7PNX: 28S ribosomal protein S2, mitochondrial

Name: PDB 7PNX: Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation a
Published: 2022-06-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation a. Determined by electron microscopy at 2.76 Å resolution. Released 15 Jun 2022.

Method: Electron microscopy
Resolution: 2.76 Å
Organism: Homo sapiens
Chains: 32
Atoms: 72,634
Mol. weight: 1217.81 kDa
Ligands: SAH, GDP, ATP, FES
Released: 15 Jun 2022

Explore 7PNX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PNX contains 378 α-helices and 202 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: 20 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
α-helix	125	1
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	147-151	5
α-helix	155-157	3
β-strand	163-165	3	3
α-helix	166-167	2
α-helix	168-180	13
α-helix	187-189	3
β-strand	190-192	3	3
α-helix	213-214	2

Chain 1: 22 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	47-48	2
β-strand	49-50	2	7
α-helix	51-55	5
α-helix	56-59	4
α-helix	66-68	3
β-strand	86	1	31
α-helix	89-91	3
α-helix	96-98	3
α-helix	103-106	4
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	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	239-242	4
α-helix	257-272	16
α-helix	280-283	4
α-helix	287-301	15
α-helix	306-319	14

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: 41 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	59-60	2
β-strand	61-64	4	36
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	154-162	9
α-helix	166-178	13
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	291-303	13
α-helix	309-325	17
α-helix	332-341	10
α-helix	346-349	4
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	410-414	5
α-helix	415-426	12
α-helix	429-440	12
β-strand	441	1	35
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	509-518	10
α-helix	525-535	11
α-helix	542-560	19
α-helix	563-566	4
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 a: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	73-77	5
α-helix	89-109	21
α-helix	115-120	6
β-strand	124-129	6	24
β-strand	136-140	5	24
α-helix	141-143	3
α-helix	146-167	22
α-helix	171-173	3
α-helix	177-178	2
β-strand	179-183	5	24
α-helix	188-199	12
α-helix	233-237	5
α-helix	241-255	15
α-helix	284-286	3
α-helix	291-297	7
β-strand	314-315	2	7

Chain b: 26 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	73-74	2
α-helix	77-84	8
β-strand	91-94	4	27
α-helix	101-109	9
β-strand	114-117	4	27
α-helix	122-131	10
β-strand	139-140	2	27
α-helix	146-156	11
β-strand	163	1	28
β-strand	165-169	5	27
α-helix	174-178	5
α-helix	180-182	3
β-strand	191	1	29
α-helix	205-206	2
α-helix	207-213	7
α-helix	216-221	6
α-helix	222-226	5
α-helix	227	1
α-helix	232-245	14
β-strand	250	1	29
α-helix	251-260	10
α-helix	264-268	5
β-strand	271	1	30
β-strand	277	1	30
α-helix	282-292	11
α-helix	295-309	15
β-strand	310	1	28
α-helix	311	1
α-helix	314	1
β-strand	315-320	6	27
α-helix	323-333	11
α-helix	341	1
α-helix	346-357	12
α-helix	371-373	3
β-strand	375-376	2	27
α-helix	382	1
β-strand	383	1	27
α-helix	387-392	6
α-helix	394-396	3
β-strand	400-406	7	27

Chain B: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	54-58	5
α-helix	59-63	5
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	106-109	4	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: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	10
α-helix	59-61	3
β-strand	62	1	11
β-strand	66	1	11
β-strand	70-71	2	12
α-helix	82-99	18
β-strand	104	1	12
β-strand	109-113	5	12
β-strand	116-124	9	12
α-helix	129-147	19
β-strand	151-158	8	12
α-helix	161-163	3
β-strand	165-166	2	10

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
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

20 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7PNX_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

>7PNX_2 28S ribosomal protein S2, mitochondrial (chains B)
MATSSAALPRILGAGARAPSRWLGFLGKATPRPARPSRRTLGSATALMIRESEDSTDFND
KILNEPLKHSDFFNVKELFSVRSLFDARVHLGHKAGCRHRFMEPYIFGSRLDHDIIDLEQ
TATHLQLALNFTAHMAYRKGIILFISRNRQFSYLIENMARDCGEYAHTRYFRGGMLTNAR
LLFGPTVRLPDLIIFLHTLNNIFEPHVAVRDAAKMNIPTVGIVDTNCNPCLITYPVPGND
DSPLAVHLYCRLFQTAITRAKEKRQQVEALYRLQGQKEPGDQGPAHPPGADMSHSL

Sequence of entity 3 (C), FASTA

>7PNX_3 28S ribosomal protein S24, mitochondrial (chains C)
MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNRAARVRVSKGDKPVTYEEAHAPH
YIAHRKGWLSLHTGNLDGEDHAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEIC
AVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHLQTVPSKVVYKYL

Sequence of entity 4 (D), FASTA

>7PNX_4 28S ribosomal protein S5, mitochondrial (chains D)
MATAVRAVGCLPVLCSGTAGHLLGRQCSLNTLPAASILAWKSVLGNGHLSSLGTRDTHPY
ASLSRALQTQCCISSPSHLMSQQYRPYSFFTKLTADELWKGALAETGAGAKKGRGKRTKK
KKRKDLNRGQIIGEGRYGFLWPGLNVPLMKNGAVQTIAQRSKEEQEKVEADMIQQREEWD
RKKKMKVKRERGWSGNSWGGISLGPPDPGPCGETYEDFDTRILEVRNVFTMTAKEGRKKS
IRVLVAVGNGKGAAGFSIGKATDRMDAFRKAKNRAVHHLHYIERYEDHTIFHDISLRFKR
THIKMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSINMLSLTQGLFRGLSRQETHQ
QLADKKGLHVVEIREECGPLPIVVASPRGPLRKDPEPEDEVPDVKLDWEDVKTAQGMKRS
VWSNLKRAAT

Sequence of entity 5 (E), FASTA

>7PNX_5 28S ribosomal protein S6, mitochondrial (chains E)
MPRYELALILKAMQRPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNR
GGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKHPLTQELKECEGIVPVPLAEKLYST
KKRKK

Sequence of entity 6 (F), FASTA

>7PNX_6 28S ribosomal protein S7, mitochondrial (chains F)
MAAPAVKVARGWSGLALGVRRAVLQLPGLTQVRWSRYSPEFKDPLIDKEYYRKPVEELTE
EEKYVRELKKTQLIKAAPAGKTSSVFEDPVISKFTNMMMIGGNKVLARSLMIQTLEAVKR
KQFEKYHAASAEEQATIERNPYTIFHQALKNCEPMIGLVPILKGGRFYQVPVPLPDRRRR
FLAMKWMITECRDKKHQRTLMPEKLSHKLLEAFHNQGPVIKRKHDLHKMAEANRALAHYR
WW

Sequence of entity 7 (G), FASTA

>7PNX_7 28S ribosomal protein S9, mitochondrial (chains G)
MAAPCVSYGGAVSYRLLLWGRGSLARKQGLWKTAAPELQTNVRSQILRLRHTAFVIPKKN
VPTSKRETYTEDFIKKQIEEFNIGKRHLANMMGEDPETFTQEDIDRAIAYLFPSGLFEKR
ARPVMKHPEQIFPRQRAIQWGEDGRPFHYLFYTGKQSYYSLMHDVYGMLLNLEKHQSHLQ
AKSLLPEKTVTRDVIGSRWLIKEELEEMLVEKLSDLDYMQFIRLLEKLLTSQCGAAEEEF
VQRFRRSVTLESKKQLIEPVQYDEQGMAFSKSEGKRKTAKAEAIVYKHGSGRIKVNGIDY
QLYFPITQDREQLMFPFHFVDRLGKHDVTCTVSGGGRSAQAGAIRLAMAKALCSFVTEDE
VEWMRQAGLLTTDPRVRERKKPGQEGARRKFTWKKR

Sequence of entity 8 (H), FASTA

>7PNX_8 28S ribosomal protein S10, mitochondrial (chains H)
MAARTAFGAVCRRLWQGLGNFSVNTSKGNTAKNGGLLLSTNMKWVQFSNLHVDVPKDLTK
PVVTISDEPDILYKRLSVLVKGHDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTL
LQSVHIYKKHRVQYEMRTLYRCLELEHLTGSTADVYLEYIQRNLPEGVAMEVTKTQLEQL
PEHIKEPIWETLSEEKEESKS

Sequence of entity 9 (I), FASTA

>7PNX_9 28S ribosomal protein S11, mitochondrial (chains I)
MQAVRNAGSRFLRSWTWPQTAGRVVARTPAGTICTGARQLQDAAAKQKVEQNAAPSHTKF
SIYPPIPGEESSLRWAGKKFEEIPIAHIKASHNNTQIQVVSASNEPLAFASCGTEGFRNA
KKGTGIAAQTAGIAAAARAKQKGVIHIRVVVKGLGPGRLSAMHGLIMGGLEVISITDNTP
IPHXGCRPRKARKL

Sequence of entity 10 (J), FASTA

>7PNX_10 28S ribosomal protein S12, mitochondrial (chains J)
MSWSGLLHGLNTSLTCGPALVPRLWATCSMATLNQMHRLGPPKRPPRKLGPTEGRPQLKG
VVLCTFTRKPKKPNSANRKCCRVRLSTGREAVCFIPGEGHTLQEHQIVLVEGGRTQDLPG
VKLTVVRGKYDCGHVQKK

Sequence of entity 11 (K), FASTA

>7PNX_11 28S ribosomal protein S14, mitochondrial (chains K)
MAAFMLGSLLRTFKQMVPSSASGQVRSHYVDWRMWRDVKRRKMAYEYADERLRINSLRKN
TILPKILQDVADEEIAALPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQL
SGIQRATW

Sequence of entity 12 (L), FASTA

>7PNX_12 28S ribosomal protein S15, mitochondrial (chains L)
MLRVAWRTLSLIRTRAVTQVLVPGLPGGGSAKFPFNQWGLQPRSLLLQAARGYVVRKPAQ
SRLDDDPPPSTLLKDYQNVPGIEKVDDVVKRLLSLEMANKKEMLKIKQEQFMKKIVANPE
DTRSLEARIIALSVKIRSYEEHLEKHRKDKAHKRYLLMSIDQRKKMLKNLRNTNYDVFEK
ICWGLGIEYTFPPLYYRRAHRRFVTKKALCIRVFQETQKLKKRRRALKAAAAAQKQAKRR
NPDSPAKAIPKTLKDSQ

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	64
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	1

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

Primary citation

Mechanism of mitoribosomal small subunit biogenesis and preinitiation. Itoh, Y., Khawaja, A., Laptev, I. et al. Nature (2022) 606:603-608. DOI 10.1038/s41586-022-04795-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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