+
Open data
-
Basic information
Entry | Database: PDB / ID: 8b5r | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | p97-p37-SPI substrate complex | ||||||||||||
![]() |
| ||||||||||||
![]() | CHAPERONE / AAA+ ATPase / p97 / VCP / Cdc48 / unfoldase / protein phosphatase-1 / protein maturation | ||||||||||||
Function / homology | ![]() negative regulation of protein localization to centrosome / PTW/PP1 phosphatase complex / positive regulation of mitotic centrosome separation / regulation of nucleocytoplasmic transport / nuclear membrane reassembly / protein phosphatase regulator activity / protein phosphatase 1 binding / lamin binding / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process ...negative regulation of protein localization to centrosome / PTW/PP1 phosphatase complex / positive regulation of mitotic centrosome separation / regulation of nucleocytoplasmic transport / nuclear membrane reassembly / protein phosphatase regulator activity / protein phosphatase 1 binding / lamin binding / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / spindle pole centrosome / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / microtubule organizing center / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / myosin phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / protein-serine/threonine phosphatase / ubiquitin-specific protease binding / Triglyceride catabolism / Maturation of hRSV A proteins / ubiquitin-like protein ligase binding / entrainment of circadian clock by photoperiod / MHC class I protein binding / Golgi organization / phosphatase activity / establishment of mitotic spindle orientation / phosphoprotein phosphatase activity / cleavage furrow / blastocyst development / RHOH GTPase cycle / autophagosome maturation / autophagosome assembly / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / negative regulation of smoothened signaling pathway / enzyme regulator activity / ERAD pathway / ATP metabolic process / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / endoplasmic reticulum unfolded protein response / positive regulation of protein dephosphorylation / positive regulation of glial cell proliferation / Attachment and Entry / Resolution of Sister Chromatid Cohesion / lipid droplet / viral genome replication / proteasome complex / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / RHO GTPases Activate Formins / Hh mutants are degraded by ERAD / macroautophagy / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / RAF activation / Translesion Synthesis by POLH / circadian regulation of gene expression / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / neuron differentiation / regulation of circadian rhythm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å | ||||||||||||
![]() | van den Boom, J. / Marini, G. / Meyer, H. / Saibil, H. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural basis of ubiquitin-independent PP1 complex disassembly by p97. Authors: Johannes van den Boom / Guendalina Marini / Hemmo Meyer / Helen R Saibil / ![]() ![]() Abstract: The AAA+-ATPase p97 (also called VCP or Cdc48) unfolds proteins and disassembles protein complexes in numerous cellular processes, but how substrate complexes are loaded onto p97 and disassembled is ...The AAA+-ATPase p97 (also called VCP or Cdc48) unfolds proteins and disassembles protein complexes in numerous cellular processes, but how substrate complexes are loaded onto p97 and disassembled is unclear. Here, we present cryo-EM structures of p97 in the process of disassembling a protein phosphatase-1 (PP1) complex by extracting an inhibitory subunit from PP1. We show that PP1 and its partners SDS22 and inhibitor-3 (I3) are loaded tightly onto p97, surprisingly via a direct contact of SDS22 with the p97 N-domain. Loading is assisted by the p37 adapter that bridges two adjacent p97 N-domains underneath the substrate complex. A stretch of I3 is threaded into the central channel of the spiral-shaped p97 hexamer, while other elements of I3 are still attached to PP1. Thus, our data show how p97 arranges a protein complex between the p97 N-domain and central channel, suggesting a hold-and-extract mechanism for p97-mediated disassembly. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 672.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 458.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 111.3 KB | Display | |
Data in CIF | ![]() | 185.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15861MC C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 3 types, 8 molecules ABCDEFPS
#1: Protein | Mass: 90265.695 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | | Mass: 37030.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P36873, protein-serine/threonine phosphatase #4: Protein | | Mass: 41616.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|
-Protein/peptide , 1 types, 1 molecules I
#2: Protein/peptide | Mass: 1890.321 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|
-UBX domain-containing protein ... , 2 types, 2 molecules XY
#5: Protein/peptide | Mass: 1123.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q14CS0 |
---|---|
#6: Protein | Mass: 9759.220 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q14CS0 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: p97 complex with p37 adaptor and SPI substrate / Type: COMPLEX / Entity ID: #1-#4, #6, #5 / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 277 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3300 nm / Nominal defocus min: 1800 nm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-
Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191477 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||
Refine LS restraints |
|