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9zjs

Human sterile alpha motif domain-containing protein 9 (SAMD9), asymmetric dimer "shell" shape

Method: ELECTRON MICROSCOPY Dmax: 135.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sterile alpha motif domain-containing protein 9

Homo sapiens

UniProt Q5K651

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 156–1589 Chain B； UniProt 156–1589 Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 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.

Other PDB Difference from Current Entry 9ZJS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7KSP Crystal structure of hSAMD9_DBD with DNA Deposited 2020-11-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 156–385（230 aa）
Chain B 156–385（230 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 20mM magnesium chloride, 20% PEG3350
Resolution 2.80 Å R-free 0.284
9ZJR Human sterile alpha motif domain-containing protein 9 (SAMD9), monomer Deposited 2025-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 156–1589（1434 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.53 Å
9ZJU Human sterile alpha motif domain-containing protein 9 (SAMD9), symmetric dimer Deposited 2025-12-05 Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 156–1589（1434 aa）
Chain B 156–1589（1434 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9ZJV Human sterile alpha motif domain-containing protein 9 (SAMD9), asymmetric dimer "wing" shape Deposited 2025-12-05 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 156–1589（1434 aa）
Chain B 156–1589（1434 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9ZJW Human sterile alpha motif domain-containing protein 9 (SAMD9), loss-of-function mutant R837A Deposited 2025-12-05 Different mutation/modification Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 156–1589（1434 aa）
Chain B 156–1589（1434 aa）
Mutation：R837A Mutation：R837A ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9ZJZ Human sterile alpha motif domain-containing protein 9 (SAMD9), loss-of-function mutant R685Q/G686C/I968C Deposited 2025-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 156–1589（1434 aa）
Mutation：R685Q,G686C,I968C ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SAMD9_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 17–1450； UniProt 156–1589 Author chain B； PDBConstruct 17–1450； UniProt 156–1589

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 9zjs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zjs
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9zjs
Deposition date deposition_date2025-12-05
Structure title titleHuman sterile alpha motif domain-containing protein 9 (SAMD9), asymmetric dimer "shell" shape
Keywords keywords;inflammasome, signal transduction ATPases with numerous domains (STAND), sterile alpha motif, poxvirus restriction factor, ANTIVIRAL PROTEIN, CYTOSOLIC PROTEIN ;; ANTIVIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.73 Å
Radius of gyration Rg (electron density) rg_electron43.08 Å
Forward intensity I(0) i0868634000.00
Molecular weight molecular_weight252520.0 kDa
Excluded volume excluded_volume319950 ų
Envelope volume envelope_volume459440 ų
Hydration-shell volume shell_volume85978 ų
Envelope diameter envelope_diameter140.6 Å
Shell Rg shell_rg51.21 Å
Envelope Rg envelope_rg41.29 Å
Shape Rg shape_rg43.07 Å
Total Rg total_rg43.54 Å
Total atoms total_atoms17804
Residues n_residues2164
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax135.4 Å
Rg (real space) rg_real43.43 Å
Rg uncertainty (real space) rg_real_error1.06 Å
I(0) (real space) i0_real8.6860e+08
I(0) uncertainty (real space) i0_real_error1.3880e+07
Rg (reciprocal space) rg_reciprocal43.73 Å
I(0) (reciprocal space) i0_reciprocal868900000.0000
Solution quality estimate total_estimate0.8931
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary60.2 Å
Skewness Skewness skewness0.037
Kurtosis Kurtosis kurtosis-0.513
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha121600000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.947
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)