9TRV | pdb_00009trv

Structure of the Plant mitochondrial pre-initiation complex 1, (SSU,mtIF3)

PDB DOI: https://doi.org/10.2210/pdb9TRV/pdb
EM Map EMD-56198: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Brassica oleracea var. botrytis, Arabidopsis thaliana
Expression System: Propioniferax innocua
Mutation(s): No

Deposited: 2025-12-28 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: 2.28 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: 1,754.02 kDa
Atom Count: 88,620
Modeled Residue Count: 8,327
Deposited Residue Count: 12,498
Unique protein chains: 38
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor IF3-1, mitochondrial	B [auth 8]	520	Arabidopsis thaliana	Mutation(s): 0 Gene Names: IF3-1, At1g34360, F7P12.8
UniProt
Find proteins for Q6NLP2 (Arabidopsis thaliana) Explore Q6NLP2 Go to UniProtKB: Q6NLP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NLP2
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S2	C [auth A]	212	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3CN01 (Brassica oleracea var. oleracea) Explore A0A0D3CN01 Go to UniProtKB: A0A0D3CN01
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UniProt Group	A0A0D3CN01
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS3m	D [auth B]	554	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A068BCX1 (Brassica oleracea var. botrytis) Explore A0A068BCX1 Go to UniProtKB: A0A068BCX1
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UniProt Group	A0A068BCX1
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S4	E [auth C]	362	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for Q6YSL2 (Brassica napus) Explore Q6YSL2 Go to UniProtKB: Q6YSL2
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6YSL2
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
S5 DRBM domain-containing protein	F [auth D]	501	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3AS28 (Brassica oleracea var. oleracea) Explore A0A0D3AS28 Go to UniProtKB: A0A0D3AS28
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UniProt Group	A0A0D3AS28
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
bS6m	G [auth E]	138	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3CIR5 (Brassica oleracea var. oleracea) Explore A0A0D3CIR5 Go to UniProtKB: A0A0D3CIR5
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UniProt Group	A0A0D3CIR5
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
uS7m,Small ribosomal subunit protein uS7m	H [auth F]	157	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S15a	I [auth G]	129	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A398AJL3 (Brassica campestris) Explore A0A398AJL3 Go to UniProtKB: A0A398AJL3
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UniProt Group	A0A398AJL3
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	J [auth H]	383	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS10 domain-containing protein	K [auth I]	228	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3CHA1 (Brassica oleracea var. oleracea) Explore A0A0D3CHA1 Go to UniProtKB: A0A0D3CHA1
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UniProt Group	A0A0D3CHA1
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S11	L [auth J]	304	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 uS12m	M [auth K]	125	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for P48857 (Brassica napus) Explore P48857 Go to UniProtKB: P48857
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48857
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
uS13m	N [auth L]	154	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3D1F0 (Brassica oleracea var. oleracea) Explore A0A0D3D1F0 Go to UniProtKB: A0A0D3D1F0
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UniProt Group	A0A0D3D1F0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS14m	O [auth M]	155	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A3P6BZM6 (Brassica oleracea) Explore A0A3P6BZM6 Go to UniProtKB: A0A3P6BZM6
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UniProt Group	A0A3P6BZM6
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS15c	P [auth N]	414	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3D1Z7 (Brassica oleracea var. oleracea) Explore A0A0D3D1Z7 Go to UniProtKB: A0A0D3D1Z7
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UniProt Group	A0A0D3D1Z7
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	Q [auth O]	136	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3ALM2 (Brassica oleracea var. oleracea) Explore A0A0D3ALM2 Go to UniProtKB: A0A0D3ALM2
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UniProt Group	A0A0D3ALM2
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS17c	R [auth P]	110	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS18c	S [auth Q]	237	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A078FCZ9 (Brassica napus) Explore A0A078FCZ9 Go to UniProtKB: A0A078FCZ9
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UniProt Group	A0A078FCZ9
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS19m	T [auth R]	212	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for P39697 (Arabidopsis thaliana) Explore P39697 Go to UniProtKB: P39697
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UniProt Group	P39697
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S21	U [auth S]	100	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3AW14 (Brassica oleracea var. oleracea) Explore A0A0D3AW14 Go to UniProtKB: A0A0D3AW14
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UniProt Group	A0A0D3AW14
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S31, mitochondrial	V [auth T]	94	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3C0Z4 (Brassica oleracea var. oleracea) Explore A0A0D3C0Z4 Go to UniProtKB: A0A0D3C0Z4
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UniProt Group	A0A0D3C0Z4
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
mS23	W [auth U]	192	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
mS26	X [auth V]	193	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0ABQ7YPD6 (Brassica napus) Explore A0ABQ7YPD6 Go to UniProtKB: A0ABQ7YPD6
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UniProt Group	A0ABQ7YPD6
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS29	Y [auth W]	483	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3CAV8 (Brassica oleracea var. oleracea) Explore A0A0D3CAV8 Go to UniProtKB: A0A0D3CAV8
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UniProt Group	A0A0D3CAV8
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
BnaC06g06470D protein	Z [auth X]	496	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A078I5F5 (Brassica napus) Explore A0A078I5F5 Go to UniProtKB: A0A078I5F5
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UniProt Group	A0A078I5F5
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
MOSC domain-containing protein	AA [auth Y]	102	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial 28S ribosomal protein S34	BA [auth Z]	153	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein	CA [auth a]	424	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
IMS import disulfide relay-system CHCH-CHCH-like Cx9C domain-containing protein	DA [auth b]	80	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A8MRX3 (Arabidopsis thaliana) Explore A8MRX3 Go to UniProtKB: A8MRX3
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UniProt Group	A8MRX3
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS38	EA [auth c]	128	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
IGR domain-containing protein	FA [auth d]	110	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3DCJ8 (Brassica oleracea var. oleracea) Explore A0A0D3DCJ8 Go to UniProtKB: A0A0D3DCJ8
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
mS45	GA [auth e]	383	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A0D3BFU2 (Brassica oleracea var. oleracea) Explore A0A0D3BFU2 Go to UniProtKB: A0A0D3BFU2
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
mS47	HA [auth f]	410	Brassica oleracea var. botrytis	Mutation(s): 0 EC: 3.1.2.4
UniProt
Find proteins for A0ABQ7BUT9 (Brassica cretica) Explore A0ABQ7BUT9 Go to UniProtKB: A0ABQ7BUT9
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UniProt Group	A0ABQ7BUT9
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS81 (rPPR8)	IA [auth g]	668	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for Q8LPF1 (Arabidopsis thaliana) Explore Q8LPF1 Go to UniProtKB: Q8LPF1
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UniProt Group	Q8LPF1
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
(rape) hypothetical protein	JA [auth h]	384	Brassica oleracea var. botrytis	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
PROP1-like PPR domain-containing protein	KA [auth i]	725	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for A0A654ECT9 (Arabidopsis thaliana) Explore A0A654ECT9 Go to UniProtKB: A0A654ECT9
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UniProt Group	A0A654ECT9
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS86	LA [auth k]	155	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for Q9FZ84 (Arabidopsis thaliana) Explore Q9FZ84 Go to UniProtKB: Q9FZ84
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UniProt Group	Q9FZ84
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein mS80 (rPPR6)	MA [auth l]	576	Brassica oleracea var. botrytis	Mutation(s): 0
UniProt
Find proteins for P0C896 (Arabidopsis thaliana) Explore P0C896 Go to UniProtKB: P0C896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C896
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Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
18S rRNA	A [auth 2]	1,611	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 NA [auth W] MOL2 format, chain NA [auth W] mmCIF format, chain NA [auth W]	NA [auth W]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain NA [auth W] Interactions & Density Focus chain NA [auth W]

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.28 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

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

9TRV | pdb_00009trv

Structure of the Plant mitochondrial pre-initiation complex 1, (SSU,mtIF3)

Literature

Missing steps of mitochondrial translation initiation identified in plants

Biological Assembly 1

Macromolecules

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

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Entity ID: 4

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Entity ID: 7

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Entity ID: 9

UniProt

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Entity ID: 10

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Entity ID: 11

UniProt

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Entity ID: 12

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Entity ID: 13

UniProt

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Entity ID: 14

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Entity ID: 15

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Entity ID: 16

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Entity ID: 17

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Entity ID: 18

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Entity ID: 19

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Entity ID: 20

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Entity ID: 21

UniProt