+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16794 | |||||||||
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Title | Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3 | |||||||||
Map data | Primary map | |||||||||
Sample |
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Keywords | Cell-autonomous immunity / intracellular pathogens / GTPase / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of protein localization to plasma membrane / negative regulation of T cell receptor signaling pathway ...GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of protein localization to plasma membrane / negative regulation of T cell receptor signaling pathway / spectrin binding / negative regulation of interleukin-2 production / defense response to protozoan / cytokine binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cellular response to interleukin-1 / regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / G protein activity / lipopolysaccharide binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / cytoplasmic vesicle membrane / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / GDP binding / Interferon gamma signaling / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / defense response to virus / defense response to bacterium / Golgi membrane / innate immune response / GTPase activity / GTP binding / enzyme binding / Golgi apparatus / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Kuhm TI / Jakobi AJ | |||||||||
Funding support | European Union, Netherlands, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3 Authors: Kuhm TI / de Agrela Pinto C / Taisne C / Huber S / Giannopolou N / Pardon E / Steyaert J / Jakobi AJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16794.map.gz | 127.1 MB | EMDB map data format | |
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Header (meta data) | emd-16794-v30.xml emd-16794.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16794_fsc.xml | 10.9 KB | Display | FSC data file |
Images | emd_16794.png | 100.9 KB | ||
Masks | emd_16794_msk_1.map | 134.6 MB | Mask map | |
Filedesc metadata | emd-16794.cif.gz | 7.1 KB | ||
Others | emd_16794_additional_1.map.gz emd_16794_half_map_1.map.gz emd_16794_half_map_2.map.gz | 1.6 MB 124.9 MB 124.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16794 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16794 | HTTPS FTP |
-Validation report
Summary document | emd_16794_validation.pdf.gz | 811 KB | Display | EMDB validaton report |
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Full document | emd_16794_full_validation.pdf.gz | 810.6 KB | Display | |
Data in XML | emd_16794_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | emd_16794_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16794 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16794 | HTTPS FTP |
-Related structure data
Related structure data | 8cqbMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16794.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Primary map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.834 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16794_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Locally sharpened map (LocScale)
File | emd_16794_additional_1.map | ||||||||||||
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Annotation | Locally sharpened map (LocScale) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_16794_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_16794_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homodimeric complex of GBP1 stabilised by GDP-AlF3
Entire | Name: Homodimeric complex of GBP1 stabilised by GDP-AlF3 |
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Components |
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-Supramolecule #1: Homodimeric complex of GBP1 stabilised by GDP-AlF3
Supramolecule | Name: Homodimeric complex of GBP1 stabilised by GDP-AlF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 134 KDa |
-Macromolecule #1: Guanylate-binding protein 1
Macromolecule | Name: Guanylate-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 68.021617 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASEIHMTGP MCLIENTNGR LMANPEALKI LSAITQPMVV VAIVGLYRTG KSYLMNKLAG KKKGFSLGST VQSHTKGIWM WCVPHPKKP GHILVLLDTE GLGDVEKGDN QNDSWIFALA VLLSSTFVYN SIGTINQQAM DQLYYVTELT HRIRSKSSPD E NENEVEDS ...String: MASEIHMTGP MCLIENTNGR LMANPEALKI LSAITQPMVV VAIVGLYRTG KSYLMNKLAG KKKGFSLGST VQSHTKGIWM WCVPHPKKP GHILVLLDTE GLGDVEKGDN QNDSWIFALA VLLSSTFVYN SIGTINQQAM DQLYYVTELT HRIRSKSSPD E NENEVEDS ADFVSFFPDF VWTLRDFSLD LEADGQPLTP DEYLTYSLKL KKGTSQKDET FNLPRLCIRK FFPKKKCFVF DR PVHRRKL AQLEKLQDEE LDPEFVQQVA DFCSYIFSNS KTKTLSGGIQ VNGPRLESLV LTYVNAISSG DLPCMENAVL ALA QIENSA AVQKAIAHYE QQMGQKVQLP TETLQELLDL HRDSEREAIE VFIRSSFKDV DHLFQKELAA QLEKKRDDFC KQNQ EASSD RCSALLQVIF SPLEEEVKAG IYSKPGGYRL FVQKLQDLKK KYYEEPRKGI QAEEILQTYL KSKESMTDAI LQTDQ TLTE KEKEIEVERV KAESAQASAK MLQEMQRKNE QMMEQKERSY QEHLKQLTEK MENDRVQLLK EQERTLALKL QEQEQL LKE GFQKESRIMK NEIQDLQTKM RRRKACTIS UniProtKB: Guanylate-binding protein 1 |
-Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Macromolecule #3: ALUMINUM FLUORIDE
Macromolecule | Name: ALUMINUM FLUORIDE / type: ligand / ID: 3 / Number of copies: 2 / Formula: AF3 |
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Molecular weight | Theoretical: 83.977 Da |
Chemical component information | ChemComp-AF3: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 7.4 Component:
Details: 5u mM HEPES pH7.4, 150 mM NaCl, 1 mM DTT, 200 uM GDP, 10 mM NaF, 300 uM AlCl3, 5 mM MgCl2 | ||||||||||||||||||||||||
Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 22 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 5214 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: RECIPROCAL / Protocol: OTHER / Target criteria: Real-space cross correlation | ||||||||
Output model | PDB-8cqb: |