7ODS: PDB entry 7ODS

Name: PDB 7ODS: State B of the human mitoribosomal large subunit assembly intermediate
Published: 2021-06-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

State B of the human mitoribosomal large subunit assembly intermediate. Determined by electron microscopy at 3.1 Å resolution. Released 23 Jun 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 58
Atoms: 108,339
Mol. weight: 1917.68 kDa
Ligands: PM8, SAM, ZN, MG
Released: 23 Jun 2021

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

Secondary structure: helices and β-sheets

7ODS contains 517 α-helices and 412 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	101-104	4
β-strand	107-109	3	36
β-strand	116-118	3	36
α-helix	124-145	22
β-strand	156-159	4	37
β-strand	173-176	4	37
α-helix	180-182	3

Chain 1: 1 helix, 4 β-strands

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

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	108-111	4
β-strand	115-116	2	46
β-strand	122-124	3	46
α-helix	133-135	3
α-helix	138-144	7
β-strand	148-149	2	46
α-helix	152-160	9
α-helix	164-167	4
β-strand	172	1	4
α-helix	178-180	3

Chain 4: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	68-69	2	53
β-strand	80-84	5	53
β-strand	87-91	5	53
α-helix	96-98	3
β-strand	100-102	3	53

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	56
β-strand	71	1	56
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	57
α-helix	117-124	8
β-strand	126-130	5	58
α-helix	134-138	5
α-helix	147	1
α-helix	150-159	10
α-helix	160-164	5
α-helix	173-188	16
α-helix	189-192	4
α-helix	196-200	5
β-strand	201-205	5	58
β-strand	209-214	6	57
β-strand	219-224	6	57
β-strand	228-232	5	58
α-helix	235-238	4
α-helix	242-246	5
α-helix	247-250	4
β-strand	259	1	59
β-strand	266-270	5	57
β-strand	276	1	57
β-strand	279	1	60
β-strand	287-294	8	58
α-helix	304-305	2
α-helix	306-329	24
β-strand	335-347	13	58
β-strand	351-361	11	58
β-strand	372-381	10	58
β-strand	385-387	3	61
β-strand	391-393	3	62
β-strand	396-399	4	62
β-strand	402-404	3	61
α-helix	408-419	12

Chain 6: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	68
α-helix	54-65	12
α-helix	74-78	5
α-helix	80-81	2
α-helix	86-88	3
β-strand	89	1	69
α-helix	92-96	5
α-helix	99-115	17
α-helix	117-124	8
α-helix	132-142	11
α-helix	144-154	11
α-helix	157-161	5
β-strand	166	1	69
β-strand	174-179	6	70
β-strand	183-187	5	70
β-strand	191-192	2	71
β-strand	203-205	3	70
β-strand	213-220	8	71
β-strand	231-241	11	71
β-strand	249-252	4	71
α-helix	259-260	2
β-strand	261	1	19
β-strand	266-275	10	71
α-helix	293-296	4
β-strand	297-298	2	71
α-helix	300-305	6
β-strand	311-321	11	71
α-helix	325-329	5
α-helix	330-334	5
α-helix	338-339	2
β-strand	340-345	6	19
α-helix	346-350	5
α-helix	352-354	3
β-strand	362	1	46
α-helix	363-369	7

Chain 7: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	37-58	22
β-strand	64-69	6	73
β-strand	78-82	5	73
α-helix	88-95	8
α-helix	97-102	6
β-strand	105-108	4	73
β-strand	111-113	3	73
α-helix	118-119	2
β-strand	123-128	6	73
α-helix	136-157	22
β-strand	158	1	74
β-strand	165-168	4	75
α-helix	174-176	3
β-strand	179-184	6	75
α-helix	188-190	3
α-helix	196-212	17
β-strand	215	1	76
β-strand	216-222	7	77
α-helix	223-229	7
α-helix	234-246	13
β-strand	251-257	7	77
β-strand	260-263	4	77
β-strand	271	1	76
α-helix	272-274	3
β-strand	275-285	11	75
β-strand	295-303	9	75
α-helix	310-321	12

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
Mitochondrial assembly of ribosomal large subunit protein 1	u	protein	234	Homo sapiens	Q96EH3 (AlphaFold model)
MIEF1 upstream open reading frame protein	v	protein	70	Homo sapiens	L0R8F8 (AlphaFold model)
Acyl carrier protein, mitochondrial	w	protein	156	Homo sapiens	O14561 (AlphaFold model)
5-methylcytosine rRNA methyltransferase NSUN4	x	protein	384	Homo sapiens	Q96CB9 (AlphaFold model)
Transcription termination factor 4, mitochondrial	y	protein	381	Homo sapiens	Q7Z6M4
rRNA methyltransferase 2, mitochondrial	z	protein	246	Homo sapiens	Q9UI43
39S ribosomal protein L32, mitochondrial	0	protein	188	Homo sapiens	Q9BYC8
39S ribosomal protein L33, mitochondrial	1	protein	65	Homo sapiens	O75394
39S ribosomal protein L34, mitochondrial	2	protein	92	Homo sapiens	Q9BQ48
39S ribosomal protein L35, mitochondrial	3	protein	188	Homo sapiens	Q9NZE8
39S ribosomal protein L36, mitochondrial	4	protein	103	Homo sapiens	Q9P0J6
39S ribosomal protein L37, mitochondrial	5	protein	423	Homo sapiens	Q9BZE1

46 more molecules are not listed.

Sequence of entity 1 (u), FASTA

>7ODS_1 Mitochondrial assembly of ribosomal large subunit protein 1 (chains u)
MGPGGRVARLLAPLMWRRAVSSVAGSAVGAEPGLRLLAVQRLPVGAAFCRACQTPNFVRG
LHSEPGLEERAEGTVNEGRPESDAADHTGPKFDIDMMVSLLRQENARDICVIQVPPEMRY
TDYFVIVSGTSTRHLHAMAFYVVKMYKHLKCKRDPHVKIEGKDTDDWLCVDFGSMVIHLM
LPETREIYELEKLWTLRSYDDQLAQIAPETVPEDFILGIEDDTSSVTPVELKCE

Sequence of entity 2 (v), FASTA

>7ODS_2 MIEF1 upstream open reading frame protein (chains v)
MAPWSREAVLSLYRALLRQGRQLRYTDRDFYFASIRREFRKNQKLEDAEARERQLEKGLV
FLNGKLGRII

Sequence of entity 3 (w), FASTA

>7ODS_3 Acyl carrier protein, mitochondrial (chains w)
MASRVLSAYVSRLPAAFAPLPRVRMLAVARPLSTALCSAGTQTRLGTLQPALVLAQVPGR
VTQLCRQYSDMPPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIM
AMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE

Sequence of entity 4 (x), FASTA

>7ODS_4 5-methylcytosine rRNA methyltransferase NSUN4 (chains x)
MAALTLRGVRELLKRVDLATVPRRHRYKKKWAATEPKFPAVRLALQNFDMTYSVQFGDLW
PSIRVSLLSEQKYGALVNNFAAWDHVSAKLEQLSAKDFVNEAISHWELQSEGGQSAAPSP
ASWACSPNLRCFTFDRGDISRFPPARPGSLGVMEYYLMDAASLLPVLALGLQPGDIVLDL
CAAPGGKTLALLQTGCCRNLAANDLSPSRIARLQKILHSYVPEEIRDGNQVRVTSWDGRK
WGELEGDTYDRVLVDVPCTTDRHSLHEEENNIFKRSRKKERQILPVLQVQLLAAGLLATK
PGGHVVYSTCSLSHLQNEYVVQGAIELLANQYSIQVQVEDLTHFRRVFMDTFCFFSSCQV
GELVIPNLMANFGPMYFCKMRRLT

Sequence of entity 5 (y), FASTA

>7ODS_5 Transcription termination factor 4, mitochondrial (chains y)
MAAFGRQVLDWHRLIPLTWACMARQTPHLGEQRRTTASLLRKLTTASNGGVIEELSCVRS
NNYVQEPECRRNLVQCLLEKQGTPVVQGSLELERVMSSLLDMGFSNAHINELLSVRRGAS
LQQLLDIISEFILLGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRVL
YCCPEIFTMRQQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDLGQLEYKFQYAYFR
MGIKHPDIVKSEYLQYSLTKIKQRHIYLERLGRYQTPDKKGQTQIPNPLLKDILRVSEAE
FLARTACTSVEEFQVFKKLLAREEEESESSTSDDKRASLDEDEDDDDEEDNDEDDNDEDD
DDEDDDEAEDNDEDEDDDEEE

Sequence of entity 6 (z), FASTA

>7ODS_6 rRNA methyltransferase 2, mitochondrial (chains z)
MAGYLKLVCVSFQRQGFHTVGSRCKNRTGAEHLWLTRHLRDPFVKAAKVESYRCRSAFKL
LEVNERHQILRPGLRVLDCGAAPGAWSQVAVQKVNAAGTDPSSPVGFVLGVDLLHIFPLE
GATFLCPADVTDPRTSQRILEVLPGRRADVILSDMAPNATGFRDLDHDRLISLCLTLLSV
TPDILQPGGTFLCKTWAGSQSRRLQRRLTEEFQNVRIIKPEASRKESSEVYFLATQYHGR
KGTVKQ

Sequence of entity 7 (0), FASTA

>7ODS_7 39S ribosomal protein L32, mitochondrial (chains 0)
MALAMLVLVVSPWSAARGVLRNYWERLLRKLPQSRPGFPSPPWGPALAVQGPAMFTEPAN
DTSGSKENSSLLDSIFWMAAPKNRRTIEVNRCRRRNPQKLIKVKNNIDVCPECGHLKQKH
VLCAYCYEKVCKETAEIRRQIGKQEGGPFKAPTIETVVLYTGETPSEQDQGKRIIERDRK
RPSWFTQN

Sequence of entity 8 (1), FASTA

>7ODS_8 39S ribosomal protein L33, mitochondrial (chains 1)
MFLSAVFFAKSKSKNILVRMVSEAGTGFCFNTKRNRLREKLTLLHYDPVVKQRVLFVEKK
KIRSL

Sequence of entity 9 (2), FASTA

>7ODS_9 39S ribosomal protein L34, mitochondrial (chains 2)
MAVLAGSLLGPTSRSAALLGGRWLQPRAWLGFPDAWGLPTPQQARGKARGNEYQPSNIKR
KNKHGWVRRLSTPAGVQVILRRMLKGRKSLSH

Sequence of entity 10 (3), FASTA

>7ODS_10 39S ribosomal protein L35, mitochondrial (chains 3)
MAASAFAGAVRAASGILRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRL
TTSERNLTCGHTSVILNRMAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIDRFLRLHCG
LWVRRKAGYKKKLWKKTPARKKRLREFVFCNKTQSKLLDKMTTSFWKRRNWYVDDPYQKY
HDRTNLKV

Sequence of entity 11 (4), FASTA

>7ODS_11 39S ribosomal protein L36, mitochondrial (chains 4)
MANLFIRKMVNPLLYLSRHTVKPRALSTFLFGSIRGAAPVAVEPGAAVRSLLSPGLLPHL
LPALGFKNKTVLKKRCKDCYLVKRRGRWYVYCKTHPRHKQRQM

Sequence of entity 12 (5), FASTA

>7ODS_12 39S ribosomal protein L37, mitochondrial (chains 5)
MALASGPARRALAGSGQLGLGGFGAPRRGAYEWGVRSTRKSEPPPLDRVYEIPGLEPITF
AGKMHFVPWLARPIFPPWDRGYKDPRFYRSPPLHEHPLYKDQACYIFHHRCRLLEGVKQA
LWLTKTKLIEGLPEKVLSLVDDPRNHIENQDECVLNVISHARLWQTTEEIPKRETYCPVI
VDNLIQLCKSQILKHPSLARRICVQNSTFSATWNRESLLLQVRGSGGARLSTKDPLPTIA
SREEIEATKNHVLETFYPISPIIDLHECNIYDVKNDTGFQEGYPYPYPHTLYLLDKANLR
PHRLQPDQLRAKMILFAFGSALAQARLLYGNDAKVLEQPVVVQSVGTDGRVFHFLVFQLN
TTDLDCNEGVKNLAWVDSDQLLYQHFWCLPVIKKRVVVEPVGPVGFKPETFRKFLALYLH
GAA

Ligands and cofactors

ID	Name	Formula	Copies
PM8	S-(2-{[N-(2-hydroxy-4-{[hydroxy(oxido)phosphino]oxy}-3,3-dimethylbutanoyl)-beta…	C21 H41 N2 O7 P S	1
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	88
N	Any 5'-monophosphate nucleotide	C5 H11 O7 P	1
FES	FE2/S2 (inorganic) cluster	Fe2 S2	1

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

Primary citation

Stepwise maturation of the peptidyl transferase region of human mitoribosomes. Lenarcic, T., Jaskolowski, M., Leibundgut, M. et al. Nat Commun (2021) 12:3671-3671. DOI 10.1038/s41467-021-23811-8 · PubMed

Other PDB entries of the same protein (UniProt Q96EH3 (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…
8QU5 2.42 Å, mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2
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…
7O9M 2.6 Å, Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4,…
7OF2 2.7 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
7OF3 2.7 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
9PRA 2.83 Å, In Situ Structure of the Human Mitoribosome Large Subunit 39S in Complex with EF-Tu
7QH7 2.89 Å, Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 4
7ODR 2.9 Å, State A of the human mitoribosomal large subunit assembly intermediate
7OF5 2.9 Å, Structure of a human mitochondrial ribosome large subunit assembly intermediate in…
8QSJ 3.0 Å, Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7

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