8e2i

Cryo-EM structure of BIRC6/Smac

Method: ELECTRON MICROSCOPY Dmax: 228.6 Å Quality: GOOD

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

Baculoviral IAP repeat-containing protein 6

Homo sapiens

UniProt Q9NR09

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 1–4857 Chain B; UniProt 1–4857 Not recorded Diablo IAP-binding mitochondrial protein × 2 (Q9NR28) Baculoviral IAP repeat-containing protein 6 × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.04 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.

21 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BIRC6_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 32–4888; UniProt 1–4857 Author chain B; PDBConstruct 32–4888; UniProt 1–4857

Diablo IAP-binding mitochondrial protein

Homo sapiens

UniProt Q9NR28

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 E; UniProt 56–239 Chain F; UniProt 56–239 Not recorded Baculoviral IAP repeat-containing protein 6 × 2 (Q9NR09) Baculoviral IAP repeat-containing protein 6 × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.04 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.

13 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DBLOH_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 2–185; UniProt 56–239 Author chain F; PDBConstruct 2–185; UniProt 56–239

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 8e2i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8e2i
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id8e2i
Deposition date deposition_date2022-08-15
Structure title titleCryo-EM structure of BIRC6/Smac
Keywords keywordsUbiquitin, E3 ligase, Apoptosis, Autophagy, IAP, LIGASE; LIGASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier72.59
Radius of gyration Rg (electron density) rg_electron72.79
Forward intensity I(0) i05667180000.00
Molecular weight molecular_weight655610.0 kDa
Excluded volume excluded_volume828250 ų
Envelope volume envelope_volume1346000 ų
Hydration-shell volume shell_volume154000 ų
Envelope diameter envelope_diameter217.3
Shell Rg shell_rg73.22
Envelope Rg envelope_rg68.71
Shape Rg shape_rg72.76
Total Rg total_rg72.90
Total atoms total_atoms92780
Residues n_residues5950
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 dmax228.6
Rg (real space) rg_real72.38
Rg uncertainty (real space) rg_real_error2.11
I(0) (real space) i0_real5.6670e+09
I(0) uncertainty (real space) i0_real_error1.2950e+08
Rg (reciprocal space) rg_reciprocal73.13
I(0) (reciprocal space) i0_reciprocal5675000000.0000
Solution quality estimate total_estimate0.8342
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary83.1
Skewness Skewness skewness0.041
Kurtosis Kurtosis kurtosis-0.788
Angular range angular_range— – 0.1100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha197400000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)