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Yorodumi- EMDB-22281: CryoEM structure of human presequence protease in partial closed ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22281 | |||||||||
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Title | CryoEM structure of human presequence protease in partial closed state 1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Partial open state / HYDROLASE | |||||||||
Function / homology | Function and homology information Mitochondrial protein import / protein targeting to mitochondrion / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases ...Mitochondrial protein import / protein targeting to mitochondrion / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / positive regulation of G2/M transition of mitotic cell cycle / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / presynaptic active zone / modulation of excitatory postsynaptic potential / regulation of peptidyl-tyrosine phosphorylation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / negative regulation of neuron differentiation / ECM proteoglycans / intracellular copper ion homeostasis / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / forebrain development / Notch signaling pathway / enzyme activator activity / neuron projection maintenance / positive regulation of protein metabolic process / positive regulation of calcium-mediated signaling / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / response to interleukin-1 / cholesterol metabolic process / positive regulation of mitotic cell cycle / extracellular matrix organization / adult locomotory behavior / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / learning / dendritic shaft / positive regulation of long-term synaptic potentiation / Mitochondrial protein degradation / central nervous system development / locomotory behavior / endosome lumen / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / visual learning / neuromuscular junction / positive regulation of non-canonical NF-kappaB signal transduction / recycling endosome / protein processing / metalloendopeptidase activity / cognition / G2/M transition of mitotic cell cycle / Golgi lumen / positive regulation of inflammatory response / neuron cellular homeostasis / positive regulation of interleukin-6 production / cellular response to amyloid-beta / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Liang WG / Zhao M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition. Authors: Wenguang G Liang / Juwina Wijaya / Hui Wei / Alex J Noble / Jordan M Mancl / Swansea Mo / David Lee / John V Lin King / Man Pan / Chang Liu / Carla M Koehler / Minglei Zhao / Clinton S ...Authors: Wenguang G Liang / Juwina Wijaya / Hui Wei / Alex J Noble / Jordan M Mancl / Swansea Mo / David Lee / John V Lin King / Man Pan / Chang Liu / Carla M Koehler / Minglei Zhao / Clinton S Potter / Bridget Carragher / Sheng Li / Wei-Jen Tang / Abstract: Presequence protease (PreP), a 117 kDa mitochondrial M16C metalloprotease vital for mitochondrial proteostasis, degrades presequence peptides cleaved off from nuclear-encoded proteins and other ...Presequence protease (PreP), a 117 kDa mitochondrial M16C metalloprotease vital for mitochondrial proteostasis, degrades presequence peptides cleaved off from nuclear-encoded proteins and other aggregation-prone peptides, such as amyloid β (Aβ). PreP structures have only been determined in a closed conformation; thus, the mechanisms of substrate binding and selectivity remain elusive. Here, we leverage advanced vitrification techniques to overcome the preferential denaturation of one of two ~55 kDa homologous domains of PreP caused by air-water interface adsorption. Thereby, we elucidate cryoEM structures of three apo-PreP open states along with Aβ- and citrate synthase presequence-bound PreP at 3.3-4.6 Å resolution. Together with integrative biophysical and pharmacological approaches, these structures reveal the key stages of the PreP catalytic cycle and how the binding of substrates or PreP inhibitor drives a rigid body motion of the protein for substrate binding and catalysis. Together, our studies provide key mechanistic insights into M16C metalloproteases for future therapeutic innovations. | |||||||||
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_22281.map.gz | 49.6 MB | EMDB map data format | |
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Header (meta data) | emd-22281-v30.xml emd-22281.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22281_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_22281.png | 164.8 KB | ||
Masks | emd_22281_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-22281.cif.gz | 6.2 KB | ||
Others | emd_22281_additional_1.map.gz emd_22281_half_map_1.map.gz emd_22281_half_map_2.map.gz | 59.9 MB 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22281 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22281 | HTTPS FTP |
-Validation report
Summary document | emd_22281_validation.pdf.gz | 957.6 KB | Display | EMDB validaton report |
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Full document | emd_22281_full_validation.pdf.gz | 957.2 KB | Display | |
Data in XML | emd_22281_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_22281_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22281 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22281 | HTTPS FTP |
-Related structure data
Related structure data | 6xovMC 6xosC 6xotC 6xouC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10937 (Title: CryoEM of PreP prepared via Chameleon / Data size: 2.2 TB / Data #1: Apo-PreP micrographs [micrographs - multiframe] / Data #2: PreP half particles [micrographs - single frame] Data #3: Citrate synthase presequence bound PreP [micrographs - multiframe] Data #4: Amyloid beta bound PreP [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22281.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.855 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_22281_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_22281_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_22281_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_22281_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : CryoEM map of Human Presequence Protease in partial close state 1
Entire | Name: CryoEM map of Human Presequence Protease in partial close state 1 |
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Components |
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-Supramolecule #1: CryoEM map of Human Presequence Protease in partial close state 1
Supramolecule | Name: CryoEM map of Human Presequence Protease in partial close state 1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Presequence protease, mitochondrial
Macromolecule | Name: Presequence protease, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 114.901461 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MHHHHHHAAA CERALQYKLG DKIHGFTVNQ VTSVPELFLT AVKLTHDDTG ARYLHLARED TNNLFSVQFR TTPMDSTGVP HILEHTVLC GSQKYPCRDP FFKMLNRSLS TFMNAFTASD YTLYPFSTQN PKDFQNLLSV YLDATFFPCL RELDFWQEGW R LEHENPSD ...String: MHHHHHHAAA CERALQYKLG DKIHGFTVNQ VTSVPELFLT AVKLTHDDTG ARYLHLARED TNNLFSVQFR TTPMDSTGVP HILEHTVLC GSQKYPCRDP FFKMLNRSLS TFMNAFTASD YTLYPFSTQN PKDFQNLLSV YLDATFFPCL RELDFWQEGW R LEHENPSD PQTPLVFKGV VFNEMKGAFT DNERIFSQHL QNRLLPDHTY SVVSGGDPLC IPELTWEQLK QFHATHYHPS NA RFFTYGN FPLEQHLKQI HEEALSKFQK IEPSTVVPAQ TPWDKPREFQ ITCGPDSFAT DPSKQTTVSV SFLLPDITDT FEA FTLSLL SSLLTSGPNS PFYKALIESG LGTDFSPDVG YNGYTREAYF SVGLQGIVEK DIETVRSLID RTIDEVVEKG FEDD RIEAL LHKIEIQMKH QSTSFGLMLT SYIASCWNHD GDPVELLKLG NQLAKFRQCL QENPKFLQEK VKQYFKNNQH KLTLS MRPD DKYHEKQAQV EATKLKQKVE ALSPGDRQQI YEKGLELRSQ QSKPQDASCL PALKVSDIEP TIPVTELDVV LTAGDI PVQ YCAQPTNGMV YFRAFSSLNT LPEELRPYVP LFCSVLTKLG CGLLDYREQA QQIELKTGGM SASPHVLPDD SHMDTYE QG VLFSSLCLDR NLPDMMQLWS EIFNNPCFEE EEHFKVLVKM TAQELANGIP DSGHLYASIR AGRTLTPAGD LQETFSGM D QVRLMKRIAE MTDIKPILRK LPRIKKHLLN GDNMRCSVNA TPQQMPQTEK AVEDFLRSIG RSKKERRPVR PHTVEKPVP SSSGGDAHVP HGSQVIRKLV MEPTFKPWQM KTHFLMPFPV NYVGECIRTV PYTDPDHASL KILARLMTAK FLHTEIREKG GAYGGGAKL SHNGIFTLYS YRDPNTIETL QSFGKAVDWA KSGKFTQQDI DEAKLSVFST VDAPVAPSDK GMDHFLYGLS D EMKQAHRE QLFAVSHDKL LAVSDRYLGT GKSTHGLAIL GPENPKIAKD PSWIIR UniProtKB: Presequence protease, mitochondrial |
-Macromolecule #2: Amyloid-beta precursor protein
Macromolecule | Name: Amyloid-beta precursor protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 4.335852 KDa |
Sequence | String: DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV UniProtKB: Amyloid-beta precursor protein |
-Macromolecule #3: Amyloid-beta precursor protein
Macromolecule | Name: Amyloid-beta precursor protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 273.33 Da |
Sequence | String: (UNK)(UNK)(UNK) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.7 Details: 20 mM Tris, pH 7.7, 150 mM NaCl, 10mM KCl, 20 mM EDTA and 1 mM 2-mercaptoethanol |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 308 K / Instrument: SPOTITON |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 6.0 sec. / Average electron dose: 66.0 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |