8PK0: 39S ribosomal protein L32, mitochondrial

Name: PDB 8PK0: human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7
Published: 2023-12-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7. Determined by electron microscopy at 3.03 Å resolution. Released 13 Dec 2023.

Method: Electron microscopy
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 58
Atoms: 108,702
Mol. weight: 1963.04 kDa
Ligands: ZN, SAM, MG, GNP
Released: 13 Dec 2023

Explore 8PK0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PK0 contains 540 α-helices and 421 β-strands across 56 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: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	84-86	3
α-helix	87-94	8
α-helix	101-103	3
β-strand	107-109	3	1
β-strand	116-118	3	1
α-helix	124-145	22
β-strand	156-159	4	2
β-strand	173-176	4	2
α-helix	180-182	3

Chain 1: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	15-22	8	20
β-strand	29-35	7	20
α-helix	39-41	3
β-strand	42-47	6	20
β-strand	52-64	13	20

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	57-64	8
α-helix	66-71	6
α-helix	73-85	13

Chain 3: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	108-113	6
β-strand	115-116	2	59
β-strand	122-124	3	59
α-helix	133-135	3
α-helix	138-144	7
β-strand	148-149	2	59
α-helix	152-161	10
α-helix	164-167	4
β-strand	172	1	60
α-helix	178-180	3

Chain 5: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	40-47	8
α-helix	48-51	4
β-strand	59	1	72
α-helix	60-62	3
β-strand	71	1	72
α-helix	72-73	2
α-helix	75-77	3
α-helix	85-87	3
α-helix	90-92	3
α-helix	93-95	3
β-strand	99-107	9	73
α-helix	117-124	8
β-strand	126-130	5	74
α-helix	134-141	8
α-helix	147	1
α-helix	150-162	13
α-helix	173-189	17
α-helix	190-192	3
α-helix	196-200	5
β-strand	201-205	5	74
β-strand	209-214	6	73
β-strand	219-224	6	73
β-strand	228-232	5	74
α-helix	235-238	4
α-helix	242-246	5
α-helix	247-249	3
β-strand	259	1	75
β-strand	266-270	5	73
β-strand	276	1	73
β-strand	279	1	76
β-strand	287-294	8	74
α-helix	304-305	2
α-helix	306-328	23
β-strand	335-347	13	74
β-strand	351-361	11	74
β-strand	372-381	10	74
β-strand	385-387	3	77
β-strand	391-393	3	78
β-strand	396-399	4	78
β-strand	402-404	3	77
α-helix	408-419	12

Chain 6: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	49	1
β-strand	50	1	66
α-helix	54-65	12
α-helix	74-77	4
α-helix	86-88	3
β-strand	89	1	90
α-helix	92-96	5
α-helix	99-115	17
α-helix	117-125	9
α-helix	132-142	11
α-helix	144-155	12
α-helix	157-160	4
α-helix	161-163	3
β-strand	166	1	90
β-strand	174-179	6	91
β-strand	183-187	5	91
β-strand	191-192	2	92
α-helix	201-202	2
β-strand	203-205	3	91
β-strand	213-220	8	92
β-strand	231-241	11	92
β-strand	249-252	4	92
α-helix	259-260	2
β-strand	261	1	67
β-strand	266-275	10	92
α-helix	293-296	4
β-strand	297-298	2	92
α-helix	303-307	5
β-strand	311-321	11	92
α-helix	325-329	5
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	67
α-helix	346-350	5
α-helix	352-355	4
β-strand	362	1	59
α-helix	365-369	5

Chain 7: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	37-58	22
β-strand	64-69	6	104
β-strand	78-82	5	104
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-108	4	104
β-strand	111-113	3	104
α-helix	117-119	3
β-strand	124-128	5	104
α-helix	136-157	22
β-strand	158	1	105
β-strand	164-168	5	106
α-helix	174-176	3
β-strand	179-185	7	106
α-helix	187-189	3
α-helix	196-212	17
α-helix	214	1
β-strand	215	1	107
β-strand	216-222	7	108
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-257	7	108
β-strand	260-263	4	108
β-strand	271	1	107
α-helix	272-274	3
β-strand	275-285	11	106
β-strand	295-303	9	106
α-helix	304-306	3
α-helix	310-320	11

Chain 8: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	104-107	4
α-helix	108-153	46
α-helix	155-162	8
β-strand	172-174	3	36
α-helix	175-176	2
β-strand	177	1	116
β-strand	189-195	7	37

48 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
39S ribosomal protein L32, mitochondrial	0	protein	188	Homo sapiens	Q9BYC8 (AlphaFold model)
39S ribosomal protein L22, mitochondrial	T	protein	206	Homo sapiens	Q9NWU5 (AlphaFold model)
Mitochondrial assembly of ribosomal large subunit protein 1	u	protein	234	Homo sapiens	Q96EH3 (AlphaFold model)
39S ribosomal protein L33, mitochondrial	1	protein	65	Homo sapiens	O75394 (AlphaFold model)
39S ribosomal protein L23, mitochondrial	U	protein	153	Homo sapiens	Q16540
MIEF1 upstream open reading frame protein	v	protein	70	Homo sapiens	L0R8F8
39S ribosomal protein L34, mitochondrial	2	protein	92	Homo sapiens	Q9BQ48
39S ribosomal protein L24, mitochondrial	V	protein	216	Homo sapiens	Q96A35
Acyl carrier protein, mitochondrial	w	protein	156	Homo sapiens	O14561
39S ribosomal protein L35, mitochondrial	3	protein	188	Homo sapiens	Q9NZE8
39S ribosomal protein L27, mitochondrial	W	protein	148	Homo sapiens	Q9P0M9
5-methylcytosine rRNA methyltransferase NSUN4	x	protein	384	Homo sapiens	Q96CB9

46 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8PK0_1 39S ribosomal protein L32, mitochondrial (chains 0)
MALAMLVLVVSPWSAARGVLRNYWERLLRKLPQSRPGFPSPPWGPALAVQGPAMFTEPAN
DTSGSKENSSLLDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKVKNNIDVCPECGHLKQKH
VLCAYCYEKVCKETAEIRRQIGKQEGGPFKAPTIETVVLYTGETPSEQDQGKRIIERDRK
RPSWFTQN

Sequence of entity 2 (T), FASTA

>8PK0_2 39S ribosomal protein L22, mitochondrial (chains T)
MAAAVLGQLGALWIHNLRSRGKLALGVLPQSYIHTSASLDISRKWEKKNKIVYPPQLPGE
PRRPAEIYHCRRQIKYSKDKMWYLAKLIRGMSIDQALAQLEFNDKKGAKIIKEVLLEAQD
MAVRDHNVEFRSNLYIAESTSGRGQCLKRIRYHGRGRFGIMEKVYCHYFVKLVEGPPPPP
EPPKTAVAHAKEYIQQLRSRTIVHTL

Sequence of entity 3 (u), FASTA

>8PK0_3 Mitochondrial assembly of ribosomal large subunit protein 1 (chains u)
MGPGGRVARLLAPLMWRRAVSSVAGSAVGAEPGLRLLAVQRLPVGAAFCRACQTPNFVRG
LHSEPGLEERAEGTVNEGRPESDAADHTGPKFDIDMMVSLLRQENARDICVIQVPPEMRY
TDYFVIVSGTSTRHLHAMAFYVVKMYKHLKCKRDPHVKIEGKDTDDWLCVDFGSMVIHLM
LPETREIYELEKLWTLRSYDDQLAQIAPETVPEDFILGIEDDTSSVTPVELKCE

Sequence of entity 4 (1), FASTA

>8PK0_4 39S ribosomal protein L33, mitochondrial (chains 1)
MFLSAVFFAKSKSKNILVRMVSEAGTGFCFNTKRNRLREKLTLLHYDPVVKQRVLFVEKK
KIRSL

Sequence of entity 5 (U), FASTA

>8PK0_5 39S ribosomal protein L23, mitochondrial (chains U)
MARNVVYPLYRLGGPQLRVFRTNFFIQLVRPGVAQPEDTVQFRIPMEMTRVDLRNYLEGI
YNVPVAAVRTRVQHGSNKRRDHRNVRIKKPDYKVAYVQLAHGQTFTFPDLFPEKDESPEG
SAADDLYSMLEEERQQRQSSDPRRGGVPSWFGL

Sequence of entity 6 (v), FASTA

>8PK0_6 MIEF1 upstream open reading frame protein (chains v)
MAPWSREAVLSLYRALLRQGRQLRYTDRDFYFASIRREFRKNQKLEDAEARERQLEKGLV
FLNGKLGRII

Sequence of entity 7 (2), FASTA

>8PK0_7 39S ribosomal protein L34, mitochondrial (chains 2)
MAVLAGSLLGPTSRSAALLGGRWLQPRAWLGFPDAWGLPTPQQARGKARGNEYQPSNIKR
KNKHGWVRRLSTPAGVQVILRRMLKGRKSLSH

Sequence of entity 8 (V), FASTA

>8PK0_8 39S ribosomal protein L24, mitochondrial (chains V)
MRLSALLALASKVTLPPHYRYGMSPPGSVADKRKNPPWIRRRPVVVEPISDEDWYLFCGD
TVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYRYIGKTMDYRGTMIPSEAPLLHRQV
KLVDPMDRKPTEIEWRFTEAGERVRVSTRSGRIIPKPEFPRADGIVPETWIDGPKDTSVE
DALERTYVPCLKTLQEEVMEAMGIKETRKYKKVYWY

Sequence of entity 9 (w), FASTA

>8PK0_9 Acyl carrier protein, mitochondrial (chains w)
MASRVLSAYVSRLPAAFAPLPRVRMLAVARPLSTALCSAGTQTRLGTLQPALVLAQVPGR
VTQLCRQYSDMPPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIM
AMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE

Sequence of entity 10 (3), FASTA

>8PK0_10 39S ribosomal protein L35, mitochondrial (chains 3)
MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRL
TTSERNLTCGHTSVILNRMAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIDRFLRLHCG
LWVRRKAGYKKKLWKKTPARKKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKY
HDRTNLKV

Sequence of entity 11 (W), FASTA

>8PK0_11 39S ribosomal protein L27, mitochondrial (chains W)
MASVVLALRTRTAVTSLLSPTPATALAVRYASKKSGGSSKNLGGKSSGRRQGIKKMEGHY
VHAGNIIATQRHFRWHPGAHVGVGKNKCLYALEEGIVRYTKEVYVPHPRNTEAVDLITRL
PKGAVLYKTFVHVVPAKPEGTFKLVAML

Sequence of entity 12 (x), FASTA

>8PK0_12 5-methylcytosine rRNA methyltransferase NSUN4 (chains x)
MAALTLRGVRELLKRVDLATVPRRHRYKKKWAATEPKFPAVRLALQNFDMTYSVQFGDLW
PSIRVSLLSEQKYGALVNNFAAWDHVSAKLEQLSAKDFVNEAISHWELQSEGGQSAAPSP
ASWACSPNLRCFTFDRGDISRFPPARPGSLGVMEYYLMDAASLLPVLALGLQPGDIVLDL
CAAPGGKTLALLQTGCCRNLAANDLSPSRIARLQKILHSYVPEEIRDGNQVRVTSWDGRK
WGELEGDTYDRVLVDVPCTTDRHSLHEEENNIFKRSRKKERQILPVLQVQLLAAGLLATK
PGGHVVYSTCSLSHLQNEYVVQGAIELLANQYSIQVQVEDLTHFRRVFMDTFCFFSSCQV
GELVIPNLMANFGPMYFCKMRRLT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
MG	Magnesium ion	Mg	96
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2
PM8	S-(2-{[N-(2-hydroxy-4-{[hydroxy(oxido)phosphino]oxy}-3,3-dimethylbutanoyl)-beta…	C21 H41 N2 O7 P S	1

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

Primary citation

Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome. Nguyen, T.G., Ritter, C., Kummer, E. Nat Commun (2023) 14:7991-7991. DOI 10.1038/s41467-023-43599-z · PubMed

Other PDB entries of the same protein (UniProt Q9BYC8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OF0 2.2 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
7QI4 2.21 Å, Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)
8RRI 2.4 Å, Human mitochondrial ribosome in complex with antibiotic tigecycline
8QU5 2.42 Å, mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2
9OLF 2.46 Å, Membrane-associated human mitoribosome in complex with TACO1
7OF7 2.5 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
7PO4 2.56 Å, Assembly intermediate of human mitochondrial ribosome large subunit (largely unfolded…
6ZM6 2.59 Å, Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA
7O9M 2.6 Å, Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4,…
7OF6 2.6 Å, Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6…
9CN3 2.62 Å, Human 39S mitoribosome in complex with antibiotic Linezolid
7QI5 2.63 Å, Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A…

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