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- PDB-6chs: Cdc48-Npl4 complex in the presence of ATP-gamma-S -

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Basic information

Entry
Database: PDB / ID: 6chs
TitleCdc48-Npl4 complex in the presence of ATP-gamma-S
Components
  • Npl4
  • Putative cell division control protein
KeywordsMOTOR PROTEIN / AAA+ / ERAD / zinc finger / ubiquitin-binding protein
Function / homologyAAA+ lid domain / CDC48 domain 2-like superfamily / CDC48, N-terminal subdomain / AAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / CDC48, domain 2 / AAA ATPase, CDC48 family / NPL4, zinc-binding putative / Nuclear pore localisation protein NPL4, C-terminal ...AAA+ lid domain / CDC48 domain 2-like superfamily / CDC48, N-terminal subdomain / AAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / CDC48, domain 2 / AAA ATPase, CDC48 family / NPL4, zinc-binding putative / Nuclear pore localisation protein NPL4, C-terminal / Aspartate decarboxylase-like domain superfamily / Vps4 oligomerisation, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Nuclear protein localization protein 4 / NPL4 family / MPN domain / MPN domain profile. / ATPase family associated with various cellular activities (AAA) / AAA-protein family signature. / Cell division protein 48 (CDC48), N-terminal domain / Cell division protein 48 (CDC48), domain 2 / NPL4 family, putative zinc binding region / Ubiquitin-like domain superfamily / Vps4 C terminal oligomerisation domain / establishment of endoplasmic reticulum localization involved in endoplasmic reticulum polarization at cell division site / SCF complex disassembly in response to cadmium stress / Cdc48p-Npl4p-Vms1p AAA ATPase complex / mitotic spindle disassembly / RQC complex / Doa10p ubiquitin ligase complex / endoplasmic reticulum membrane fusion / sterol regulatory element binding protein cleavage / cellular protein complex disassembly / ribophagy / stress-induced homeostatically regulated protein degradation pathway / ribosome-associated ubiquitin-dependent protein catabolic process / Hrd1p ubiquitin ligase ERAD-L complex / nuclear protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / cytoplasm protein quality control by the ubiquitin-proteasome system / sister chromatid biorientation / mitotic sister chromatid separation / positive regulation of histone H2B ubiquitination / molecular adaptor activity / mitotic spindle midzone / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein phosphatase regulator activity / piecemeal microautophagy of the nucleus / ER-associated misfolded protein catabolic process / VCP-NPL4-UFD1 AAA ATPase complex / protein localization to Golgi apparatus / nonfunctional rRNA decay / retrograde protein transport, ER to cytosol / ATP metabolic process / ubiquitin-dependent ERAD pathway / negative regulation of telomerase activity / ubiquitin binding / cytosolic large ribosomal subunit / positive regulation of protein localization to nucleus / ubiquitin-dependent protein catabolic process / ATPase activity / nuclear chromatin / cell division / ATP binding / identical protein binding / Uncharacterized protein / Putative cell division control protein
Function and homology information
Specimen sourceChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsKim, K.H. / Bodnar, N.O. / Walz, T. / Rapoport, T.A.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 22, 2018 / Release: Jul 4, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 4, 2018Structure modelrepositoryInitial release
1.1Jul 18, 2018Structure modelData collection / Database referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
1.2Jul 25, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: Npl4
H: Putative cell division control protein
I: Putative cell division control protein
J: Putative cell division control protein
D: Putative cell division control protein
E: Putative cell division control protein
F: Putative cell division control protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)623,17733
Polyers616,4757
Non-polymers6,70126
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide Npl4


Mass: 73880.391 Da / Num. of mol.: 1
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0009420 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0B4
#2: Protein/peptide
Putative cell division control protein / Cdc48


Mass: 90432.516 Da / Num. of mol.: 6
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0027280 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S6Y2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 12 / Formula: C10H16N5O12P3S
Comment: ATP-gamma-S (energy-carrying molecule analogue) *YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Formula: Mg / Magnesium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cdc48-Npl4/Ufd1 complex / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1,2 / Source: RECOMBINANT
Source (natural)Organism: Chaetomium thermophilum (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
150 mMHEPES1
2150 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
40.5 mMTCEP1
5100 uMATPgS1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 15 sec. / Electron dose: 1.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 9299
Image scansMovie frames/image: 50

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
9cryoSPARCinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 808059
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 91883 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00730952
ELECTRON MICROSCOPYf_angle_d0.93341904
ELECTRON MICROSCOPYf_dihedral_angle_d10.98019056
ELECTRON MICROSCOPYf_chiral_restr0.0534663
ELECTRON MICROSCOPYf_plane_restr0.0085529

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