SAXSdb — 7clv

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

TIM23 isoform 1

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–222 Chain B； UniProt 1–222	Not recorded	COX4 isoform 1 × 1 （A0A6A5PV33）	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

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 7CLV	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 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 × 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
8SCX Cryo-EM structure of the core TIM23 complex from S. cerevisiae Deposited 2023-04-05	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 × 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 2.70 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–222； UniProt 1–222 Author chain B； PDBConstruct 1–222； UniProt 1–222

COX4 isoform 1

Saccharomyces cerevisiae

UniProt A0A6A5PV33

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–25	Not recorded	TIM23 isoform 1 × 2 （A0A6A5Q5E3）	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

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 7CLV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GIQ Saccharomyces cerevisiae respiratory supercomplex III2IV Deposited 2018-05-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain d 1–155（155 aa）	Not recorded	6PH (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate × 2 HEC HEME C × 6 8PE (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate × 2 CN5 (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate × 1 UQ6 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL × 2 7PH (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 PCF 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE × 2 9PE (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate × 2 CN3 (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate × 1 CU COPPER (II) ION × 1 HEA HEME-A × 2 CUA DINUCLEAR COPPER ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å

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

View Construct and Data Evidence

UniProt name	A0A6A5PV33_YEASX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–25； UniProt 1–25

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	7clv
Deposition date deposition_date	2020-07-22
Structure title title	Solution structure of mitochondrial Tim23 channel in complex with a signaling peptide
Keywords keywords	Membrane Protein, Tim23 Channel, Presequence., PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	52.54 Å
Radius of gyration Rg (electron density) rg_electron	53.58 Å
Forward intensity I(0) i0	7560360000.00
Molecular weight molecular_weight	742210.0 kDa
Excluded volume excluded_volume	930400 Å³
Envelope volume envelope_volume	600760 Å³
Hydration-shell volume shell_volume	73293 Å³
Envelope diameter envelope_diameter	212.3 Å
Shell Rg shell_rg	59.22 Å
Envelope Rg envelope_rg	73.03 Å
Shape Rg shape_rg	53.63 Å
Total Rg total_rg	53.46 Å
Total atoms total_atoms	104775
Residues n_residues	7035
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

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

Maximum dimension Dmax dmax	205.0 Å
Rg (real space) rg_real	53.63 Å
Rg uncertainty (real space) rg_real_error	3.66 Å
I(0) (real space) i0_real	7.5600e+09
I(0) uncertainty (real space) i0_real_error	1.9410e+08
Rg (reciprocal space) rg_reciprocal	51.62 Å
I(0) (reciprocal space) i0_reciprocal	7539000000.0000
Solution quality estimate total_estimate	0.6160
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.652
Kurtosis Kurtosis kurtosis	-0.562
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4985000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.043; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.030; Smooth: 0.846

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	TIM23 isoform 1
Molecular weight formula_weight	23266.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	104775

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	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	COX4 isoform 1
Molecular weight formula_weight	2993.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MLSLRQSIRFFKPATRTLCSSRYLL

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	Escherichia coli K-12

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8. Citations (1)

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fit	/app/data/saxs_computation/cl/7clv/7clv.fit
pddf	/app/data/pr_computation/cl/7clv/7clv.pr.out
profile	/app/data/saxs_computation/cl/7clv/7clv.dat

Solution structure of mitochondrial Tim23 channel in complex with a signaling peptide

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

TIM23 isoform 1

State in the Current Structure

Other States of the Same Protein in the Database

COX4 isoform 1

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)