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Yorodumi- EMDB-22282: CryoEM structure of human presequence protease in partial close s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22282 | |||||||||
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Title | CryoEM structure of human presequence protease in partial close state 2, induced by presequence of citrate synthase | |||||||||
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 / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / enzyme activator activity / protein processing / metalloendopeptidase activity / metallopeptidase activity / mitochondrial matrix / mitochondrion / proteolysis / zinc ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Liang WG / Tang W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: CryoEM structure of human presequence protease in partial open state 2, induced by presequence of citrate synthase Authors: Liang WG / Zhao M / Tang W | |||||||||
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_22282.map.gz | 2.4 MB | EMDB map data format | |
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Header (meta data) | emd-22282-v30.xml emd-22282.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22282_fsc.xml | 3.5 KB | Display | FSC data file |
Images | emd_22282.png | 108.9 KB | ||
Masks | emd_22282_msk_1.map | 3.4 MB | Mask map | |
Filedesc metadata | emd-22282.cif.gz | 5.7 KB | ||
Others | emd_22282_additional_1.map.gz emd_22282_half_map_1.map.gz emd_22282_half_map_2.map.gz | 3.2 MB 2.4 MB 2.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22282 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22282 | HTTPS FTP |
-Related structure data
Related structure data | 6xowMC M: atomic model generated by this map C: citing same article (ref.) |
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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_22282.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.71 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_22282_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_22282_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_22282_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_22282_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CryoEM map of Human Presequence Protease in partial close state 2...
Entire | Name: CryoEM map of Human Presequence Protease in partial close state 2, induced by presequence of citrate synthase |
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Components |
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-Supramolecule #1: CryoEM map of Human Presequence Protease in partial close state 2...
Supramolecule | Name: CryoEM map of Human Presequence Protease in partial close state 2, induced by presequence of citrate synthase 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 |
-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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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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |