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- EMDB-56096: SP100 CARD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-56096
TitleSP100 CARD filament
Map data
Sample
  • Complex: SP100 CARD domain filament
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
KeywordsInnate immunity / interferon / DNA damage / cryo-EM / IMMUNE SYSTEM
Function / homology
Function and homology information


regulation of Fas signaling pathway / regulation of viral process / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway ...regulation of Fas signaling pathway / regulation of viral process / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / regulation of angiogenesis / maltose transport / maltodextrin transmembrane transport / type II interferon-mediated signaling pathway / response to retinoic acid / response to type II interferon / SUMOylation of DNA damage response and repair proteins / retinoic acid receptor signaling pathway / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to cytokine / nuclear periphery / ATP-binding cassette (ABC) transporter complex / telomere maintenance / cell chemotaxis / DNA damage response, signal transduction by p53 class mediator / PML body / kinase binding / Interferon gamma signaling / transcription corepressor activity / outer membrane-bounded periplasmic space / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / periplasmic space / chromosome, telomeric region / protein dimerization activity / nuclear body / protein domain specific binding / negative regulation of DNA-templated transcription / DNA damage response / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm
Similarity search - Function
HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain ...HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Nuclear autoantigen Sp-100
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsRabl J / Aird E / Corn J
Funding supportEuropean Union, Switzerland, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)855741-DDREAMM-ERC-2019-SyGEuropean Union
Swiss National Science Foundation310030_188858 Switzerland
European Molecular Biology Organization (EMBO)ALTF 144-2021European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionDec 16, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56096.png

Downloads & links

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Map

FileDownload / File: emd_56096.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.5322048 - 0.8002044
Average (Standard dev.)0.0009065622 (±0.021282282)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_56096_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_56096_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SP100 CARD domain filament

EntireName: SP100 CARD domain filament
Components
  • Complex: SP100 CARD domain filament
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100

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Supramolecule #1: SP100 CARD domain filament

SupramoleculeName: SP100 CARD domain filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoanti...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Nuclear autoantigen Sp-100
type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.874168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSSHHHHHH GSSMKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS A LMFNLQEP ...String:
MKSSHHHHHH GSSMKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS A LMFNLQEP YFTWPLIAAD GGYAFKYENG KYDIKDVGVD NAGAKAGLTF LVDLIKNKHM NADTDYSIAE AAFNKGETAM TI NGPWAWS NIDTSKVNYG VTVLPTFKGQ PSKPFVGVLS AGINAASPNK ELAKEFLENY LLTDEGLEAV NKDKPLGAVA LKS YEEELA KDPRIAATME NAQKGEIMPN IPQMSAFWYA VRTAVINAAS GRQTVDEALK DAQTNSSSNN NNNNNNNNLG IEEN LYFQS NATDLQRMFT EDQGVDDRLL YDIVFKHFKR NKVEISNAIK KTFPFLEGLR DRDLITNKMF EDSQDSCRNL VPVQR VVYN VLSELEKTFN LPVLEALFSD VNMQEYPDLI HIYKGFENVI H

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Nuclear autoantigen Sp-100

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMHEPES pH 8.0
150.0 mMsodium chlorideNaCl
0.05 %NP40
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 10995 / Average exposure time: 7.0 sec. / Average electron dose: 64.0 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: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
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

Final reconstructionApplied symmetry - Helical parameters - Δz: 19.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 46.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 296140
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 2890408 / Software - Name: cryoSPARC (ver. 4.4.0)
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Overall B value: 66.53
Output model

PDB-9tnz:
SP100 CARD filament

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