9TRT | pdb_00009trt

Structure of the Plant mitochondrial pre-initiation complex 3, (SSU,mtIF3,mRNA,tRNA)

PDB DOI: https://doi.org/10.2210/pdb9TRT/pdb
EM Map EMD-56197: EMDB EMDataResource
NAKB: 9TRT

Classification: RIBOSOME
Organism(s): Brassica oleracea var. botrytis
Mutation(s): No

Deposited: 2025-12-27 Released: 2026-11-04
Deposition Author(s): Skaltsogiannis, V., Giege, P., Soufari, H.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Missing steps of mitochondrial translation initiation identified in plants

Skaltsogiannis, V., Soufari, H., Giege, P.

To be published.

Macromolecule Content

Total Structure Weight: 1,777.24 kDa
Atom Count: 91,416
Modeled Residue Count: 8,554
Deposited Residue Count: 12,568
Unique protein chains: 38
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor IF3-1, mitochondrial	D [auth 8]	520	Brassica oleracea var. botrytis	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S2	E [auth A]	212	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS3m	F [auth B]	554	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S4	G [auth C]	362	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
S5 DRBM domain-containing protein	H [auth D]	501	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein bS6m	I [auth E]	138	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS7m	J [auth F]	157	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8, chloroplastic	K [auth G]	129	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	L [auth H]	383	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS10 domain-containing protein	M [auth I]	228	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S11	N [auth J]	304	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS12m	O [auth K]	125	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein uS13m	P [auth L]	154	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS14m	Q [auth M]	155	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS15c	R [auth N]	414	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	S [auth O]	136	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS17c	T [auth P]	110	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS18c	U [auth Q]	237	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS19m	V [auth R]	212	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S21	W [auth S]	100	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S31, mitochondrial	X [auth T]	94	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein mS23	Y [auth U]	192	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein mS26	Z [auth V]	193	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS29	AA [auth W]	483	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
RRM domain-containing protein	BA [auth X]	496	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
MOSC domain-containing protein	CA [auth Y]	102	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal Protein S34, mitochondrial	DA [auth Z]	153	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein	EA [auth a]	424	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain-containing protein	FA [auth b]	80	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS38	GA [auth c]	128	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
IGR domain-containing protein	HA [auth d]	110	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein mS45	IA [auth e]	383	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein mS47	JA [auth f]	410	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS81 (rPPR8)	KA [auth g]	668	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylyl cyclase	LA [auth h]	384	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
PROP1-like PPR domain-containing protein	MA [auth i]	725	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
RRM domain-containing protein	NA [auth k]	153	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS80 (rPPR6)	OA [auth l]	576	Brassica oleracea var. botrytis	Mutation(s): 0
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
18S rRNA	A [auth 2]	1,601	Brassica oleracea var. botrytis
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Molecule	Chains	Length	Organism
Entity ID: 2
initiator tRNA	B [auth 5]	77	Brassica oleracea var. botrytis
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
mRNA	C [auth 6]	5	Brassica oleracea var. botrytis
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain PA [auth W] MOL2 format, chain PA [auth W] mmCIF format, chain PA [auth W]	PA [auth W]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain PA [auth W] Interactions & Density Focus chain PA [auth W]

Non-standard Monomers 1 Unique
ID	Chains	Type	Formula	2D Diagram
UNK Query on UNK	J [auth F]	L-PEPTIDE LINKING	C₄ H₉ N O₂

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Skaltsogiannis, V.

Giege, P.

Soufari, H.

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--
Agence Nationale de la Recherche (ANR)	France	--

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release

9TRT | pdb_00009trt

Structure of the Plant mitochondrial pre-initiation complex 3, (SSU,mtIF3,mRNA,tRNA)

Literature

Missing steps of mitochondrial translation initiation identified in plants

Biological Assembly 1

Macromolecules

Entity ID: 4

Entity Groups

Sequence Annotations

Entity ID: 5

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Entity ID: 12

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Entity ID: 25

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Entity ID: 26

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Entity ID: 27

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Entity ID: 28

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