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Yorodumi- PDB-7b7z: DeAMPylation complex of monomeric FICD and AMPylated BiP (state 1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b7z | ||||||
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Title | DeAMPylation complex of monomeric FICD and AMPylated BiP (state 1) | ||||||
Components |
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Keywords | HYDROLASE / FICD / Fic / HYPE / BiP / Grp78 / AMPylation / deAMPylation / deAMPylase / ER stress / Complex / adenylation / adenylylation / Hsp70 / chaperone / transferase | ||||||
Function / homology | Function and homology information protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / negative regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / protein adenylylation / regulation of IRE1-mediated unfolded protein response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / post-translational protein targeting to membrane, translocation / negative regulation of GTPase activity ...protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / negative regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / protein adenylylation / regulation of IRE1-mediated unfolded protein response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / post-translational protein targeting to membrane, translocation / negative regulation of GTPase activity / non-chaperonin molecular chaperone ATPase / response to unfolded protein / negative regulation of protein-containing complex assembly / Hsp70 protein binding / response to endoplasmic reticulum stress / ATP-dependent protein folding chaperone / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / melanosome / protein-folding chaperone binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Cricetulus griseus (Chinese hamster) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Perera, L.A. / Ron, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD. Authors: Perera, L.A. / Preissler, S. / Zaccai, N.R. / Prevost, S. / Devos, J.M. / Haertlein, M. / Ron, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b7z.cif.gz | 379 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b7z.ent.gz | 299.6 KB | Display | PDB format |
PDBx/mmJSON format | 7b7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/7b7z ftp://data.pdbj.org/pub/pdb/validation_reports/b7/7b7z | HTTPS FTP |
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-Related structure data
Related structure data | 7b80C 5o4pS 6i7lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules BA
#1: Protein | Mass: 57543.043 Da / Num. of mol.: 1 / Mutation: T229A, V461F Source method: isolated from a genetically manipulated source Details: Covalent modification of T518 with AMP moiety / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: HSPA5, GRP78, I79_019946 / Production host: Escherichia coli M15 (bacteria) References: UniProt: G3I8R9, non-chaperonin molecular chaperone ATPase |
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#2: Protein | Mass: 39383.984 Da / Num. of mol.: 1 / Mutation: L258D, H363A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FICD, HIP13, HYPE, UNQ3041/PRO9857 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q9BVA6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
-Non-polymers , 4 types, 963 molecules
#3: Chemical | ChemComp-AMP / |
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#4: Chemical | ChemComp-MES / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 10% PEG 4000 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→105.63 Å / Num. obs: 115633 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.299 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5639 / CC1/2: 0.585 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5O4P, 6I7L Resolution: 1.7→74.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.281 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.79 Å2 / Biso mean: 28.996 Å2 / Biso min: 10.56 Å2
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Refinement step | Cycle: final / Resolution: 1.7→74.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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