6lul

NMR structure and dynamics studies of yeast respiratory super-complex factor 2 in micelles

Method: SOLUTION NMR Dmax: 113.7 Å Quality: GOOD

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

Respiratory supercomplex factor 2, mitochondrial

Saccharomyces cerevisiae S288C

UniProt P53721

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–224 Chain B; UniProt 1–224 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions:pH 5;323 K;Ionic strength (raw mmCIF value) 25;Pressure 1 NMR sample composition:0.5 mM [U-99% 15N] Rcf2, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5 mM 15N_2H Rcf2, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5 mM 15N_2H_13C Rcf2, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5 mM 15N_50%-2H_13C Rcf2, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5 mM 15N_2H_13C-IVL Rcf2, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5 mM 50% [13C, 15N] and 50% [12C, 14N] Rcf2, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:0.5 mM [13C, 15N] Rcf2, 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.

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

View Construct and Data Evidence
UniProt name RCF2_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–224; UniProt 1–224 Author chain B; PDBConstruct 1–224; UniProt 1–224

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6lul

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6lul
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6lul
Deposition date deposition_date2020-01-29
Structure title titleNMR structure and dynamics studies of yeast respiratory super-complex factor 2 in micelles
Keywords keywordsmembrane protein, respiratory supercomplex factor, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier32.99
Radius of gyration Rg (electron density) rg_electron32.81
Forward intensity I(0) i07679190000.00
Molecular weight molecular_weight759580.0 kDa
Excluded volume excluded_volume957410 ų
Envelope volume envelope_volume257590 ų
Hydration-shell volume shell_volume54102 ų
Envelope diameter envelope_diameter131.5
Shell Rg shell_rg45.15
Envelope Rg envelope_rg39.68
Shape Rg shape_rg32.80
Total Rg total_rg33.02
Total atoms total_atoms107880
Residues n_residues6720
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax113.7
Rg (real space) rg_real33.11
Rg uncertainty (real space) rg_real_error1.10
I(0) (real space) i0_real7.6790e+09
I(0) uncertainty (real space) i0_real_error1.4690e+08
Rg (reciprocal space) rg_reciprocal33.06
I(0) (reciprocal space) i0_reciprocal7679000000.0000
Solution quality estimate total_estimate0.7980
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary30.8
Skewness Skewness skewness0.374
Kurtosis Kurtosis kurtosis-0.343
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16150000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.873; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (1)

9. Files and Curves (10)