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Yorodumi- EMDB-23455: Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23455 | |||||||||
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Title | Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos in the presence of ATP and sub-stoichiometric NMS-873 (Class 3) | |||||||||
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Sample |
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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 / 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 / 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 / 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 / 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 / RHOH GTPase cycle / autophagosome maturation / 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 / lipid droplet / viral genome replication / proteasome complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / cytoplasmic stress granule / Aggrephagy / 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 / Neddylation / site of double-strand break / cellular response to heat / 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 / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / glutamatergic synapse / lipid binding / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.58 Å | |||||||||
Authors | Pan M / Yu Y / Liu L / Zhao M | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Mechanistic insight into substrate processing and allosteric inhibition of human p97. Authors: Man Pan / Yuanyuan Yu / Huasong Ai / Qingyun Zheng / Yuan Xie / Lei Liu / Minglei Zhao / Abstract: p97 processes ubiquitinated substrates and plays a central role in cellular protein homeostasis. Here, we report a series of cryo-EM structures of the substrate-engaged human p97 complex with ...p97 processes ubiquitinated substrates and plays a central role in cellular protein homeostasis. Here, we report a series of cryo-EM structures of the substrate-engaged human p97 complex with resolutions ranging from 2.9 to 3.8 Å that captured 'power-stroke'-like motions of both the D1 and D2 ATPase rings of p97. A key feature of these structures is the critical conformational changes of the intersubunit signaling (ISS) motifs, which tighten the binding of nucleotides and neighboring subunits and contribute to the spiral staircase conformation of the D1 and D2 rings. In addition, we determined the cryo-EM structure of human p97 in complex with NMS-873, a potent p97 inhibitor, at a resolution of 2.4 Å. The structures showed that NMS-873 binds at a cryptic groove in the D2 domain and interacts with the ISS motif, preventing its conformational change and thus blocking substrate translocation allosterically. | |||||||||
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_23455.map.gz | 97.9 MB | EMDB map data format | |
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Header (meta data) | emd-23455-v30.xml emd-23455.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23455_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_23455.png | 171.9 KB | ||
Masks | emd_23455_msk_1.map | 125 MB | Mask map | |
Others | emd_23455_additional_1.map.gz emd_23455_half_map_1.map.gz emd_23455_half_map_2.map.gz | 116.3 MB 98.4 MB 98.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23455 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23455 | HTTPS FTP |
-Validation report
Summary document | emd_23455_validation.pdf.gz | 541.9 KB | Display | EMDB validaton report |
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Full document | emd_23455_full_validation.pdf.gz | 541.5 KB | Display | |
Data in XML | emd_23455_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_23455_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23455 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23455 | HTTPS FTP |
-Related structure data
Related structure data | 7lmyC 7lmzC 7ln0C 7ln1C 7ln2C 7ln3C 7ln4C 7ln5C 7ln6C 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_23455.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23455_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_23455_additional_1.map | ||||||||||||
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-Half map: #2
File | emd_23455_half_map_1.map | ||||||||||||
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-Half map: #1
File | emd_23455_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos ...
Entire | Name: Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos in the presence of ATP and sub-stoichiometric NMS-873 |
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Components |
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-Supramolecule #1: Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos ...
Supramolecule | Name: Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos in the presence of ATP and sub-stoichiometric NMS-873 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
-Macromolecule #1: Human p97 (A232E/E578Q)
Macromolecule | Name: Human p97 (A232E/E578Q) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVC IVLSDDTCSD EKIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI D DTVEGITG NLFEVYLKPY FLEAYRPIRK GDIFLVRGGM RAVEFKVVET ...String: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVC IVLSDDTCSD EKIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI D DTVEGITG NLFEVYLKPY FLEAYRPIRK GDIFLVRGGM RAVEFKVVET DPSPYCIVAP DT VIHCEGE PIKREDEEES LNEVGYDDIG GCRKQLAQIK EMVELPLRHP ALFKEIGVKP PRG ILLYGP PGTGKTLIAR AVANETGAFF FLINGPEIMS KLAGESESNL RKAFEEAEKN APAI IFIDE LDAIAPKREK THGEVERRIV SQLLTLMDGL KQRAHVIVMA ATNRPNSIDP ALRRF GRFD REVDIGIPDA TGRLEILQIH TKNMKLADDV DLEQVANETH GHVGADLAAL CSEAAL QAI RKKMDLIDLE DETIDAEVMN SLAVTMDDFR WALSQSNPSA LRETVVEVPQ VTWEDIG GL EDVKRELQEL VQYPVEHPDK FLKFGMTPSK GVLFYGPPGC GKTLLAKAIA NECQANFI S IKGPELLTMW FGESEANVRE IFDKARQAAP CVLFFDQLDS IAKARGGNIG DGGGAADRV INQILTEMDG MSTKKNVFII GATNRPDIID PAILRPGRLD QLIYIPLPDE KSRVAILKAN LRKSPVAKD VDLEFLAKMT NGFSGADLTE ICQRACKLAI RESIESEIRR ERERQTNPSA M EVEEDDPV PEIRRDHFEE AMRFARRSVS DNDIRKYEMF AQTLQQSRGF GSFRFPSGNQ GG AGPSQGS GGGTGGSVYT EDNDDDLYG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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