7AIH | pdb_00007aih

The Large subunit of the Kinetoplastid mitochondrial ribosome

PDB DOI: https://doi.org/10.2210/pdb7AIH/pdb
EM Map EMD-11796: EMDB EMDataResource
NAKB: 7AIH

Classification: RIBOSOME
Organism(s): Leishmania major
Mutation(s): No

Deposited: 2020-09-27 Released: 2021-04-28
Deposition Author(s): Soufari, H., Waltz, F., Parrot, C., Bochler, A., Hashem, Y.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis.

Soufari, H., Waltz, F., Parrot, C., Durrieu-Gaillard, S., Bochler, A., Kuhn, L., Sissler, M., Hashem, Y.

(2020) Proc Natl Acad Sci U S A 117: 29851-29861

PubMed: 33168716 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2011301117
Primary Citation Related Structures:
7AIH, 7AM2, 7ANE, 7AOR

PubMed Abstract:
Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in Trypanosoma brucei already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans Leishmania tarentolae and Trypanosoma cruzi mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.

Organizational Affiliation

Institut Européen de Chimie et Biologie, U1212 INSERM, UMR5320 CNRS, Université de Bordeaux, F-33600 Pessac, France.

Macromolecule Content

Total Structure Weight: 5,045 kDa
Atom Count: 143,667
Modeled Residue Count: 16,092
Deposited Residue Count: 27,994
Unique protein chains: 70
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L3-like protein	A	467	Leishmania major	Mutation(s): 0
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
uL4m	B	436	Leishmania major	Mutation(s): 0
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL_L9 domain-containing protein	C	262	Leishmania major	Mutation(s): 0
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
uL10m	D	204	Leishmania major	Mutation(s): 0
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ribosomal protein L11	E	346	Leishmania major	Mutation(s): 0
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13-like protein	F	171	Leishmania major	Mutation(s): 0
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal_L18e/L15P domain-containing protein	G	374	Leishmania major	Mutation(s): 0
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal_L16 domain-containing protein	H	168	Leishmania major	Mutation(s): 0
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 50S ribosomal protein L17	I	305	Leishmania major	Mutation(s): 0
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
bL19m	J	144	Leishmania major	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
bL20	K	194	Leishmania major	Mutation(s): 0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
bL21m	L	186	Leishmania major	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
uL22m	M	279	Leishmania major	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
uL23m	N	252	Leishmania major	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
uL24m	O	476	Leishmania major	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
bL27m	P	185	Leishmania major	Mutation(s): 0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
bL28m	Q	234	Leishmania major	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
uL29m	R	480	Leishmania major	Mutation(s): 0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
uL30m	S	409	Leishmania major	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
bL32m	T	83	Leishmania major	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
bL33m	U	118	Leishmania major	Mutation(s): 0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
bL35m	V	151	Leishmania major	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
bL36m	W	186	Leishmania major	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
mL38	X	513	Leishmania major	Mutation(s): 0
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
mL40	Y	292	Leishmania major	Mutation(s): 0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
mL41	Z	197	Leishmania major	Mutation(s): 0
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
mL94	AA [auth BA]	167	Leishmania major	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
UA	BA [auth UA]	203	Leishmania major	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
mL95	CA [auth BB]	156	Leishmania major	Mutation(s): 0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
mL89	DA [auth Aw]	187	Leishmania major	Mutation(s): 0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
bL31m	EA [auth Bj]	185	Leishmania major	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
mL76	FA [auth An]	331	Leishmania major	Mutation(s): 0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
mL74	GA [auth Al]	346	Leishmania major	Mutation(s): 0
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	HA [auth BI]	266	Leishmania major	Mutation(s): 0 EC: 5.2.1.8
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
mL93	IA [auth Az]	152	Leishmania major	Mutation(s): 0
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
mL86	JA [auth At]	183	Leishmania major	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
mL96	KA [auth BC]	147	Leishmania major	Mutation(s): 0
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
L51_S25_CI-B8 domain-containing protein	LA [auth Ab]	262	Leishmania major	Mutation(s): 0
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
mL69	MA [auth Ai]	479	Leishmania major	Mutation(s): 0
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
mL80	NA [auth Ap]	240	Leishmania major	Mutation(s): 0
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
mL87	OA [auth Au]	186	Leishmania major	Mutation(s): 0
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
mL42	PA [auth Aa]	195	Leishmania major	Mutation(s): 0
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
mL79	QA [auth Ao]	284	Leishmania major	Mutation(s): 0
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
mL70	RA [auth BM]	457	Leishmania major	Mutation(s): 0
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
mL84	SA [auth Ar]	205	Leishmania major	Mutation(s): 0
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
mL72	TA [auth Aj]	503	Leishmania major	Mutation(s): 0
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	UA [auth BH]	229	Leishmania major	Mutation(s): 0 EC: 5.2.1.8
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
mL75	VA [auth Am]	340	Leishmania major	Mutation(s): 0
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
mL82	WA [auth Aq]	341	Leishmania major	Mutation(s): 0
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
mL98	XA [auth BE]	118	Leishmania major	Mutation(s): 0
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
mL73	YA [auth Ak]	323	Leishmania major	Mutation(s): 0
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
mL52,mL52	ZA [auth BP]	254	Leishmania major	Mutation(s): 0
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
mL49	AB [auth Ad]	237	Leishmania major	Mutation(s): 0
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
mL99	BB [auth BF]	109	Leishmania major	Mutation(s): 0
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
mL88	CB [auth Av]	192	Leishmania major	Mutation(s): 0
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
mL63	DB [auth Af]	155	Leishmania major	Mutation(s): 0
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
mL85	EB [auth As]	249	Leishmania major	Mutation(s): 0
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
mL53	FB [auth Ae]	311	Leishmania major	Mutation(s): 0
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
MRP-L46 domain-containing protein	GB [auth Ac]	291	Leishmania major	Mutation(s): 0
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
mL68	HB [auth Ah]	570	Leishmania major	Mutation(s): 0
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Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
mL97	IB [auth BD]	102	Leishmania major	Mutation(s): 0
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
C2H2-type domain-containing protein	JB [auth Ay]	174	Leishmania major	Mutation(s): 0
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
mL54/69	KB [auth Ag]	244	Leishmania major	Mutation(s): 0
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Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM zinc-binding domain-containing protein	LB [auth Ax]	216	Leishmania major	Mutation(s): 0
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Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ribosomal protein L2	MB [auth BL]	380	Leishmania major	Mutation(s): 0
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Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ribosomal protein L14	NB [auth BO]	190	Leishmania major	Mutation(s): 0
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Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
mL100	OB [auth BG]	1,347	Leishmania major	Mutation(s): 0
UniProt
Find proteins for A0A504WW14 (Leishmania donovani) Explore A0A504WW14 Go to UniProtKB: A0A504WW14
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UniProt Group	A0A504WW14
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Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
UB	PB [auth UB]	67	Leishmania major	Mutation(s): 0
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Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
UC	QB [auth UC]	144	Leishmania major	Mutation(s): 0
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Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
UD	RB [auth UD]	95	Leishmania major	Mutation(s): 0
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Molecule	Chains	Length	Organism
Entity ID: 71
Ribosomal RNA	SB [auth 1]	9,070	Leishmania major
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Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain WB [auth Ag] MOL2 format, chain WB [auth Ag] mmCIF format, chain WB [auth Ag]	WB [auth Ag]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain WB [auth Ag] Interactions & Density Focus chain WB [auth Ag]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain TB [auth T] SDF format, chain UB [auth W] SDF format, chain VB [auth BD] SDF format, chain XB [auth Ax] SDF format, chain YB [auth Ax] SDF format, chain ZB [auth BG] MOL2 format, chain TB [auth T] MOL2 format, chain UB [auth W] MOL2 format, chain VB [auth BD] MOL2 format, chain XB [auth Ax] MOL2 format, chain YB [auth Ax] MOL2 format, chain ZB [auth BG] mmCIF format, chain TB [auth T] mmCIF format, chain UB [auth W] mmCIF format, chain VB [auth BD] mmCIF format, chain XB [auth Ax] mmCIF format, chain YB [auth Ax] mmCIF format, chain ZB [auth BG]	TB [auth T] UB [auth W] VB [auth BD] XB [auth Ax] YB [auth Ax] TB [auth T], UB [auth W], VB [auth BD], XB [auth Ax], YB [auth Ax], ZB [auth BG]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain TB [auth T] Focus chain UB [auth W] Focus chain VB [auth BD] Focus chain XB [auth Ax] Focus chain YB [auth Ax] Focus chain ZB [auth BG] Interactions & Density Focus chain TB [auth T] Focus chain UB [auth W] Focus chain VB [auth BD] Focus chain XB [auth Ax] Focus chain YB [auth Ax] Focus chain ZB [auth BG]

Non-standard Monomers 1 Unique
ID	Chains	Type	Formula	2D Diagram
UNK Query on UNK	BA [auth UA], PB [auth UB], QB [auth UC], RB [auth UD]	L-PEPTIDE LINKING	C₄ H₉ N O₂

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-28

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	France	--

Revision History (Full details and data files)

Version 1.0: 2021-04-28
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary
Version 1.2: 2025-12-17
Changes: Data collection

7AIH | pdb_00007aih

The Large subunit of the Kinetoplastid mitochondrial ribosome

Literature

Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis.

Biological Assembly 1

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