SAXSdb — 8scx

▼

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

Mitochondrial import inner membrane translocase subunit TIM17

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–158	Not recorded	Mitochondrial import inner membrane translocase subunit TIM23 × 1 （A0A6A5Q5E3） Mitochondrial import inner membrane translocase subunit TIM44 × 1 （A0A6A5Q2Y5） Antibody Fab fragment light chain × 1 Antibody Fab fragment heavy chain × 1 CDL CARDIOLIPIN × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8SCX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8E1M Cryo-EM structure of the endogenous core TIM23 complex from S. cerevisiae Deposited 2022-08-10	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–158（158 aa）	Not recorded	CDL CARDIOLIPIN × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5PVU8_YEASX
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

UniProt A0A6A5Q5E3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain B； UniProt 1–222	Not recorded	Mitochondrial import inner membrane translocase subunit TIM17 × 1 （A0A6A5PVU8） Mitochondrial import inner membrane translocase subunit TIM44 × 1 （A0A6A5Q2Y5） Antibody Fab fragment light chain × 1 Antibody Fab fragment heavy chain × 1 CDL CARDIOLIPIN × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8SCX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7CLV Solution structure of mitochondrial Tim23 channel in complex with a signaling peptide Deposited 2020-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–222（222 aa） Chain B 1–222（222 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；313.75 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR measurement conditions pH 5；313.75 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.5 mM 2H, 15N Tim23, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 uM 2H, 15N, 13C Tim23_unlabeled_Peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM 15N, 13C Tim23_unlabeled_Peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM 50% 2H, 13C, 15N Tim23_unlabeled_Peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM IVL-selectively_labeled_Tim23_unlabeled_peptide Tim23_unlabeled_Peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM 50%unlabeled/50%labeled_Tim23_unlabeled_peptide Tim23_unlabeled_Peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 nM 50%unlabeled/50%labeled_Tim23_unlabeled_peptide [15N, 13C]-peptide_unlabeled_Tim23, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8E1M Cryo-EM structure of the endogenous core TIM23 complex from S. cerevisiae Deposited 2022-08-10	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–222（222 aa）	Not recorded	CDL CARDIOLIPIN × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q5E3_YEASX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–222； UniProt 1–222

Mitochondrial import inner membrane translocase subunit TIM44

Saccharomyces cerevisiae

UniProt A0A6A5Q2Y5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain C； UniProt 1–431	Not recorded	Mitochondrial import inner membrane translocase subunit TIM17 × 1 （A0A6A5PVU8） Mitochondrial import inner membrane translocase subunit TIM23 × 1 （A0A6A5Q5E3） Antibody Fab fragment light chain × 1 Antibody Fab fragment heavy chain × 1 CDL CARDIOLIPIN × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8SCX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8E1M Cryo-EM structure of the endogenous core TIM23 complex from S. cerevisiae Deposited 2022-08-10	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–431（431 aa）	Not recorded	CDL CARDIOLIPIN × 1 PTY PHOSPHATIDYLETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6A5Q2Y5_YEASX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–431； UniProt 1–431

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8scx
Deposition date deposition_date	2023-04-05
Structure title title	Cryo-EM structure of the core TIM23 complex from S. cerevisiae
Keywords keywords	TRANSLOCASE; TRANSLOCASE
Experimental Method method	ELECTRON MICROSCOPY

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.94 Å
Radius of gyration Rg (electron density) rg_electron	32.48 Å
Forward intensity I(0) i0	105206000.00
Molecular weight molecular_weight	81732.0 kDa
Excluded volume excluded_volume	102410 Å³
Envelope volume envelope_volume	135780 Å³
Hydration-shell volume shell_volume	35967 Å³
Envelope diameter envelope_diameter	115.4 Å
Shell Rg shell_rg	38.20 Å
Envelope Rg envelope_rg	32.35 Å
Shape Rg shape_rg	32.46 Å
Total Rg total_rg	33.04 Å
Total atoms total_atoms	5753
Residues n_residues	760
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	106.3 Å
Rg (real space) rg_real	33.00 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	1.0520e+08
I(0) uncertainty (real space) i0_real_error	1.7030e+06
Rg (reciprocal space) rg_reciprocal	32.98 Å
I(0) (reciprocal space) i0_reciprocal	105200000.0000
Solution quality estimate total_estimate	0.8992
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.4 Å
Skewness Skewness skewness	0.314
Kurtosis Kurtosis kurtosis	-0.546
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10910000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.908

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

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	5753

MSADHSRDPCPIVILNDFGGAFAMGAIGGVVWHGIKGFRNSPLGERGSGAMSAIKARAPVLGGNFGVWGGLFSTFDCAVKAVRKREDPWNAIIAGFFTGGALAVRGGWRHTRNSSITCACLLGVIEGVGLMFQRYAAWQAKPMAPPLPEAPSSQPLQA

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 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

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 3 Entity 3 polymer

Description description	Mitochondrial import inner membrane translocase subunit TIM44
Molecular weight formula_weight	48933.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MHRSTFIRTSGTSSRTLTARYRSQYTGLLVARVLFSTSTTRAQGGNPRSPLQIFRDTFKKEWEKSQELQENIKTLQDASGKLGESEAYKKAREAYLKAQRGSTIVGKTLKKTGETMEHIATKAWESELGKNTRKAAAATAKKLDESFEPVRQTKIYKEVSEVIDDGESSRYGGFITKEQRRLKRERDLASGKRHRAVKSNEDAGTAVVATNIESKESFGKKVEDFKEKTVVGRSIQSLKNKLWDESENPLIVVMRKITNKVGGFFAETESSRVYSQFKLMDPTFSNESFTRHLREYIVPEILEAYVKGDVKVLKKWFSEAPFNVYAAQQKIFKEQDVYADGRILDIRGVEIVSAKLLAPQDIPVLVVGCRAQEINLYRKKKTGEIAAGDEANILMSSYAMVFTRDPEQIDDDETEGWKILEFVRGGSRQFT

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 4 Entity 4 polymer

Description description	Antibody Fab fragment light chain
Molecular weight formula_weight	26173.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MEKDTLLLWVLLLWVPGSTGDIVLTQSPASLAVSLGQRATISCRASESVDIYGISFMNWFQQKPGQPPKLLIYATSNQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 5 Entity 5 polymer

Description description	Antibody Fab fragment heavy chain
Molecular weight formula_weight	25495.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MAVLVLLLCLVTFPSCVLSQVQLKQSGPGLVQPSQSLSITCTVSGFSLTTYGVHWVRQSPGKGLEWLGVMWRGGSTDFNAAFMSRLSITKDNSKSQVFFKMNSLQADDTAIYYCARYGNYDAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	734.0 kDa
Source method src_method	syn
Copy count entity_count	1

▶

8. Citations (1)

▶

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	2.70 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	159958

fit	/app/data/saxs_computation/sc/8scx/8scx.fit
pddf	/app/data/pr_computation/sc/8scx/8scx.pr.out
profile	/app/data/saxs_computation/sc/8scx/8scx.dat

Cryo-EM structure of the core TIM23 complex from S. cerevisiae

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

Mitochondrial import inner membrane translocase subunit TIM23

State in the Current Structure

Other States of the Same Protein in the Database

Mitochondrial import inner membrane translocase subunit TIM44

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)