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- PDB-37id: Human sterile alpha motif domain-containing protein 9 (SAMD9), lo... -

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Basic information

Entry
Database: PDB / ID: 37id
TitleHuman sterile alpha motif domain-containing protein 9 (SAMD9), loss-of-function mutant Q514S/R515S/R522S/R553S/Q565S/R593S
ComponentsSterile alpha motif domain-containing protein 9
KeywordsIMMUNE SYSTEM / inflammasome / signal transductionATPases with numerous domains (STAND) / sterile alpha motif. poxvirusrestriction factor / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


endosomal vesicle fusion / innate immune response / cytosol / cytoplasm
Similarity search - Function
SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Sterile alpha motif domain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMou, Z. / Zhang, F. / Dai, X. / Xiang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al151638 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM151043 United States
CitationJournal: To Be Published
Title: Human sterile alpha motif domain-containing protein 9 (SAMD9), loss-of-function mutant Q514S/R515S/R522S/R553S/Q565S/R593S
Authors: Mou, Z. / Zhang, F. / Dai, X. / Xiang, Y.
History
DepositionJul 21, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sterile alpha motif domain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,9013
Polymers166,3691
Non-polymers5312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Sterile alpha motif domain-containing protein 9 / SAM domain-containing protein 9


Mass: 166369.422 Da / Num. of mol.: 1 / Mutation: Q514S,R515S,R522S,R553S,Q565S,R593S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMD9, C7orf5, DRIF1, KIAA2004, OEF1 / Production host: Homo sapiens (human) / References: UniProt: Q5K651
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human sterile alpha motif domain-containing protein 9 (SAMD9)
Type: COMPLEX
Details: Human sterile alpha motif domain-containing protein 9 (SAMD9), loss-of-function mutant Q514S/R515S/R522S/R553S/Q565S/R593S
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.167 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49919 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049331
ELECTRON MICROSCOPYf_angle_d0.46712580
ELECTRON MICROSCOPYf_dihedral_angle_d6.6021232
ELECTRON MICROSCOPYf_chiral_restr0.041383
ELECTRON MICROSCOPYf_plane_restr0.0031584

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