9j9b

Substrate-engaged TIM23 complex from yeast

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mitochondrial import inner membrane translocase subunit TIM17

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 7	Mitochondrial import inner membrane translocase subunit TIM23 × 1 （P32897） Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP × 1 （P00175,Q01852） Protein MGR2 × 1 （Q02889） anti-Tim44-Fab H chain × 1 anti-Tim44-Fab L chain × 1 Substrate × 1 CARDIOLIPIN × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TIM17_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158

Mitochondrial import inner membrane translocase subunit TIM23

Saccharomyces cerevisiae S288C

UniProt P32897

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 7	Mitochondrial import inner membrane translocase subunit TIM17 × 1 （P39515） Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP × 1 （P00175,Q01852） Protein MGR2 × 1 （Q02889） anti-Tim44-Fab H chain × 1 anti-Tim44-Fab L chain × 1 Substrate × 1 CARDIOLIPIN × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TIM23_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–222； UniProt 1–222

Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP

synthetic construct

UniProt P00175

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 7	Mitochondrial import inner membrane translocase subunit TIM17 × 1 （P39515） Mitochondrial import inner membrane translocase subunit TIM23 × 1 （P32897） Protein MGR2 × 1 （Q02889） anti-Tim44-Fab H chain × 1 anti-Tim44-Fab L chain × 1 Substrate × 1 CARDIOLIPIN × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYB2_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 432–476； UniProt 121–165

Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP

synthetic construct

UniProt Q01852

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 7	Mitochondrial import inner membrane translocase subunit TIM17 × 1 （P39515） Mitochondrial import inner membrane translocase subunit TIM23 × 1 （P32897） Protein MGR2 × 1 （Q02889） anti-Tim44-Fab H chain × 1 anti-Tim44-Fab L chain × 1 Substrate × 1 CARDIOLIPIN × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TIM44_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–431； UniProt 1–431

Protein MGR2

Saccharomyces cerevisiae S288C

UniProt Q02889

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 7	Mitochondrial import inner membrane translocase subunit TIM17 × 1 （P39515） Mitochondrial import inner membrane translocase subunit TIM23 × 1 （P32897） Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP × 1 （P00175,Q01852） anti-Tim44-Fab H chain × 1 anti-Tim44-Fab L chain × 1 Substrate × 1 CARDIOLIPIN × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MGR2_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–113； UniProt 1–113

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9j9b
Deposition date deposition_date	2024-08-22
Structure title title	Substrate-engaged TIM23 complex from yeast
Keywords keywords	Mitochondrial protein import, TOM / TIM23 protein translocation, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9j9b__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9j9b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9j9b__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	33.73 Å
Rg (electron density)	33.25 Å
Total Rg	33.90 Å
Atom count	6047
Residues	790
Excluded volume	107790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9j9b__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Mitochondrial import inner membrane translocase subunit TIM17
Molecular weight formula_weight	16602.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6047

MSADHSRDPCPIVILNDFGGAFAMGAIGGVVWHGIKGFRNSPLGERGSGAMSAIKARAPVLGGNFGVWGGLFSTFDCAVKAVRKREDPWNAIIAGFFTGGALAVRGGWRHTRNSSITCACLLGVIEGVGLMFQRYAAWQAKPMAPPLPEAPSSQPLQA

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	Mitochondrial import inner membrane translocase subunit TIM23
Molecular weight formula_weight	23266.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSWLFGDKTPTDDANAAVGGQDTTKPKELSLKQSLGFEPNINNIISGPGGMHVDTARLHPLAGLDKGVEYLDLEEEQLSSLEGSQGLIPSRGWTDDLCYGTGAVYLLGLGIGGFSGMMQGLQNIPPNSPGKLQLNTVLNHITKRGPFLGNNAGILALSYNIINSTIDALRGKHDTAGSIGAGALTGALFKSSKGLKPMGYSSAMVAAACAVWCSVKKRLLEK

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 3 Entity 3 polymer

Description description	Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP
Molecular weight formula_weight	84451.1 kDa
EC 编号 ec_number	1.1.2.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MHRSTFIRTSGTSSRTLTARYRSQYTGLLVARVLFSTSTTRAQGGNPRSPLQIFRDTFKKEWEKSQELQENIKTLQDASGKLGESEAYKKAREAYLKAQRGSTIVGKTLKKTGETMEHIATKAWESELGKNTRKAAAATAKKLDESFEPVRQTKIYKEVSEVIDDGESSRYGGFITKEQRRLKRERDLASGKRHRAVKSNEDAGTAVVATNIESKESFGKKVEDFKEKTVVGRSIQSLKNKLWDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPEILEAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQDIPVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTRDPEQIDDDETEGWKILEFVRGGSRQFTPNHPGGQDVIKFNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSGSGSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGSAGLEVLFQGPANGGSAWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Saccharomyces cerevisiae

Entity 4 Entity 4 polymer

Description description	Protein MGR2
Molecular weight formula_weight	12264.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MPPLPQNYAQQQPSNWDKFKMGLMMGTTVGVCTGILFGGFAIATQGPGPDGVVRTLGKYIAGSAGTFGLFMSIGSIIRSDSESSPMSHPNLNLQQQARLEMWKLRAKYGIRKD

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 5 Entity 5 polymer

Description description	anti-Tim44-Fab H chain
Molecular weight formula_weight	25635.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MDWTWRVFCLLAVAPGAHSQVQLKQSGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSPGKGLEWLGVMWRGGSTDFNAAFMSRLSITKDNSKSQVFFKMNSLQADDTAIYYCARYGNYDAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 6 Entity 6 polymer

Description description	anti-Tim44-Fab L chain
Molecular weight formula_weight	26140.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MVLQTQVFISLLLWISGAYGDIVLTQSPASLAVSLGQRATISCRASESVDIYGISFMNWFQQKPGQPPKLLIYATSNQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 7 Entity 7 polymer

Description description	Substrate
Molecular weight formula_weight	1294.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

XXXXXXXXXXXXXXX

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 8 Entity 8 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1464.0 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.830 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.83 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	160770

Substrate-engaged TIM23 complex from yeast

1. Protein Identity and Related Structures Protein Identity & Related Structures

Mitochondrial import inner membrane translocase subunit TIM17

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Mitochondrial import inner membrane translocase subunit TIM23

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Mitochondrial import inner membrane translocase subunit TIM44,L-lactate dehydrogenase (cytochrome),sfGFP

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein MGR2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9j9b__assembly_1__model_1

9j9b__assembly_1__model_1 | I(q)

9j9b__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

7. Citations (1)