+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2319 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM of full-length p97-FAF1 protein complex | |||||||||
Map data | Reconstruction of full-length p97-FAF1 protein complex | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information positive regulation of protein catabolic process => GO:0045732 / RHOH GTPase cycle / HSF1 activation / : / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Ovarian tumor domain proteases ...positive regulation of protein catabolic process => GO:0045732 / RHOH GTPase cycle / HSF1 activation / : / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / cytoplasmic sequestering of NF-kappaB / cell death / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport / Neddylation / flavin adenine dinucleotide catabolic process / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / aggresome assembly / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / positive regulation of ATP biosynthetic process / regulation of synapse organization / positive regulation of DNA replication / ATPase complex / ubiquitin-specific protease binding / regulation of protein catabolic process / MHC class I protein binding / autophagosome maturation / NF-kappaB binding / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / regulation of cell adhesion / translesion synthesis / interstrand cross-link repair / ERAD pathway / ATP metabolic process / negative regulation of smoothened signaling pathway / heat shock protein binding / Neutrophil degranulation / proteasome complex / viral genome replication / lipid droplet / ubiquitin binding / macroautophagy / positive regulation of protein-containing complex assembly / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / autophagy / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / nuclear envelope / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / site of double-strand break / cellular response to heat / protein phosphatase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein domain specific binding / DNA repair / DNA damage response / ubiquitin protein ligase binding / lipid binding / glutamatergic synapse / synapse / endoplasmic reticulum membrane / protein-containing complex binding / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.0 Å | |||||||||
Authors | Ewens CA / Kloppsteck P / McKeown C / Ebong I-O / Robinson C / Zhang X / Freemont P | |||||||||
Citation | Journal: J Biol Chem / Year: 2014 Title: The p97-FAF1 protein complex reveals a common mode of p97 adaptor binding. Authors: Caroline A Ewens / Silvia Panico / Patrik Kloppsteck / Ciaran McKeown / Ima-Obong Ebong / Carol Robinson / Xiaodong Zhang / Paul S Freemont / Abstract: p97, also known as valosin-containing protein, is a versatile participant in the ubiquitin-proteasome system. p97 interacts with a large network of adaptor proteins to process ubiquitylated ...p97, also known as valosin-containing protein, is a versatile participant in the ubiquitin-proteasome system. p97 interacts with a large network of adaptor proteins to process ubiquitylated substrates in different cellular pathways, including endoplasmic reticulum-associated degradation and transcription factor activation. p97 and its adaptor Fas-associated factor-1 (FAF1) both have roles in the ubiquitin-proteasome system during NF-κB activation, although the mechanisms are unknown. FAF1 itself also has emerging roles in other cell-cycle pathways and displays altered expression levels in various cancer cell lines. We have performed a detailed study the p97-FAF1 interaction. We show that FAF1 binds p97 stably and in a stoichiometry of 3 to 6. Cryo-EM analysis of p97-FAF1 yielded a 17 Å reconstruction of the complex with FAF1 above the p97 ring. Characteristics of p97-FAF1 uncovered in this study reveal common features in the interactions of p97, providing mechanistic insight into how p97 mediates diverse functionalities. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2319.map.gz | 798.8 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2319-v30.xml emd-2319.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | 2319-for-emdb-2.png | 78.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2319 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2319 | HTTPS FTP |
-Validation report
Summary document | emd_2319_validation.pdf.gz | 191.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_2319_full_validation.pdf.gz | 191 KB | Display | |
Data in XML | emd_2319_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2319 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2319 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_2319.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of full-length p97-FAF1 protein complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.52 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Full-length p97-FAF1
Entire | Name: Full-length p97-FAF1 |
---|---|
Components |
|
-Supramolecule #1000: Full-length p97-FAF1
Supramolecule | Name: Full-length p97-FAF1 / type: sample / ID: 1000 Oligomeric state: One hexamer of p97 bound to one trimer of FAF1 Number unique components: 2 |
---|---|
Molecular weight | Theoretical: 780 KDa / Method: Theoretical |
-Macromolecule #1: p97
Macromolecule | Name: p97 / type: protein_or_peptide / ID: 1 / Name.synonym: VCP / Details: full-length, wild-type / Number of copies: 1 / Oligomeric state: hexamer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) / synonym: House Mouse |
Molecular weight | Experimental: 550 KDa / Theoretical: 550 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta 2 / Recombinant plasmid: PET28b |
Sequence | UniProtKB: Transitional endoplasmic reticulum ATPase |
-Macromolecule #2: Fas-associated factor 1
Macromolecule | Name: Fas-associated factor 1 / type: protein_or_peptide / ID: 2 / Details: N-terminally His6-tagged, full-length, wild-type / Number of copies: 1 / Oligomeric state: trimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) / synonym: House Mouse |
Molecular weight | Theoretical: 230 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta2 / Recombinant plasmid: pProEx |
Sequence | UniProtKB: FAS-associated factor 1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
---|---|
Buffer | pH: 7.4 / Details: 20mM HEPES, 150mM KCl |
Grid | Details: holey carbon, quantifoil, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: 3sec blot, 0sec drain |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
---|---|
Temperature | Min: 94 K / Max: 104 K / Average: 94 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Date | Dec 20, 2011 |
Image recording | Category: CCD / Film or detector model: GENERIC TVIPS / Digitization - Sampling interval: 1.76 µm / Number real images: 281 / Average electron dose: 10 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.1 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: each micrograph |
---|---|
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: Imagic / Number images used: 4500 |
Final angle assignment | Details: Imagic |
Final two d classification | Number classes: 457 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: a |
---|---|
Software | Name: chimera, WEDA |
Details | domains were separately fitted and taking account of symmetry |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: a / Chain - #1 - Chain ID: b |
---|---|
Software | Name: chimera, WEDA |
Details | domains were separately fitted and taking account of symmetry |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |