+Open data
-Basic information
Entry | Database: PDB / ID: 7brq | ||||||||||||
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Title | Crystal structure of human FAM134B LIR fused to human GABARAP | ||||||||||||
Components | Reticulophagy regulator 1,Gamma-aminobutyric acid receptor-associated protein | ||||||||||||
Keywords | MEMBRANE PROTEIN / autophagy / endoplasmic reticulum | ||||||||||||
Function / homology | Function and homology information endoplasmic reticulum-autophagosome adaptor activity / : / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / cis-Golgi network / phosphatidylethanolamine binding / endoplasmic reticulum organization / cellular response to nitrogen starvation / TBC/RABGAPs ...endoplasmic reticulum-autophagosome adaptor activity / : / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / cis-Golgi network / phosphatidylethanolamine binding / endoplasmic reticulum organization / cellular response to nitrogen starvation / TBC/RABGAPs / reticulophagy / white fat cell differentiation / microtubule associated complex / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / mitophagy / extrinsic apoptotic signaling pathway via death domain receptors / collagen catabolic process / autophagosome assembly / autophagosome / smooth endoplasmic reticulum / protein targeting / sperm midpiece / sensory perception of pain / microtubule cytoskeleton organization / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / negative regulation of neuron apoptotic process / microtubule / lysosome / nuclear body / Golgi membrane / ubiquitin protein ligase binding / synapse / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.404 Å | ||||||||||||
Authors | Yamasaki, A. / Noda, N.N. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Nat Commun / Year: 2020 Title: Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes. Authors: Mochida, K. / Yamasaki, A. / Matoba, K. / Kirisako, H. / Noda, N.N. / Nakatogawa, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7brq.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7brq.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 7brq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7brq_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 7brq_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 7brq_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 7brq_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/7brq ftp://data.pdbj.org/pub/pdb/validation_reports/br/7brq | HTTPS FTP |
-Related structure data
Related structure data | 7brnC 7brtC 7bruC 1gnuS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 16118.130 Da / Num. of mol.: 1 / Mutation: F3S,V4T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAM134B, GABARAP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H6L5, UniProt: O95166 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1.91 M ammonium sulfate, 0.1 M sodium citrate pH 5.5, 0.18 M potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.404→40.95 Å / Num. obs: 24609 / % possible obs: 97.71 % / Redundancy: 9.7 % / Biso Wilson estimate: 20.05 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07419 / Rpim(I) all: 0.02491 / Rrim(I) all: 0.07837 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.404→1.454 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.6313 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 2058 / CC1/2: 0.755 / CC star: 0.928 / Rpim(I) all: 0.2538 / Rrim(I) all: 0.6831 / % possible all: 82.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GNU Resolution: 1.404→40.946 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.46 Å2 / Biso mean: 30.2026 Å2 / Biso min: 9.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.404→40.946 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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