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- EMDB-31633: human Serine beta-lactamase-like protein LACTB truncation variant -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31633 | |||||||||
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Title | human Serine beta-lactamase-like protein LACTB truncation variant | |||||||||
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![]() | mitochondrial intermembrane space protease / CYTOSOLIC PROTEIN / HYDROLASE | |||||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases) / regulation of lipid metabolic process / lipid metabolic process / peptidase activity / mitochondrion / proteolysis / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
![]() | Zhang MH / Yang MJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the catalytic activity of filamentous human serine beta-lactamase-like protein LACTB. Authors: Minghui Zhang / Laixing Zhang / Runyu Guo / Chun Xiao / Jian Yin / Sensen Zhang / Maojun Yang / ![]() Abstract: Serine beta-lactamase-like protein (LACTB) is a mammalian mitochondrial serine protease that can specifically hydrolyze peptide bonds adjacent to aspartic acid residues and is structurally related to ...Serine beta-lactamase-like protein (LACTB) is a mammalian mitochondrial serine protease that can specifically hydrolyze peptide bonds adjacent to aspartic acid residues and is structurally related to prokaryotic penicillin-binding proteins. Here, we determined the cryoelectron microscopy structures of human LACTB (hLACTB) filaments from wild-type protein, a middle region deletion mutant, and in complex with the inhibitor Z-AAD-CMK at 3.0-, 3.1-, and 2.8-Å resolution, respectively. Structural analysis and activity assays revealed that three interfaces are required for the assembly of hLACTB filaments and that the formation of higher order helical structures facilitates its cleavage activity. Further structural and enzymatic analyses of middle region deletion constructs indicated that, while this region is necessary for substrate hydrolysis, it is not required for filament formation. Moreover, the inhibitor-bound structure showed that hLACTB may cleave peptide bonds adjacent to aspartic acid residues. These findings provide the structural basis underlying hLACTB catalytic activity. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.3 KB 9.3 KB | Display Display | ![]() |
Images | ![]() | 30.7 KB | ||
Filedesc metadata | ![]() | 5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 381.5 KB | Display | ![]() |
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Full document | ![]() | 381.1 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7v21MC ![]() 7v1yC ![]() 7v1zC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.97 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 : mitochondrial intermembrane space protease truncation
Entire | Name: mitochondrial intermembrane space protease truncation |
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Components |
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-Supramolecule #1: mitochondrial intermembrane space protease truncation
Supramolecule | Name: mitochondrial intermembrane space protease truncation / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Serine beta-lactamase-like protein LACTB, mitochondrial
Macromolecule | Name: Serine beta-lactamase-like protein LACTB, mitochondrial type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 47.029566 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPAAPAQSPA APDPEASPLA EPPQEQSLAP WSPQTPAPPC SRCFARAIES SRDLLHRIKD EVGAPGIVVG VSVDGKEVWS EGLGYADVE NRVPCKPETV MRIASISKSL TMVALAKLWE AGKLDLDIPV QHYVPEFPEK EYEGEKVSVT TRLLISHLSG I RHYGELYL ...String: GPAAPAQSPA APDPEASPLA EPPQEQSLAP WSPQTPAPPC SRCFARAIES SRDLLHRIKD EVGAPGIVVG VSVDGKEVWS EGLGYADVE NRVPCKPETV MRIASISKSL TMVALAKLWE AGKLDLDIPV QHYVPEFPEK EYEGEKVSVT TRLLISHLSG I RHYGELYL REKFENSIES LRLFKNDPLF FKPGSQFLYS TFGYTLLAAI VERASGCKYL DYMQKIFHDL DMLTTVQEEN EP VIYNRAR FYVYNKKKRL VNTPYVDNSY KWAGGGFLST VGDLLKFGNA MLYGYQVGLF KNSNENLLPG YLKPETMVMM WTP VPNTEM SWDKEGKYAM AWGVVERKQT YGSCRKQRHY ASHTGGAVGA SSVLLVLPEE LDTETINNKV PPRGIIVSII CNMQ SVGLN STALKIALEF DKDRSD UniProtKB: Serine beta-lactamase-like protein LACTB, mitochondrial, Serine beta-lactamase-like protein LACTB, mitochondrial |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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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) / 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 |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120786 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: RANDOM ASSIGNMENT |