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Open data
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Basic information
Entry | Database: PDB / ID: 6chs | ||||||
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Title | Cdc48-Npl4 complex in the presence of ATP-gamma-S | ||||||
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![]() | MOTOR PROTEIN / AAA+ / ERAD / zinc finger / ubiquitin-binding protein | ||||||
Function / homology | ![]() : / endoplasmic reticulum polarization => GO:0061163 / mitotic sister chromatid separation / mitotic spindle midzone / protein localization to Golgi apparatus / mitotic spindle disassembly / mRNA transport / ubiquitin binding / protein transport / ubiquitin-dependent protein catabolic process ...: / endoplasmic reticulum polarization => GO:0061163 / mitotic sister chromatid separation / mitotic spindle midzone / protein localization to Golgi apparatus / mitotic spindle disassembly / mRNA transport / ubiquitin binding / protein transport / ubiquitin-dependent protein catabolic process / nuclear membrane / cell division / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
![]() | Kim, K.H. / Bodnar, N.O. / Walz, T. / Rapoport, T.A. | ||||||
![]() | ![]() Title: Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4. Authors: Nicholas O Bodnar / Kelly H Kim / Zhejian Ji / Thomas E Wales / Vladimir Svetlov / Evgeny Nudler / John R Engen / Thomas Walz / Tom A Rapoport / ![]() Abstract: Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains ...Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains two stacked ATPase rings (D1 and D2) and six N-terminal (N) domains. Cdc48 binds various cofactors, including the Ufd1-Npl4 heterodimer. Here, we report structures of the Cdc48-Ufd1-Npl4 complex from Chaetomium thermophilum. Npl4 interacts through its UBX-like domain with a Cdc48 N domain, and it uses two Zn-finger domains to anchor the enzymatically inactive Mpr1-Pad1 N-terminal (MPN) domain, homologous to domains found in several isopeptidases, to the top of the D1 ATPase ring. The MPN domain of Npl4 is located above Cdc48's central pore, a position similar to the MPN domain from deubiquitinase Rpn11 in the proteasome. Our results indicate that Npl4 is unique among Cdc48 cofactors and suggest a mechanism for binding and translocation of polyubiquitinated substrates into the ATPase. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 758.3 KB | Display | ![]() |
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PDB format | ![]() | 616.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 108.8 KB | Display | |
Data in CIF | ![]() | 162.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7476MC ![]() 7477C ![]() 7478C ![]() 7479C ![]() 6cddC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 73880.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0009420 / Production host: ![]() ![]() | ||||||
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#2: Protein | Mass: 90432.516 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0027280 / Production host: ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-AGS / #5: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cdc48-Npl4/Ufd1 complex / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 15 sec. / Electron dose: 1.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 9299 |
Image scans | Movie frames/image: 50 |
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Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 808059 | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91883 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||
Refine LS restraints |
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