8QRN: Mt-SSU in GTPBP8 knock-out cells, state 4

Name: PDB 8QRN: mt-SSU in GTPBP8 knock-out cells, state 4
Published: 2024-06-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

mt-SSU in GTPBP8 knock-out cells, state 4. Determined by electron microscopy at 2.98 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 2.98 Å
Organism: Homo sapiens
Chains: 34
Atoms: 73,195
Mol. weight: 1248.2 kDa
Ligands: NAD, SPM, SRY, MG
Released: 26 Jun 2024

Explore 8QRN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QRN contains 344 α-helices and 212 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, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	11-25	15
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	55-58	4
β-strand	62	1	2
α-helix	64-66	3
α-helix	68-70	3
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	147-151	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: 19 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	52-55	4
α-helix	66-69	4
β-strand	86	1	24
β-strand	87	1	7
α-helix	89-91	3
α-helix	96	1
β-strand	97	1	7
α-helix	98	1
α-helix	104-107	4
α-helix	116-124	9
α-helix	132-134	3
α-helix	143-146	4
β-strand	149-157	9	8
β-strand	162	1	9
α-helix	166-168	3
β-strand	171-176	6	8
α-helix	184-194	11
α-helix	195-197	3
β-strand	198-199	2	8
β-strand	204-209	6	8
α-helix	215-233	19
α-helix	239-241	3
α-helix	257-272	16
α-helix	280-285	6
α-helix	287-300	14
α-helix	303-304	2
α-helix	306-319	14

Chain 2: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	3-5	3
α-helix	18-19	2
α-helix	34-39	6
α-helix	47-58	12
α-helix	67-93	27
α-helix	99-100	2
α-helix	101-108	8

Chain 3: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	133-147	15
α-helix	151-179	29
α-helix	185-186	2

Chain 4: 38 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	59-60	2
β-strand	61-64	4	37
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	158-161	4
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	309-323	15
α-helix	332-341	10
α-helix	342-344	3
α-helix	346-362	17
α-helix	369-379	11
α-helix	387-400	14
α-helix	410-413	4
α-helix	414-426	13
α-helix	432-438	7
α-helix	444-447	4
α-helix	451-468	18
α-helix	474-480	7
α-helix	487-489	3
α-helix	490-502	13
α-helix	509-518	10
α-helix	525-536	12
α-helix	542-560	19
α-helix	573-586	14
α-helix	589-592	4
α-helix	596-601	6
α-helix	604-607	4
α-helix	608-621	14
α-helix	624-637	14
α-helix	640-653	14
α-helix	656-665	10

Chain 7: 22 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	160-162	3
α-helix	167-172	6
β-strand	177-178	2	27
α-helix	180-181	2
β-strand	182-187	6	28
α-helix	193-201	9
β-strand	218-223	6	28
β-strand	229-234	6	28
α-helix	239-241	3
α-helix	242-251	10
β-strand	254-258	5	28
α-helix	267-279	13
β-strand	283-287	5	28
α-helix	297-306	10
β-strand	311	1	29
α-helix	312-314	3
β-strand	318	1	29
β-strand	319-322	4	28
β-strand	324	1	30
β-strand	329	1	30
α-helix	331-345	15
β-strand	348-349	2	27
β-strand	356-365	10	31
β-strand	369-378	10	31
β-strand	381	1	32
β-strand	386-389	4	31
β-strand	392-395	4	31
β-strand	399-400	2	31
β-strand	406	1	31
β-strand	410	1	32
β-strand	415-419	5	31
β-strand	421	1	31
α-helix	425-426	2
β-strand	430-434	5	31
α-helix	437-478	42
α-helix	486-497	12
α-helix	504-506	3
α-helix	510-512	3
β-strand	515-522	8	33
β-strand	524	1	31
α-helix	525-535	11
β-strand	545-553	9	33
α-helix	558-567	10
β-strand	570-574	5	33
α-helix	580-589	10
β-strand	592-596	5	33
α-helix	599-613	15
α-helix	615-616	2
β-strand	617-636	20	34
β-strand	639-651	13	34
β-strand	653-654	2	35
β-strand	658-663	6	34
β-strand	666-671	6	34
β-strand	673-677	5	34
β-strand	678	1	36
β-strand	681	1	36
β-strand	685-686	2	35
β-strand	691-696	6	34
α-helix	701-703	3
β-strand	708-717	10	34
α-helix	718-721	4

Chain B: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	55-59	5
α-helix	60-64	5
α-helix	66-68	3
α-helix	81-85	5
β-strand	91	1	4
α-helix	100-105	6
β-strand	106-109	4	4
β-strand	114-116	3	4
α-helix	118-137	20
β-strand	142-145	4	5
α-helix	149-151	3
α-helix	152-161	10
β-strand	165-167	3	5
α-helix	179-182	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: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	10
α-helix	59-61	3
β-strand	70-71	2	11
α-helix	82-99	18
β-strand	104	1	11
β-strand	109-113	5	11
β-strand	116-124	9	11
α-helix	129-146	18
β-strand	151-158	8	11
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

22 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8QRN_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

>8QRN_2 28S ribosomal protein S2, mitochondrial (chains B)
MATSSAALPRILGAGARAPSRWLGFLGKATPRPARPSRRTLGSATALMIRESEDSTDFND
KILNEPLKHSDFFNVKELFSVRSLFDARVHLGHKAGCRHRFMEPYIFGSRLDHDIIDLEQ
TATHLQLALNFTAHMAYRKGIILFISRNRQFSYLIENMARDCGEYAHTRYFRGGMLTNAR
LLFGPTVRLPDLIIFLHTLNNIFEPHVAVRDAAKMNIPTVGIVDTNCNPCLITYPVPGND
DSPLAVHLYCRLFQTAITRAKEKRQQVEALYRLQGQKEPGDQGPAHPPGADMSHSL

Sequence of entity 3 (C), FASTA

>8QRN_3 28S ribosomal protein S24, mitochondrial (chains C)
MAASVCSGLLGPRVLSWSRELPCAWRALHTSPVCAKNRAARVRVSKGDKPVTYEEAHAPH
YIAHRKGWLSLHTGNLDGEDHAAERTVEDVFLRKFMWGTFPGCLADQLVLKRRGNQLEIC
AVVLRQLSPHKYYFLVGYSETLLSYFYKCPVRLHLQTVPSKVVYKYL

Sequence of entity 4 (D), FASTA

>8QRN_4 28S ribosomal protein S5, mitochondrial (chains D)
MATAVRAVGCLPVLCSGTAGHLLGRQCSLNTLPAASILAWKSVLGNGHLSSLGTRDTHPY
ASLSRALQTQCCISSPSHLMSQQYRPYSFFTKLTADELWKGALAETGAGAKKGRGKRTKK
KKRKDLNRGQIIGEGRYGFLWPGLNVPLMKNGAVQTIAQRSKEEQEKVEADMIQQREEWD
RKKKMKVKRERGWSGNSWGGISLGPPDPGPCGETYEDFDTRILEVRNVFTMTAKEGRKKS
IRVLVAVGNGKGAAGFSIGKATDRMDAFRKAKNRAVHHLHYIERYEDHTIFHDISLRFKR
THIKMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSINMLSLTQGLFRGLSRQETHQ
QLADKKGLHVVEIREECGPLPIVVASPRGPLRKDPEPEDEVPDVKLDWEDVKTAQGMKRS
VWSNLKRAAT

Sequence of entity 5 (E), FASTA

>8QRN_5 28S ribosomal protein S6, mitochondrial (chains E)
MPRYELALILKAMQRPETAATLKRTIEALMDRGAIVRDLENLGERALPYRISAHSQQHNR
GGYFLVDFYAPTAAVESMVEHLSRDIDVIRGNIVKHPLTQELKECEGIVPVPLAEKLYST
KKRKK

Sequence of entity 6 (F), FASTA

>8QRN_6 28S ribosomal protein S7, mitochondrial (chains F)
MAAPAVKVARGWSGLALGVRRAVLQLPGLTQVRWSRYSPEFKDPLIDKEYYRKPVEELTE
EEKYVRELKKTQLIKAAPAGKTSSVFEDPVISKFTNMMMIGGNKVLARSLMIQTLEAVKR
KQFEKYHAASAEEQATIERNPYTIFHQALKNCEPMIGLVPILKGGRFYQVPVPLPDRRRR
FLAMKWMITECRDKKHQRTLMPEKLSHKLLEAFHNQGPVIKRKHDLHKMAEANRALAHYR
WW

Sequence of entity 7 (G), FASTA

>8QRN_7 28S ribosomal protein S9, mitochondrial (chains G)
MAAPCVSYGGAVSYRLLLWGRGSLARKQGLWKTAAPELQTNVRSQILRLRHTAFVIPKKN
VPTSKRETYTEDFIKKQIEEFNIGKRHLANMMGEDPETFTQEDIDRAIAYLFPSGLFEKR
ARPVMKHPEQIFPRQRAIQWGEDGRPFHYLFYTGKQSYYSLMHDVYGMLLNLEKHQSHLQ
AKSLLPEKTVTRDVIGSRWLIKEELEEMLVEKLSDLDYMQFIRLLEKLLTSQCGAAEEEF
VQRFRRSVTLESKKQLIEPVQYDEQGMAFSKSEGKRKTAKAEAIVYKHGSGRIKVNGIDY
QLYFPITQDREQLMFPFHFVDRLGKHDVTCTVSGGGRSAQAGAIRLAMAKALCSFVTEDE
VEWMRQAGLLTTDPRVRERKKPGQEGARRKFTWKKR

Sequence of entity 8 (H), FASTA

>8QRN_8 28S ribosomal protein S10, mitochondrial (chains H)
MAARTAFGAVCRRLWQGLGNFSVNTSKGNTAKNGGLLLSTNMKWVQFSNLHVDVPKDLTK
PVVTISDEPDILYKRLSVLVKGHDKAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTL
LQSVHIYKKHRVQYEMRTLYRCLELEHLTGSTADVYLEYIQRNLPEGVAMEVTKTQLEQL
PEHIKEPIWETLSEEKEESKS

Sequence of entity 9 (I), FASTA

>8QRN_9 28S ribosomal protein S11, mitochondrial (chains I)
MQAVRNAGSRFLRSWTWPQTAGRVVARTPAGTICTGARQLQDAAAKQKVEQNAAPSHTKF
SIYPPIPGEESSLRWAGKKFEEIPIAHIKASHNNTQIQVVSASNEPLAFASCGTEGFRNA
KKGTGIAAQTAGIAAAARAKQKGVIHIRVVVKGLGPGRLSAMHGLIMGGLEVISITDNTP
IPHNGCRPRKARKL

Sequence of entity 10 (J), FASTA

>8QRN_10 28S ribosomal protein S12, mitochondrial (chains J)
MSWSGLLHGLNTSLTCGPALVPRLWATCSMATLNQMHRLGPPKRPPRKLGPTEGRPQLKG
VVLCTFTRKPKKPNSANRKCCRVRLSTGREAVCFIPGEGHTLQEHQIVLVEGGRTQDLPG
VKLTVVRGKYDCGHVQKK

Sequence of entity 11 (K), FASTA

>8QRN_11 28S ribosomal protein S14, mitochondrial (chains K)
MAAFMLGSLLRTFKQMVPSSASGQVRSHYVDWRMWRDVKRRKMAYEYADERLRINSLRKN
TILPKILQDVADEEIAALPRDSCPVRIRNRCVMTSRPRGVKRRWRLSRIVFRHLADHGQL
SGIQRATW

Sequence of entity 12 (L), FASTA

>8QRN_12 28S ribosomal protein S15, mitochondrial (chains L)
MLRVAWRTLSLIRTRAVTQVLVPGLPGGGSAKFPFNQWGLQPRSLLLQAARGYVVRKPAQ
SRLDDDPPPSTLLKDYQNVPGIEKVDDVVKRLLSLEMANKKEMLKIKQEQFMKKIVANPE
DTRSLEARIIALSVKIRSYEEHLEKHRKDKAHKRYLLMSIDQRKKMLKNLRNTNYDVFEK
ICWGLGIEYTFPPLYYRRAHRRFVTKKALCIRVFQETQKLKKRRRALKAAAAAQKQAKRR
NPDSPAKAIPKTLKDSQ

Ligands and cofactors

ID	Name	Formula	Copies
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	1
SPM	Spermine	C10 H26 N4	1
SRY	Streptomycin	C21 H39 N7 O12	1
MG	Magnesium ion	Mg	58
ZN	Zinc ion	Zn	1
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1
FME	N-formylmethionine	C6 H11 N O3 S	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

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

Primary citation

GTPBP8 plays a role in mitoribosome formation in human mitochondria. Cipullo, M., Valentin Gese, G., Gopalakrishna, S. et al. Nat Commun (2024) 15:5664-5664. DOI 10.1038/s41467-024-50011-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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