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- EMDB-16794: Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3 -

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Basic information

Entry
Database: EMDB / ID: EMD-16794
TitleCryo-EM structure of the human GBP1 dimer bound to GDP-AlF3
Map dataPrimary map
Sample
  • Complex: Homodimeric complex of GBP1 stabilised by GDP-AlF3
    • Protein or peptide: Guanylate-binding protein 1
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: ALUMINUM FLUORIDEAluminium fluoride
  • Ligand: MAGNESIUM ION
KeywordsCell-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 interleukin-2 production ...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 interleukin-2 production / negative regulation of T cell receptor signaling pathway / spectrin binding / cytokine binding / defense response to protozoan / 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 / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKuhm TI / Jakobi AJ
Funding supportEuropean Union, Netherlands, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)852880European Union
Netherlands Organisation for Scientific Research (NWO)NWO.STU.018-2.007 Netherlands
CitationJournal: 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
DepositionMar 4, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16794.png

Downloads & links

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Map

FileDownload / File: emd_16794.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 328 pix.
= 273.552 Å		0.83 Å/pix.
x 328 pix.
= 273.552 Å		0.83 Å/pix.
x 328 pix.
= 273.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-2.143496 - 3.13021
Average (Standard dev.)0.00024753826 (±0.043452296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 273.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16794_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Locally sharpened map (LocScale)

Fileemd_16794_additional_1.map
AnnotationLocally sharpened map (LocScale)
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_16794_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_16794_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimeric complex of GBP1 stabilised by GDP-AlF3

EntireName: Homodimeric complex of GBP1 stabilised by GDP-AlF3
Components
  • Complex: Homodimeric complex of GBP1 stabilised by GDP-AlF3
    • Protein or peptide: Guanylate-binding protein 1
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: ALUMINUM FLUORIDEAluminium fluoride
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Homodimeric complex of GBP1 stabilised by GDP-AlF3

SupramoleculeName: Homodimeric complex of GBP1 stabilised by GDP-AlF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 134 KDa

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Macromolecule #1: Guanylate-binding protein 1

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.021617 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Macromolecule #3: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 3 / Number of copies: 2 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE / Aluminium fluoride

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / 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

Concentration0.7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chlorideSodium chloride
1.0 mMC4H10O2S2Dithiothreitol
200.0 uMC10H15N5O11P2Guanosine diphosphate
10.0 mMNaFSodium fluoride
300.0 uMAlCl3Aluminium chloride
5.0 mMMgCl2Magnesium chloride

Details: 5u mM HEPES pH7.4, 150 mM NaCl, 1 mM DTT, 200 uM GDP, 10 mM NaF, 300 uM AlCl3, 5 mM MgCl2
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 22 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 447651
Details: 447,651 particles were used to perform ab initio reconstruction to generate five different models. Three classes were selected for heterogeneous refinements without imposing symmetry. A ...Details: 447,651 particles were used to perform ab initio reconstruction to generate five different models. Three classes were selected for heterogeneous refinements without imposing symmetry. A single class with 147095 particles was used for non-uniform refinement.
Startup modelType of model: OTHER / Details: Startup model was generated ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 147095
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1fn5

chain_id: A, residue_range: 323-478, source_name: PDB, initial_model_type: experimental model

2b92

chain_id: A, residue_range: 6-304, source_name: PDB, initial_model_type: experimental model

2b92

chain_id: B, residue_range: 6-304, source_name: PDB, initial_model_type: experimental model
RefinementSpace: RECIPROCAL / Protocol: OTHER / Target criteria: Real-space cross correlation
Output model

PDB-8cqb:
Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3

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