SAXSdb — 8e2j

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

Diablo IAP-binding mitochondrial protein

Homo sapiens

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 56–239 Chain B； UniProt 56–239	Not recorded	Baculoviral IAP repeat-containing protein 6 × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.44 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 8E2J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FEW CRYSTAL STRUCTURE OF SMAC/DIABLO Deposited 2000-07-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 56–239（184 aa） Fragment：SMAC/DIABLO	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；276 K；Dioxane, Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 276.0K	Resolution 2.20 Å R-free 0.259
1FEW CRYSTAL STRUCTURE OF SMAC/DIABLO Deposited 2000-07-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 56–239（184 aa） Fragment：SMAC/DIABLO	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；276 K；Dioxane, Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 276.0K	Resolution 2.20 Å R-free 0.259
1G3F NMR STRUCTURE OF A 9 RESIDUE PEPTIDE FROM SMAC/DIABLO COMPLEXED TO THE BIR3 DOMAIN OF XIAP Deposited 2000-10-24	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 × 2 PDB declaration: dimeric	Chain B 56–64（9 aa） Fragment：9 RESIDUE PEPTIDE	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7.2；300 K；Pressure 1 NMR sample composition 1 mM protein/peptide complex, 120 mM NaCl, 1mM DTT, 10mM phosphate \| 90% h20, 10% d20	Resolution not provided
1G73 CRYSTAL STRUCTURE OF SMAC BOUND TO XIAP-BIR3 DOMAIN Deposited 2000-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 56–217（162 aa） Fragment：RESIDUES 1-162	Mutation：F33D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；297 K；100 mM Citrate, pH5.5 5% PEG4000 10% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.00 Å R-free 0.268
1G73 CRYSTAL STRUCTURE OF SMAC BOUND TO XIAP-BIR3 DOMAIN Deposited 2000-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 56–217（162 aa） Fragment：RESIDUES 1-162	Mutation：F33D	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；297 K；100 mM Citrate, pH5.5 5% PEG4000 10% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.00 Å R-free 0.268
1TW6 Structure of an ML-IAP/XIAP chimera bound to a 9mer peptide derived from Smac Deposited 2004-06-30	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 × 2 PDB declaration: dimeric	Chain C 56–64（9 aa） Fragment：Smac residues 1-9	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；lithium sulfate, Bis-tris, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.71 Å R-free 0.171
1TW6 Structure of an ML-IAP/XIAP chimera bound to a 9mer peptide derived from Smac Deposited 2004-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 56–64（9 aa） Fragment：Smac residues 1-9	Not recorded	ZN ZINC ION × 1 LI LITHIUM ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；lithium sulfate, Bis-tris, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.71 Å R-free 0.171
1TW6 Structure of an ML-IAP/XIAP chimera bound to a 9mer peptide derived from Smac Deposited 2004-06-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 56–64（9 aa） Fragment：Smac residues 1-9 Chain D 56–64（9 aa） Fragment：Smac residues 1-9	Not recorded	ZN ZINC ION × 4 LI LITHIUM ION × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；lithium sulfate, Bis-tris, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.71 Å R-free 0.171
1TW6 Structure of an ML-IAP/XIAP chimera bound to a 9mer peptide derived from Smac Deposited 2004-06-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 56–64（9 aa） Fragment：Smac residues 1-9 Chain D 56–64（9 aa） Fragment：Smac residues 1-9	Not recorded	ZN ZINC ION × 2 LI LITHIUM ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；lithium sulfate, Bis-tris, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.71 Å R-free 0.171
1TW6 Structure of an ML-IAP/XIAP chimera bound to a 9mer peptide derived from Smac Deposited 2004-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 56–64（9 aa） Fragment：Smac residues 1-9	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；lithium sulfate, Bis-tris, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.71 Å R-free 0.171
1XB0 Structure of the BIR domain of IAP-like protein 2 Deposited 2004-08-27	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 × 12 PDB declaration: dodecameric	Chain G 56–62（7 aa） Chain H 56–62（7 aa） Chain I 56–62（7 aa） Chain J 56–62（7 aa） Chain K 56–62（7 aa） Chain L 56–62（7 aa）	Not recorded	ZN ZINC ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；295 K；5% PEG3000, 100mM sodium acetate, 100mM Zinc acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.244
1XB1 The Structure of the BIR domain of IAP-like protein 2 Deposited 2004-08-27	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 × 12 PDB declaration: dodecameric	Chain G 56–62（7 aa） Chain H 56–62（7 aa） Chain I 56–62（7 aa） Chain J 56–62（7 aa） Chain K 56–62（7 aa） Chain L 56–62（7 aa）	Not recorded	ZN ZINC ION × 23	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；295 K；5% PEG3000, 100mM Na acetate, 100mM Zinc acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.277
1XB1 The Structure of the BIR domain of IAP-like protein 2 Deposited 2004-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain G 56–62（7 aa） Chain H 56–62（7 aa） Chain I 56–62（7 aa） Chain J 56–62（7 aa） Chain K 56–62（7 aa） Chain L 56–62（7 aa）	Not recorded	ZN ZINC ION × 46	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；295 K；5% PEG3000, 100mM Na acetate, 100mM Zinc acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.277
3UIH crystal structure of human Survivin in complex with Smac/DIABLO(1-15) peptide Deposited 2011-11-04	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 56–70（15 aa） Fragment：unp residues 1-15 Chain Q 56–70（15 aa） Fragment：unp residues 1-15	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M potassium thiocyanate, 10% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.245
3UIJ Crystal structure of human Survivin K62Y/H80W mutant in complex with Smac/DIABLO(1-15) peptide Deposited 2011-11-04	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 56–70（15 aa） Fragment：unp residues 1-15 Chain Q 56–70（15 aa） Fragment：unp residues 1-15	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M sodium bromide, 12% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.71 Å R-free 0.242
4TX5 Crystal structure of Smac-DIABLO (in space group P65) Deposited 2014-07-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 56–239（184 aa） Fragment：UNP Residues 56-239 Chain B 56–239（184 aa） Fragment：UNP Residues 56-239	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 6 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；30% MPD, 0.1 M Sodium Acetate, 0.02 M Calcium Chloride.	Resolution 1.80 Å R-free 0.202
6JX6 Tetrameric form of Smac Deposited 2019-04-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 56–239（184 aa） Chain B 56–239（184 aa） Chain C 56–239（184 aa） Chain D 56–239（184 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；296 K；200mM Potassium Phosphate Monobasic, 20% PEG 3350	Resolution 2.81 Å R-free 0.264
8ATO Structure of the giant inhibitor of apoptosis, BIRC6 bound to the regulator SMAC Deposited 2022-08-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 56–239（184 aa） Chain D 56–239（184 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8AUW Cryo-EM structure of human BIRC6 in complex with SMAC. Deposited 2022-08-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 56–239（184 aa） Chain D 56–239（184 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.20 Å
8E2I Cryo-EM structure of BIRC6/Smac Deposited 2022-08-15	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 56–239（184 aa） Chain F 56–239（184 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å

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	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–185； UniProt 56–239 Author chain B； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8e2j
Deposition date deposition_date	2022-08-15
Structure title title	Cryo-EM structure of BIRC6/Smac (from local refinement 1)
Keywords keywords	Ubiquitin, E3 ligase, Apoptosis, Autophagy, IAP, LIGASE; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	35.80 Å
Radius of gyration Rg (electron density) rg_electron	36.25 Å
Forward intensity I(0) i0	40067200.00
Molecular weight molecular_weight	47144.0 kDa
Excluded volume excluded_volume	57783 Å³
Envelope volume envelope_volume	85840 Å³
Hydration-shell volume shell_volume	23180 Å³
Envelope diameter envelope_diameter	147.1 Å
Shell Rg shell_rg	34.81 Å
Envelope Rg envelope_rg	39.07 Å
Shape Rg shape_rg	36.30 Å
Total Rg total_rg	35.99 Å
Total atoms total_atoms	6466
Residues n_residues	460
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	140.1 Å
Rg (real space) rg_real	36.71 Å
Rg uncertainty (real space) rg_real_error	2.07 Å
I(0) (real space) i0_real	4.0070e+07
I(0) uncertainty (real space) i0_real_error	7.9510e+05
Rg (reciprocal space) rg_reciprocal	36.15 Å
I(0) (reciprocal space) i0_reciprocal	40050000.0000
Solution quality estimate total_estimate	0.6498
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.764
Kurtosis Kurtosis kurtosis	-0.024
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4007000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.188; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.031; Smooth: 0.848

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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	Diablo IAP-binding mitochondrial protein
Molecular weight formula_weight	22161.6 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	6466

MAVPIAQKSEPHSLSSEALMRRAVSLVTDSTSTFLSQTTYALIEAITEYTKAVYTLTSLYRQYTSLLGKMNSEEEDEVWQVIIGARAEMTSKHQEYLKLETTWMTAVGLSEMAAEAAYQTGADQASITARNHIQLVKLQVEEVHQLSRKAETKLAEAQIEELRQKTQEEGEERAESEQEAYLREDHHHHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Baculoviral IAP repeat-containing protein 6
Molecular weight formula_weight	4869.0 kDa
EC 编号 ec_number	6.-.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

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8. Citations (1)

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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	3.44 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	192025

fit	/app/data/saxs_computation/e2/8e2j/8e2j.fit
pddf	/app/data/pr_computation/e2/8e2j/8e2j.pr.out
profile	/app/data/saxs_computation/e2/8e2j/8e2j.dat

Cryo-EM structure of BIRC6/Smac (from local refinement 1)

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

Diablo IAP-binding mitochondrial protein

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 (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)