 (AlphaFold model)
28S ribosomal protein S5, mitochondrial	D	protein	430	Homo sapiens	P82675 (AlphaFold model)
28S ribosomal protein S6, mitochondrial	E	protein	125	Homo sapiens	P82932 (AlphaFold model)
28S ribosomal protein S7, mitochondrial	F	protein	242	Homo sapiens	Q9Y2R9
28S ribosomal protein S9, mitochondrial	G	protein	396	Homo sapiens	P82933
28S ribosomal protein S10, mitochondrial	H	protein	201	Homo sapiens	P82664
28S ribosomal protein S11, mitochondrial	I	protein	194	Homo sapiens	P82912
28S ribosomal protein S12, mitochondrial	J	protein	138	Homo sapiens	O15235
28S ribosomal protein S14, mitochondrial	K	protein	128	Homo sapiens	O60783
28S ribosomal protein S15, mitochondrial	L	protein	257	Homo sapiens	P82914

19 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9H54_1 12S mitochondrial rRNA (chains A)
AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCC
CGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGC
AGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAA
CCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCG
UGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUU
UUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUG
ACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCA
AACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAA
CUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAU
AUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUG
CUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAG
UACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACA
UUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUA
GCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCC
CGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAU
AGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAACC

Sequence of entity 2 (B), FASTA

>9H54_2 28S ribosomal protein S2, mitochondrial (chains B)
MATSSAALPRILGAGARAPSRWLGFLGKATPRPARPSRRTLGSATALMIRESEDSTDFND
KILNEPLKHSDFFNVKELFSVRSLFDARVHLGHKAGCRHRFMEPYIFGSRLDHDIIDLEQ
TATHLQLALNFTAHMAYRKGIILFISRNRQFSYLIENMARDCGEYAHTRYFRGGMLTNAR
LLFGPTVRLPDLIIFLHTLNNIFEPHVAVRDAAKMNIPTVGIVDTNCNPCLITYPVPGND
DSPLAVHLYCRLFQTAITRAKEKRQQVEALYRLQGQKEPGDQGPAHPPGADMSHSL

Sequence of entity 3 (C), FASTA

>9H54_3 28S ribosomal protein S24, mitochondrial (chains C)
MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNRAARVRVSKGDKPVTYEEAHAPH
YIAHRKGWLSLHTGNLDGEDHAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEIC
AVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHLQTVPSKVVYKYL

Sequence of entity 4 (D), FASTA

>9H54_4 28S ribosomal protein S5, mitochondrial (chains D)
MATAVRAVGCLPVLCSGTAGHLLGRQCSLNTLPAASILAWKSVLGNGHLSSLGTRDTHPY
ASLSRALQTQCCISSPSHLMSQQYRPYSFFTKLTADELWKGALAETGAGAKKGRGKRTKK
KKRKDLNRGQIIGEGRYGFLWPGLNVPLMKNGAVQTIAQRSKEEQEKVEADMIQQREEWD
RKKKMKVKRERGWSGNSWGGISLGPPDPGPCGETYEDFDTRILEVRNVFTMTAKEGRKKS
IRVLVAVGNGKGAAGFSIGKATDRMDAFRKAKNRAVHHLHYIERYEDHTIFHDISLRFKR
THIKMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSINMLSLTQGLFRGLSRQETHQ
QLADKKGLHVVEIREECGPLPIVVASPRGPLRKDPEPEDEVPDVKLDWEDVKTAQGMKRS
VWSNLKRAAT

Sequence of entity 5 (E), FASTA

>9H54_5 28S ribosomal protein S6, mitochondrial (chains E)
MPRYELALILKAMQRPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNR
GGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKHPLTQELKECEGIVPVPLAEKLYST
KKRKK

Sequence of entity 6 (F), FASTA

>9H54_6 28S ribosomal protein S7, mitochondrial (chains F)
MAAPAVKVARGWSGLALGVRRAVLQLPGLTQVRWSRYSPEFKDPLIDKEYYRKPVEELTE
EEKYVRELKKTQLIKAAPAGKTSSVFEDPVISKFTNMMMIGGNKVLARSLMIQTLEAVKR
KQFEKYHAASAEEQATIERNPYTIFHQALKNCEPMIGLVPILKGGRFYQVPVPLPDRRRR
FLAMKWMITECRDKKHQRTLMPEKLSHKLLEAFHNQGPVIKRKHDLHKMAEANRALAHYR
WW

Sequence of entity 7 (G), FASTA

>9H54_7 28S ribosomal protein S9, mitochondrial (chains G)
MAAPCVSYGGAVSYRLLLWGRGSLARKQGLWKTAAPELQTNVRSQILRLRHTAFVIPKKN
VPTSKRETYTEDFIKKQIEEFNIGKRHLANMMGEDPETFTQEDIDRAIAYLFPSGLFEKR
ARPVMKHPEQIFPRQRAIQWGEDGRPFHYLFYTGKQSYYSLMHDVYGMLLNLEKHQSHLQ
AKSLLPEKTVTRDVIGSRWLIKEELEEMLVEKLSDLDYMQFIRLLEKLLTSQCGAAEEEF
VQRFRRSVTLESKKQLIEPVQYDEQGMAFSKSEGKRKTAKAEAIVYKHGSGRIKVNGIDY
QLYFPITQDREQLMFPFHFVDRLGKHDVTCTVSGGGRSAQAGAIRLAMAKALCSFVTEDE
VEWMRQAGLLTTDPRVRERKKPGQEGARRKFTWKKR

Sequence of entity 8 (H), FASTA

>9H54_8 28S ribosomal protein S10, mitochondrial (chains H)
MAARTAFGAVCRRLWQGLGNFSVNTSKGNTAKNGGLLLSTNMKWVQFSNLHVDVPKDLTK
PVVTISDEPDILYKRLSVLVKGHDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTL
LQSVHIYKKHRVQYEMRTLYRCLELEHLTGSTADVYLEYIQRNLPEGVAMEVTKTQLEQL
PEHIKEPIWETLSEEKEESKS

Sequence of entity 9 (I), FASTA

>9H54_9 28S ribosomal protein S11, mitochondrial (chains I)
MQAVRNAGSRFLRSWTWPQTAGRVVARTPAGTICTGARQLQDAAAKQKVEQNAAPSHTKF
SIYPPIPGEESSLRWAGKKFEEIPIAHIKASHNNTQIQVVSASNEPLAFASCGTEGFRNA
KKGTGIAAQTAGIAAAARAKQKGVIHIRVVVKGLGPGRLSAMHGLIMGGLEVISITDNTP
IPHXGCRPRKARKL

Sequence of entity 10 (J), FASTA

>9H54_10 28S ribosomal protein S12, mitochondrial (chains J)
MSWSGLLHGLNTSLTCGPALVPRLWATCSMATLNQMHRLGPPKRPPRKLGPTEGRPQLKG
VVLCTFTRKPKKPNSANRKCCRVRLSTGREAVCFIPGEGHTLQEHQIVLVEGGRTQDLPG
VKLTVVRGKYDCGHVQKK

Sequence of entity 11 (K), FASTA

>9H54_11 28S ribosomal protein S14, mitochondrial (chains K)
MAAFMLGSLLRTFKQMVPSSASGQVRSHYVDWRMWRDVKRRKMAYEYADERLRINSLRKN
TILPKILQDVADEEIAALPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQL
SGIQRATW

Sequence of entity 12 (L), FASTA

>9H54_12 28S ribosomal protein S15, mitochondrial (chains L)
MLRVAWRTLSLIRTRAVTQVLVPGLPGGGSAKFPFNQWGLQPRSLLLQAARGYVVRKPAQ
SRLDDDPPPSTLLKDYQNVPGIEKVDDVVKRLLSLEMANKKEMLKIKQEQFMKKIVANPE
DTRSLEARIIALSVKIRSYEEHLEKHRKDKAHKRYLLMSIDQRKKMLKNLRNTNYDVFEK
ICWGLGIEYTFPPLYYRRAHRRFVTKKALCIRVFQETQKLKKRRRALKAAAAAQKQAKRR
NPDSPAKAIPKTLKDSQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	42
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	2

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

Primary citation

Pseudouridine synthase PUS1 and initiation factor mtIF2 are human mitoribosomal small subunit assembly factors. Singh, V., Shiriaev, D., Bilalli, L. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-74700-x · PubMed

Other PDB entries of the same protein (UniProt Q9Y399 (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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