7AOR | pdb_00007aor

mt-SSU from Trypanosoma cruzi in complex with mt-IF-3.

PDB DOI: https://doi.org/10.2210/pdb7AOR/pdb
EM Map EMD-11846: EMDB EMDataResource
NAKB: 7AOR

Classification: RIBOSOME
Organism(s): Trypanosoma cruzi strain CL Brener, Trypanosoma cruzi
Mutation(s): No

Deposited: 2020-10-15 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: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.1 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: 7,881.46 kDa
Atom Count: 173,743
Modeled Residue Count: 20,276
Deposited Residue Count: 39,249
Unique protein chains: 55
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mS35	A [auth u]	874	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mS33	B [auth s]	180	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mS29	C [auth r]	500	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
uS19	D [auth n]	172	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
uS14m	E [auth h]	166	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
uS10m	F [auth e]	818	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
mS72	G [auth az]	163	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
mS71	H [auth ay]	218	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
mS70	I [auth ax]	172	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
mS69	J [auth aw]	186	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodanese domain-containing protein	K [auth au]	247	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
mS58	L [auth ak]	314	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
mS57	M [auth aj]	396	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
mS55	N [auth ag]	581	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
mS54	O [auth af]	677	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
mS53	P [auth ae]	678	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
mS52	Q [auth l]	714	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
mS50	R [auth ac]	1,152	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
mS49	S [auth ab]	1,175	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
mS51	T [auth ad]	810	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
bS18m	U [auth m]	319	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
uS15m	V [auth i]	429	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
uS11m	W [auth f]	325	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
uS8m	X [auth c]	285	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
uS9m	Y [auth d]	445	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
mS73	Z [auth ba]	217	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
mS68	AA [auth av]	237	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
mS66	BA [auth at]	259	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
AKAP7_NLS domain-containing protein	CA [auth ar]	268	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
mS63	DA [auth aq]	299	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
mS62	EA [auth ap]	277	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
mS61	FA [auth ao]	283	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
mS56	GA [auth ai]	410	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
mS60	HA [auth an]	293	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
mS47	IA [auth z]	1,181	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Sod_Fe_C domain-containing protein	JA [auth y]	449	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase, putative	KA [auth x]	345	Trypanosoma cruzi strain CL Brener	Mutation(s): 0 EC: 1.15.1.1
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein FYV4, mitochondrial	LA [auth w]	186	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
mS37	MA [auth v]	215	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
mS38	NA [auth bb]	238	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Trafficking protein particle complex subunit	OA [auth t]	256	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
mS59	PA [auth al]	308	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
mS26	QA [auth q]	442	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
mS23	RA [auth p]	308	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
mS22	SA [auth Ca]	603	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
bS21m	TA [auth g]	193	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
bS16m	UA [auth j]	189	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
bS6m	VA [auth b]	160	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
MURF5	WA [auth bd]	90	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal_S5_C domain-containing protein	XA [auth a]	434	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
mt-iF3	YA [auth bc]	376	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
mS48	ZA [auth aa]	1,827	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
30S Ribosomal protein S17-like protein	AB [auth k]	309	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for A0A2V2XQ88 (Trypanosoma cruzi) Explore A0A2V2XQ88 Go to UniProtKB: A0A2V2XQ88
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UniProt Group	A0A2V2XQ88
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome protein S12	BB [auth be]	82	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for A0A2H4T2H0 (Trypanosoma cruzi) Explore A0A2H4T2H0 Go to UniProtKB: A0A2H4T2H0
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UniProt Group	A0A2H4T2H0
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
mS65	CB [auth as]	261	Trypanosoma cruzi strain CL Brener	Mutation(s): 0
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Molecule	Chains	Length	Organism
Entity ID: 56
RNA (478-MER)	DB [auth A], EB [auth 2]	8,129	Trypanosoma cruzi strain CL Brener
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain FB [auth r] MOL2 format, chain FB [auth r] mmCIF format, chain FB [auth r]	FB [auth r]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain FB [auth r] Interactions & Density Focus chain FB [auth r]
UTP (Subject of Investigation/LOI) Query on UTP Download:Ideal Coordinates CCD File SDF format, chain HB [auth aj] MOL2 format, chain HB [auth aj] mmCIF format, chain HB [auth aj]	HB [auth aj]	URIDINE 5'-TRIPHOSPHATE C₉ H₁₅ N₂ O₁₅ P₃ PGAVKCOVUIYSFO-XVFCMESISA-N		Interactions Focus chain HB [auth aj] Interactions & Density Focus chain HB [auth aj]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain IB [auth at] SDF format, chain LB [auth aa] SDF format, chain KB [auth y] SDF format, chain JB [auth at] MOL2 format, chain IB [auth at] MOL2 format, chain LB [auth aa] MOL2 format, chain KB [auth y] MOL2 format, chain JB [auth at] mmCIF format, chain IB [auth at] mmCIF format, chain LB [auth aa] mmCIF format, chain KB [auth y] mmCIF format, chain JB [auth at]	IB [auth at], JB [auth at], KB [auth y], LB [auth aa]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain IB [auth at] Focus chain JB [auth at] Focus chain KB [auth y] Focus chain LB [auth aa] Interactions & Density Focus chain IB [auth at] Focus chain JB [auth at] Focus chain KB [auth y] Focus chain LB [auth aa]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain GB [auth r] MOL2 format, chain GB [auth r] mmCIF format, chain GB [auth r]	GB [auth r]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GB [auth r] Interactions & Density Focus chain GB [auth r]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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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 2.0: 2021-06-23
Changes: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Structure summary

7AOR | pdb_00007aor

mt-SSU from Trypanosoma cruzi in complex with mt-IF-3.

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

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Entity ID: 10

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Entity ID: 11

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Entity ID: 12

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Entity ID: 14

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Entity Groups

Sequence Annotations

Entity ID: 20

Entity Groups

Sequence Annotations

Entity ID: 21

Entity Groups

Sequence Annotations

Entity ID: 22

Entity Groups

Sequence Annotations

Entity ID: 23

Entity Groups

Sequence Annotations

Entity ID: 24

Entity Groups

Sequence Annotations

Entity ID: 25

Entity Groups