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Yorodumi- PDB-7fgm: The complex crystals structure of the FAF1 UBL1_L-Hsp70 NBD with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fgm | ||||||
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Title | The complex crystals structure of the FAF1 UBL1_L-Hsp70 NBD with ADP and phosphate | ||||||
Components |
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Keywords | CHAPERONE/INHIBITOR / CHAPERONE-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information ooplasm / positive regulation of endoribonuclease activity / denatured protein binding / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / cytoplasmic sequestering of NF-kappaB / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus ...ooplasm / positive regulation of endoribonuclease activity / denatured protein binding / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / cytoplasmic sequestering of NF-kappaB / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / regulation of protein catabolic process / mRNA catabolic process / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / NF-kappaB binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / cellular response to unfolded protein / regulation of cell adhesion / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / ATP metabolic process / protein folding chaperone / inclusion body / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / positive regulation of DNA replication / ubiquitin binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of interleukin-8 production / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / positive regulation of protein catabolic process / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nuclear envelope / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / blood microparticle / protein stabilization / nuclear speck / ribonucleoprotein complex / cadherin binding / positive regulation of apoptotic process / protein domain specific binding / negative regulation of cell population proliferation / focal adhesion / signaling receptor binding / centrosome / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kim, E.E. / ParK, J.K. / Shin, S.C. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: J Mol Cell Biol / Year: 2022 Title: The complex of Fas-associated factor 1 with Hsp70 stabilizes the adherens junction integrity by suppressing RhoA activation Authors: Song, S. / Park, J.K. / Shin, S.C. / Lee, J.J. / Hong, S.K. / Song, I.K. / Kim, B. / Song, E.J. / Lee, K.J. / Kim, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fgm.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fgm.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 7fgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fgm_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7fgm_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7fgm_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 7fgm_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/7fgm ftp://data.pdbj.org/pub/pdb/validation_reports/fg/7fgm | HTTPS FTP |
-Related structure data
Related structure data | 7fgnC 1s3xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 AB
#1: Protein | Mass: 42084.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSP72, HSPA1, HSX70 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DMV8 |
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#2: Protein | Mass: 9467.923 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAF1, UBXD12, UBXN3A, CGI-03 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNN5 |
-Non-polymers , 4 types, 357 molecules
#3: Chemical | ChemComp-ADP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-PO4 / |
#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: 3.81 Å3/Da / Density % sol: 67.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 200 mM Imidazole-malate pH 8.5 12 % PEG 10,000 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 14, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 40339 / % possible obs: 99.9 % / Redundancy: 16.3 % / Rmerge(I) obs: 0.098 / Χ2: 0.776 / Net I/σ(I): 7 / Num. measured all: 656487 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S3X Resolution: 2.2→30.763 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 17.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.22 Å2 / Biso mean: 24.6049 Å2 / Biso min: 9.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→30.763 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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