SAXSdb — 3dxr

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

Mitochondrial import inner membrane translocase subunit TIM9

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Mitochondrial import inner membrane translocase subunit TIM10 × 3 （P87108） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 12	Mitochondrial import inner membrane translocase subunit TIM10 × 6 （P87108） water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TIM9_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–89； UniProt 1–87

Mitochondrial import inner membrane translocase subunit TIM10

Saccharomyces cerevisiae

UniProt P87108

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Mitochondrial import inner membrane translocase subunit TIM9 × 3 （O74700） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 12	Mitochondrial import inner membrane translocase subunit TIM9 × 6 （O74700） water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TIM10_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–95； UniProt 1–93

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	3dxr
Deposition date deposition_date	2008-07-24
Structure title title	Crystal structure of the yeast inter-membrane space chaperone assembly TIM9.10
Keywords keywords	;Alpha-Propeller; Helix-Turn-Helix; Intramolecular Disulfides., Chaperone, Inner membrane, Membrane, Metal-binding, Mitochondrion, Protein transport, Translocation, Transport, Zinc ;; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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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.

3dxr__assembly_1__model_1

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

Download this curve (.dat)

3dxr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dxr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.34 Å
Rg (electron density)	22.26 Å
Total Rg	23.15 Å
Atom count	3087
Residues	414
Excluded volume	54255 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dxr__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dxr__assembly_2__model_1`	dodecameric （12）	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 (3)

Entity 1 Entity 1 polymer

Description description	Mitochondrial import inner membrane translocase subunit TIM9
Molecular weight formula_weight	10360.8 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	1072

GSMDALNSKEQQEFQKVVEQKQMKDFMRLYSNLVERCFTDCVNDFTTSKLTNKEQTCIMKCSEKFLKHSERVGQRFQEQNAALGQGLGR

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Mitochondrial import inner membrane translocase subunit TIM10
Molecular weight formula_weight	10457.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSMSFLGFGGGQPQLSSQQKIQAAEAELDLVTDMFNKLVNNCYKKCINTSYSEGELNKNESSCLDRCVAKYFETNVQVGENMQKMGQSFNAAGKF

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3dxra_
Class class	g — Small proteins
Fold Fold fold	g.83 — Tim10-like
Superfamily Superfamily superfamily	g.83.1 — Tim10-like
Family Family family	g.83.1.0 — automated matches

Domain ID domain_id	d3dxrb_
Class class	g — Small proteins
Fold Fold fold	g.83 — Tim10-like
Superfamily Superfamily superfamily	g.83.1 — Tim10-like
Family Family family	g.83.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3dxrA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	810 — Mitochondrial import inner membrane translocase subunit tim13 like domains

Domain ID domain_id	3dxrB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	810 — Mitochondrial import inner membrane translocase subunit tim13 like domains

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Unit-cell length a length_a	58.198 Å
Unit-cell length b length_b	58.198 Å
Unit-cell length c length_c	243.731 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2470
R_work r_work	0.2450
R_free r_free	0.2750

Crystal structure of the yeast inter-membrane space chaperone assembly TIM9.10

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

Mitochondrial import inner membrane translocase subunit TIM9

State in the Current Structure

Other States of the Same Protein in the Database

Mitochondrial import inner membrane translocase subunit TIM10

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dxr__assembly_1__model_1

3dxr__assembly_1__model_1 | I(q)

3dxr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the yeast inter-membrane space chaperone assembly TIM9.10

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

Mitochondrial import inner membrane translocase subunit TIM9

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 TIM10

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

3dxr__assembly_1__model_1

3dxr__assembly_1__model_1 | I(q)

3dxr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)