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- EMDB-78192: Human sterile alpha motif domain-containing protein 9 (SAMD9), lo... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-78192
TitleHuman sterile alpha motif domain-containing protein 9 (SAMD9), loss-of-function mutant R1562E/I1567R/E1568I
Map data
Sample
  • Complex: SAMD9
    • Protein or peptide: Sterile alpha motif domain-containing protein 9
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsinflammasome / signal transductionATPases with numerous domains (STAND) / sterile alpha motif. poxvirusrestriction factor / ANTIVIRAL PROTEIN / IMMUNE SYSTEM
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
Sterile alpha motif domain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsMou Z / Zhang F / Dai X / Xiang Y
Funding support United States, 2 items
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 R1562E/I1567R/E1568I
Authors: Mou Z / Zhang F / Dai X / Xiang Y
History
DepositionJul 21, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78192.png

Downloads & links

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Map

FileDownload / File: emd_78192.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.7019447 - 1.4445953
Average (Standard dev.)-0.00024995324 (±0.03197296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_78192_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_78192_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SAMD9

EntireName: SAMD9
Components
  • Complex: SAMD9
    • Protein or peptide: Sterile alpha motif domain-containing protein 9
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: SAMD9

SupramoleculeName: SAMD9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 168 KDa

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Macromolecule #1: Sterile alpha motif domain-containing protein 9

MacromoleculeName: Sterile alpha motif domain-containing protein 9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 166.731984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SIDLTCVSYP FDEFSNPYRY KLDFSLQPET GPGNLIDPIH EFKAFTNTAT ATEEDVKMKF SNEVFRFASA CMNSRTNGTI HFGVKDKPH GKIVGIKVTN DTKEALINHF NLMINKYFED HQVQQAKKCI REPRFVEVLL PNSTLSDRFV IEVDIIPQFS E CQYDYFQI ...String:
SIDLTCVSYP FDEFSNPYRY KLDFSLQPET GPGNLIDPIH EFKAFTNTAT ATEEDVKMKF SNEVFRFASA CMNSRTNGTI HFGVKDKPH GKIVGIKVTN DTKEALINHF NLMINKYFED HQVQQAKKCI REPRFVEVLL PNSTLSDRFV IEVDIIPQFS E CQYDYFQI KMQNYNNKIW EQSKKFSLFV RDGTSSKDIT KNKVDFRAFK ADFKTLAESR KAAEEKFRAK TNKKEREGPK LV KLLTGNQ DLLDNSYYEQ YILVTNKCHP DQTKHLDFLK EIKWFAVLEF DPESNINGVV KAYKESRVAN LHFPSVYVEQ KTT PNETIS TLNLYHQPSW IFCNGRLDLD SEKYKPFDPS SWQRERASDV RKLISFLTHE DIMPRGKFLV VFLLLSSVDD PRDP LIETF CAFYQDLKGM ENILCICVHP HIFQGWKDLL EARLIKHQDE ISSQCISALS LEEINGTILK LKSVTQSSKR LLPSI GLST VLLKKEEDIM TALEIICENE CEGTLLEKDK NKFLEFKASK EEDFYRGGKV SWWNFYFSSE SYSSPFVKRD KYERLE AMI QNCADSSKPT STKIIHLYHH PGCGGTTLAM HILWELRKKF RCAVLKNKTV DFSEIGEQVT SLITYGAMNR QEYVPVL LL VDDFEEQDNV YLLQYSIQTA IAKKYIRYEK PLVIILNCMR SQNPEKSARI PDSIAVIQQL SPKEQRAFEL KLKEIKEQ H KNFEDFYSFM IMKTNFNKEY IENVVRNILK GQNIFTKEAK LFSFLALLNS YVPDTTISLS QCEKFLGIGN KKAFWGTEK FEDKMGTYST ILIKTEVIEC GNYCGVRIIH SLIAEFSLEE LKKSYHLNKS QIMLDMLTEN LFFDTGMGKS KFLQDMHTLL LTRHRDEHE GETGNWFSPF IEALHKDEGN EAVEAVLLES IHRFNPNAFI CQALARHFYI KKKDFGNALN WAKQAKIIEP D NSYISDTL GQVYKSKIRW WIEENGGNGN ISVDDLIALL DLAEHASSAF KESQQQSEDR EYEVKERLYP KSKRRYDTYN IA GYQGEIE VGLYTIQILQ LIPFFDNKNE LSKRYMVNFV SGSSDIPGDP NNEYKLALKN YIPYLTKLKF SLKKSFDFFD EYF VLLKPR NNIKQNEEAK TRRKVAGYFK KYVDIFCLLE ESQNNTGLGS KFSEPLQVER CRRNLVALKA DKFSGLLEYL IKSQ EDAIS TMKCIVNEYT FLLEQCTVKI QSKEKLNFIL ANIILSCIQP TSRLVKPVEK LKDQLREVLQ PIGLTYQFSE PYFLA SLLF WPENQQLDQH SEQMKEYAQA LKNSFKGQYK HMHRTKQPIA YFFLGKGKRL ERLVHKGKID QCFKKTPDIN SLWQSG DVW KEEKVQELLL RLQGRAENNC LYIEYGINEK ITIPITPAFL GQLESGRSRI KVSFYLGFSI GGPLAYDIEI V

UniProtKB: Sterile alpha motif domain-containing protein 9

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaCIsodium chloride
50.0 mMTrisTris(hydroxymethyl)aminome
1.0 mMDTTDithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 103396
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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