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- PDB-7v21: human Serine beta-lactamase-like protein LACTB truncation variant -
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Open data
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Basic information
Entry | Database: PDB / ID: 7v21 | ||||||
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Title | human Serine beta-lactamase-like protein LACTB truncation variant | ||||||
![]() | Serine beta-lactamase-like protein LACTB, mitochondrial | ||||||
![]() | HYDROLASE / mitochondrial intermembrane space protease / CYTOSOLIC PROTEIN | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å | ||||||
![]() | Zhang, M.H. / Yang, M.J. | ||||||
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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 265.4 KB | Display | ![]() |
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PDB format | ![]() | 215.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 718.7 KB | Display | ![]() |
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Full document | ![]() | 727.8 KB | Display | |
Data in XML | ![]() | 41.6 KB | Display | |
Data in CIF | ![]() | 64 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31633MC ![]() 7v1yC ![]() 7v1zC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 47029.566 Da / Num. of mol.: 4 / Mutation: deletions 224-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P83111, Hydrolases; Acting on peptide bonds (peptidases) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: mitochondrial intermembrane space protease truncation / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120786 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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