+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24302 | |||||||||
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Title | p47-bound p97-R155H mutant with ATPgammaS | |||||||||
Map data | p47-bound p97-R155H mutant with ATPgammaS | |||||||||
Sample |
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Keywords | AAA+ ATPase / MOTOR PROTEIN / HYDROLASE / HYDROLASE-Lipid Binding Protein complex | |||||||||
Function / homology | Function and homology information negative regulation of protein localization to centrosome / RHOH GTPase cycle / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / positive regulation of Lys63-specific deubiquitinase activity / Golgi stack / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair ...negative regulation of protein localization to centrosome / RHOH GTPase cycle / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / positive regulation of Lys63-specific deubiquitinase activity / Golgi stack / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / 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 / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / MHC class I protein binding / Golgi organization / establishment of mitotic spindle orientation / RHOH GTPase cycle / autophagosome maturation / autophagosome assembly / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ERAD pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / viral genome replication / proteasome complex / lipid droplet / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / Hh mutants are degraded by ERAD / macroautophagy / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / ADP binding / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / chromosome / Neddylation / site of double-strand break / cellular response to heat / ATPase binding / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / membrane fusion / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.23 Å | |||||||||
Authors | Nandi P / Li S | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Int J Mol Sci / Year: 2021 Title: Structural and Functional Analysis of Disease-Linked p97 ATPase Mutant Complexes. Authors: Purbasha Nandi / Shan Li / Rod Carlo A Columbres / Feng Wang / Dewight R Williams / Yu-Ping Poh / Tsui-Fen Chou / Po-Lin Chiu / Abstract: IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase ...IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase malfunction remains unclear. To understand how the mutation alters the ATPase regulation, we assembled a full-length p97 with its p47 cofactor and first visualized their structures using single-particle cryo-EM. More than one-third of the population was the dodecameric form. Nucleotide presence dissociates the dodecamer into two hexamers for its highly elevated function. The N-domains of the p97 mutant all show up configurations in ADP- or ATPS-bound states. Our functional and structural analyses showed that the p47 binding is likely to impact the p97 ATPase activities via changing the conformations of arginine fingers. These functional and structural analyses underline the ATPase dysregulation with the miscommunication between the functional modules of the p97. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24302.map.gz | 49.8 MB | EMDB map data format | |
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Header (meta data) | emd-24302-v30.xml emd-24302.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_24302.png | 74.7 KB | ||
Filedesc metadata | emd-24302.cif.gz | 6.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24302 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24302 | HTTPS FTP |
-Validation report
Summary document | emd_24302_validation.pdf.gz | 538.6 KB | Display | EMDB validaton report |
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Full document | emd_24302_full_validation.pdf.gz | 538.2 KB | Display | |
Data in XML | emd_24302_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_24302_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24302 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24302 | HTTPS FTP |
-Related structure data
Related structure data | 7r7sMC 7l5wC 7l5xC 7r7tC 7r7uC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10920 (Title: Cryo-EM dataset of mutant p97R155H-p47 in presence of ATPγS collected using Thermo Fisher/FEI Titan Krios TEM Gatan K2 Summit DED camera Data size: 280.3 Data #1: Motion corrected dose-weighted micrographs for the cryo-EM dataset of disease mutant p97R155H-p47 in presence of ADP. [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24302.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | p47-bound p97-R155H mutant with ATPgammaS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.413 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : p47-bound p97-R155H mutant with ATPgammaS
Entire | Name: p47-bound p97-R155H mutant with ATPgammaS |
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Components |
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-Supramolecule #1: p47-bound p97-R155H mutant with ATPgammaS
Supramolecule | Name: p47-bound p97-R155H mutant with ATPgammaS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: p47-bound p97-R155H mutant with ATPgammaS |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 723 KDa |
-Macromolecule #1: Transitional endoplasmic reticulum ATPase
Macromolecule | Name: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 89.417773 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVHGGMR A VEFKVVET ...String: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVHGGMR A VEFKVVET DPSPYCIVAP DTVIHCEGEP IKREDEEESL NEVGYDDIGG CRKQLAQIKE MVELPLRHPA LFKAIGVKPP RG ILLYGPP GTGKTLIARA VANETGAFFF LINGPEIMSK LAGESESNLR KAFEEAEKNA PAIIFIDELD AIAPKREKTH GEV ERRIVS QLLTLMDGLK QRAHVIVMAA TNRPNSIDPA LRRFGRFDRE VDIGIPDATG RLEILQIHTK NMKLADDVDL EQVA NETHG HVGADLAALC SEAALQAIRK KMDLIDLEDE TIDAEVMNSL AVTMDDFRWA LSQSNPSALR ETVVEVPQVT WEDIG GLED VKRELQELVQ YPVEHPDKFL KFGMTPSKGV LFYGPPGCGK TLLAKAIANE CQANFISIKG PELLTMWFGE SEANVR EIF DKARQAAPCV LFFDELDSIA KARGGNIGDG GGAADRVINQ ILTEMDGMST KKNVFIIGAT NRPDIIDPAI LRPGRLD QL IYIPLPDEKS RVAILKANLR KSPVAKDVDL EFLAKMTNGF SGADLTEICQ RACKLAIRES IESEIRRERE RQTNPSAM E VEEDDPVPEI RRDHFEEAMR FARRSVSDND IRKYEMFAQT LQQSRGFGSF RFPSGNQGGA GPSQGSGGGT GGSVYTEDN DDDLYG UniProtKB: Transitional endoplasmic reticulum ATPase |
-Macromolecule #2: NSFL1 cofactor p47
Macromolecule | Name: NSFL1 cofactor p47 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 40.731855 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAEERQDALR EFVAVTGAEE DRARFFLESA GWDLQIALAS FYEDGGDEDI VTISQATPSS VSRGTAPSDN RVTSFRDLIH DQDEEEEEE EGQRFYAGGS ERSGQQIVGP PRKKSPNELV DDLFKGAKEH GAVAVERVTK SPGETSKPRP FAGGGYRLGA A PEEESAYV ...String: MAEERQDALR EFVAVTGAEE DRARFFLESA GWDLQIALAS FYEDGGDEDI VTISQATPSS VSRGTAPSDN RVTSFRDLIH DQDEEEEEE EGQRFYAGGS ERSGQQIVGP PRKKSPNELV DDLFKGAKEH GAVAVERVTK SPGETSKPRP FAGGGYRLGA A PEEESAYV AGERRRHSGQ DVHVVLKLWK TGFSLDNGDL RSYQDPSNAQ FLESIRRGEV PAELRRLAHG GQVNLDMEDH RD EDFVKPK GAFKAFTGEG QKLGSTAPQV LNTSSPAQQA ENEAKASSSI LINEAEPTTN IQIRLADGGR LVQKFNHSHR ISD IRLFIV DARPAMAATS FVLMTTFPNK ELADENQTLK EANLLNAVIV QRLT UniProtKB: NSFL1 cofactor p47 |
-Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 12 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: C-flat-2/1 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 292 K / Instrument: FEI VITROBOT MARK IV / Details: The grid was blotted for 6 seconds.. | ||||||||||||
Details | The protein sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Coma free - Residual tilt: 0.001 mrad |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 2796 / Average electron dose: 44.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 48077 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |