8h93

Structure of dimeric mouse SCMC core complex

Method: ELECTRON MICROSCOPY Dmax: 201.5 Å Quality: GOOD

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

NACHT, LRR and PYD domains-containing protein 5

Mus musculus

UniProt Q9R1M5

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 105–1163 Chain D; UniProt 105–1163 Not recorded Transducin-like enhancer protein 6 × 2 (Q9WVB3) Oocyte-expressed protein homolog × 2 (Q9CWE6) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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.

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NALP5_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1059; UniProt 105–1163 Author chain D; PDBConstruct 1–1059; UniProt 105–1163

Transducin-like enhancer protein 6

Mus musculus

UniProt Q9WVB3

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–581 Chain E; UniProt 1–581 Not recorded NACHT, LRR and PYD domains-containing protein 5 × 2 (Q9R1M5) Oocyte-expressed protein homolog × 2 (Q9CWE6) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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.

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TLE6_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–581; UniProt 1–581 Author chain E; PDBConstruct 1–581; UniProt 1–581

Oocyte-expressed protein homolog

Mus musculus

UniProt Q9CWE6

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 1–164 Chain F; UniProt 1–164 Not recorded NACHT, LRR and PYD domains-containing protein 5 × 2 (Q9R1M5) Transducin-like enhancer protein 6 × 2 (Q9WVB3) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.01 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.

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OOEP_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–164; UniProt 1–164 Author chain F; PDBConstruct 1–164; UniProt 1–164

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 8h93

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8h93
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8h93
Deposition date deposition_date2022-10-24
Structure title titleStructure of dimeric mouse SCMC core complex
Keywords keywordsoocyte, subcortical, complex, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier63.98
Radius of gyration Rg (electron density) rg_electron65.52
Forward intensity I(0) i01385120000.00
Molecular weight molecular_weight316650.0 kDa
Excluded volume excluded_volume397970 ų
Envelope volume envelope_volume601770 ų
Hydration-shell volume shell_volume80078 ų
Envelope diameter envelope_diameter221.9
Shell Rg shell_rg60.82
Envelope Rg envelope_rg63.86
Shape Rg shape_rg65.59
Total Rg total_rg65.13
Total atoms total_atoms22191
Residues n_residues2810
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 dmax201.5
Rg (real space) rg_real64.97
Rg uncertainty (real space) rg_real_error1.69
I(0) (real space) i0_real1.3850e+09
I(0) uncertainty (real space) i0_real_error2.9460e+07
Rg (reciprocal space) rg_reciprocal63.01
I(0) (reciprocal space) i0_reciprocal1380000000.0000
Solution quality estimate total_estimate0.7685
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary48.4
Skewness Skewness skewness0.531
Kurtosis Kurtosis kurtosis-0.600
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0006
Highest regularization parameter α highest_alpha108300000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.695; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.869; Smooth: 0.036

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)