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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24529 | |||||||||
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Title | Cryo-EM structure of human p97-D592N mutant bound to ADP. | |||||||||
![]() | Cryo-EM structure of human p97-D592N bound to ADP. | |||||||||
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![]() | p97 / VCP / TERA / Inhibitor / CB-5083 / HYDROLASE | |||||||||
Function / homology | ![]() : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / cytoplasm protein quality control / Derlin-1 retrotranslocation complex ...: / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / cytoplasm protein quality control / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / positive regulation of oxidative phosphorylation / : / aggresome assembly / mitotic spindle disassembly / deubiquitinase activator activity / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / negative regulation of protein localization to chromatin / vesicle-fusing ATPase / positive regulation of mitochondrial membrane potential / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / translesion synthesis / interstrand cross-link repair / proteasomal protein catabolic process / Protein methylation / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / Josephin domain DUBs / ERAD pathway / lipid droplet / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / proteasome complex / viral genome replication / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / negative regulation of smoothened signaling pathway / macroautophagy / positive regulation of protein-containing complex assembly / ABC-family proteins mediated transport / establishment of protein localization / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / autophagy / Aggrephagy / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / cytoplasmic stress granule / positive regulation of protein catabolic process / azurophil granule lumen / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / double-strand break repair / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / ciliary basal body / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / lipid binding / DNA damage response / endoplasmic reticulum membrane / Neutrophil degranulation / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / protein-containing complex / ATP hydrolysis activity / RNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Caffrey B / Zhu X | |||||||||
![]() | ![]() Title: AAA+ ATPase p97/VCP mutants and inhibitor binding disrupt inter-domain coupling and subsequent allosteric activation. Authors: Brian Caffrey / Xing Zhu / Alison Berezuk / Katharine Tuttle / Sagar Chittori / Sriram Subramaniam / ![]() Abstract: The human AAA+ ATPase p97, also known as valosin-containing protein, a potential target for cancer therapeutics, plays a vital role in the clearing of misfolded proteins. p97 dysfunction is also ...The human AAA+ ATPase p97, also known as valosin-containing protein, a potential target for cancer therapeutics, plays a vital role in the clearing of misfolded proteins. p97 dysfunction is also known to play a crucial role in several neurodegenerative disorders, such as MultiSystem Proteinopathy 1 (MSP-1) and Familial Amyotrophic Lateral Sclerosis (ALS). However, the structural basis of its role in such diseases remains elusive. Here, we present cryo-EM structural analyses of four disease mutants p97, p97, p97, p97, as well as p97, implicated in resistance to the drug CB-5083, a potent p97 inhibitor. Our cryo-EM structures demonstrate that these mutations affect nucleotide-driven allosteric activation across the three principal p97 domains (N, D1, and D2) by predominantly interfering with either (1) the coupling between the D1 and N-terminal domains (p97 and p97), (2) the interprotomer interactions (p97), or (3) the coupling between D1 and D2 nucleotide domains (p97, p97). We also show that binding of the competitive inhibitor, CB-5083, to the D2 domain prevents conformational changes similar to those seen for mutations that affect coupling between the D1 and D2 domains. Our studies enable tracing of the path of allosteric activation across p97 and establish a common mechanistic link between active site inhibition and defects in allosteric activation by disease-causing mutations and have potential implications for the design of novel allosteric compounds that can modulate p97 function. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 32.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.7 KB 11.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.7 KB | Display | ![]() |
Images | ![]() | 53 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 515.5 KB | Display | ![]() |
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Full document | ![]() | 515.1 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rlgMC ![]() 7rl6C ![]() 7rl7C ![]() 7rl9C ![]() 7rlaC ![]() 7rlbC ![]() 7rlcC ![]() 7rldC ![]() 7rlfC ![]() 7rlhC ![]() 7rliC ![]() 7rljC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM structure of human p97-D592N bound to ADP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.296 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Full-length Hexameric p97-D592N mutant.
Entire | Name: Full-length Hexameric p97-D592N mutant. |
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Components |
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-Supramolecule #1: Full-length Hexameric p97-D592N mutant.
Supramolecule | Name: Full-length Hexameric p97-D592N mutant. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 540 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: ![]() |
Molecular weight | Theoretical: 91.230664 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: HHHHHHGTSE NLYFQGASGA DSKGDDLSTA ILKQKNRPNR LIVDEAINED NSVVSLSQPK MDELQLFRGD TVLLKGKKRR EAVCIVLSD DTCSDEKIRM NRVVRNNLRV RLGDVISIQP CPDVKYGKRI HVLPIDDTVE GITGNLFEVY LKPYFLEAYR P IRKGDIFL ...String: HHHHHHGTSE NLYFQGASGA DSKGDDLSTA ILKQKNRPNR LIVDEAINED NSVVSLSQPK MDELQLFRGD TVLLKGKKRR EAVCIVLSD DTCSDEKIRM NRVVRNNLRV RLGDVISIQP CPDVKYGKRI HVLPIDDTVE GITGNLFEVY LKPYFLEAYR P IRKGDIFL VRGGMRAVEF KVVETDPSPY CIVAPDTVIH CEGEPIKRED EEESLNEVGY DDIGGCRKQL AQIKEMVELP LR HPALFKA IGVKPPRGIL LYGPPGTGKT LIARAVANET GAFFFLINGP EIMSKLAGES ESNLRKAFEE AEKNAPAIIF IDE LDAIAP KREKTHGEVE RRIVSQLLTL MDGLKQRAHV IVMAATNRPN SIDPALRRFG RFDREVDIGI PDATGRLEIL QIHT KNMKL ADDVDLEQVA NETHGHVGAD LAALCSEAAL QAIRKKMDLI DLEDETIDAE VMNSLAVTMD DFRWALSQSN PSALR ETVV EVPQVTWEDI GGLEDVKREL QELVQYPVEH PDKFLKFGMT PSKGVLFYGP PGCGKTLLAK AIANECQANF ISIKGP ELL TMWFGESEAN VREIFDKARQ AAPCVLFFDE LDSIAKARGG NIGNGGGAAD RVINQILTEM DGMSTKKNVF IIGATNR PD IIDPAILRPG RLDQLIYIPL PDEKSRVAIL KANLRKSPVA KDVDLEFLAK MTNGFSGADL TEICQRACKL AIRESIES E IRRERERQTN PSAMEVEEDD PVPEIRRDHF EEAMRFARRS VSDNDIRKYE MFAQTLQQSR GFGSFRFPSG NQGGAGPSQ GSGGGTGGSV YTEDNDDDLY G UniProtKB: Transitional endoplasmic reticulum ATPase |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | 2D array |
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Sample preparation
Concentration | 2 mg/mL | |||||||||||||||||||||
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Buffer | pH: 8 Component:
Details: Protein Storage Buffer with ADP. | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 6940 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |