+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24518 | |||||||||
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Title | Cryo-EM structure of human p97-R155H mutant bound to ADP. | |||||||||
Map data | Cryo-EM structure of human full-length p97-R155H mutant bound to ADP. | |||||||||
Sample |
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Keywords | p97 / VCP / TERA / Inhibitor / CB-5083 / HYDROLASE | |||||||||
Function / homology | Function and homology information positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding ...positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / aggresome assembly / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / regulation of synapse organization / positive regulation of ATP biosynthetic process / ubiquitin-specific protease binding / ATPase complex / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / HSF1 activation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / proteasomal protein catabolic process / translesion synthesis / Protein methylation / interstrand cross-link repair / ATP metabolic process / negative regulation of smoothened signaling pathway / ERAD pathway / endoplasmic reticulum unfolded protein response / Attachment and Entry / proteasome complex / viral genome replication / lipid droplet / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / positive regulation of protein-containing complex assembly / ADP binding / Translesion Synthesis by POLH / establishment of protein localization / ABC-family proteins mediated transport / : / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / positive regulation of canonical Wnt signaling pathway / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / 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 / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / lipid binding / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Caffrey B / Zhu X / Berezuk A / Tuttle K / Chittori S / Subramaniam S | |||||||||
Citation | Journal: J Biol Chem / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24518.map.gz | 31.7 MB | EMDB map data format | |
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Header (meta data) | emd-24518-v30.xml emd-24518.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24518_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_24518.png | 60.3 KB | ||
Filedesc metadata | emd-24518.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24518 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24518 | HTTPS FTP |
-Validation report
Summary document | emd_24518_validation.pdf.gz | 499.6 KB | Display | EMDB validaton report |
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Full document | emd_24518_full_validation.pdf.gz | 499.1 KB | Display | |
Data in XML | emd_24518_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_24518_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24518 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24518 | HTTPS FTP |
-Related structure data
Related structure data | 7rl6MC 7rl7C 7rl9C 7rlaC 7rlbC 7rlcC 7rldC 7rlfC 7rlgC 7rlhC 7rliC 7rljC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24518.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of human full-length p97-R155H mutant bound to ADP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0125 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 : Full-length Hexameric p97-R155H mutant
Entire | Name: Full-length Hexameric p97-R155H mutant |
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Components |
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-Supramolecule #1: Full-length Hexameric p97-R155H mutant
Supramolecule | Name: Full-length Hexameric p97-R155H mutant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
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: Homo sapiens (human) |
Molecular weight | Theoretical: 91.472969 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKHHHHHHGT SENLYFQGAS GADSKGDDLS TAILKQKNRP NRLIVDEAIN EDNSVVSLSQ PKMDELQLFR GDTVLLKGKK RREAVCIVL SDDTCSDEKI RMNRVVRNNL RVRLGDVISI QPCPDVKYGK RIHVLPIDDT VEGITGNLFE VYLKPYFLEA Y RPIRKGDI ...String: MKHHHHHHGT SENLYFQGAS GADSKGDDLS TAILKQKNRP NRLIVDEAIN EDNSVVSLSQ PKMDELQLFR GDTVLLKGKK RREAVCIVL SDDTCSDEKI RMNRVVRNNL RVRLGDVISI QPCPDVKYGK RIHVLPIDDT VEGITGNLFE VYLKPYFLEA Y RPIRKGDI FLVHGGMRAV EFKVVETDPS PYCIVAPDTV IHCEGEPIKR EDEEESLNEV GYDDIGGCRK QLAQIKEMVE LP LRHPALF KAIGVKPPRG ILLYGPPGTG KTLIARAVAN ETGAFFFLIN GPEIMSKLAG ESESNLRKAF EEAEKNAPAI IFI DELDAI APKREKTHGE VERRIVSQLL TLMDGLKQRA HVIVMAATNR PNSIDPALRR FGRFDREVDI GIPDATGRLE ILQI HTKNM KLADDVDLEQ VANETHGHVG ADLAALCSEA ALQAIRKKMD LIDLEDETID AEVMNSLAVT MDDFRWALSQ SNPSA LRET VVEVPQVTWE DIGGLEDVKR ELQELVQYPV EHPDKFLKFG MTPSKGVLFY GPPGCGKTLL AKAIANECQA NFISIK GPE LLTMWFGESE ANVREIFDKA RQAAPCVLFF DELDSIAKAR GGNIGDGGGA ADRVINQILT EMDGMSTKKN VFIIGAT NR PDIIDPAILR PGRLDQLIYI PLPDEKSRVA ILKANLRKSP VAKDVDLEFL AKMTNGFSGA DLTEICQRAC KLAIRESI E SEIRRERERQ TNPSAMEVEE DDPVPEIRRD HFEEAMRFAR RSVSDNDIRK YEMFAQTLQQ SRGFGSFRFP SGNQGGAGP SQGSGGGTGG SVYTEDNDDD LYG 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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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Concentration | 2 mg/mL | |||||||||||||||||||||
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Buffer | pH: 8 Component:
Details: Protein Storage Buffer with ADP. | |||||||||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 4410 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |