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- EMDB-31630: Serine beta-lactamase-like protein LACTB in complex with inhibitor -

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Basic information

Entry
Database: EMDB / ID: EMD-31630
TitleSerine beta-lactamase-like protein LACTB in complex with inhibitor
Map data
Sample
  • Organelle or cellular component: Mitochondrial intermembrane space protease.
    • Protein or peptide: Serine beta-lactamase-like protein LACTB, mitochondrial
  • Protein or peptide: ALA-ALA-B3S
Keywordsmitochondrial intermembrane space protease / CYTOSOLIC PROTEIN / HYDROLASE
Function / homology
Function and homology information


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
: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Serine beta-lactamase-like protein LACTB, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsZhang MH / Yang MJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31671049 China
CitationJournal: Structure / Year: 2022
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
DepositionAug 7, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7v1y
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7v1y
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31630.png

Downloads & links

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Map

FileDownload / File: emd_31630.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 301.28 Å		1.08 Å/pix.
x 280 pix.
= 301.28 Å		1.08 Å/pix.
x 280 pix.
= 301.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.03
Minimum - Maximum-0.13448273 - 0.20984434
Average (Standard dev.)0.00030389518 (±0.005150041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 301.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0761.0761.076
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z301.280301.280301.280
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1340.2100.000

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Supplemental data

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Sample components

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Entire : Mitochondrial intermembrane space protease.

EntireName: Mitochondrial intermembrane space protease.
Components
  • Organelle or cellular component: Mitochondrial intermembrane space protease.
    • Protein or peptide: Serine beta-lactamase-like protein LACTB, mitochondrial
  • Protein or peptide: ALA-ALA-B3S

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Supramolecule #1: Mitochondrial intermembrane space protease.

SupramoleculeName: Mitochondrial intermembrane space protease. / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55 kDa/nm

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Macromolecule #1: Serine beta-lactamase-like protein LACTB, mitochondrial

MacromoleculeName: 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)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.889445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPAAPAQSPA APDPEASPLA EPPQEQSLAP WSPQTPAPPC SRCFARAIES SRDLLHRIKD EVGAPGIVVG VSVDGKEVWS EGLGYADVE NRVPCKPETV MRIASISKSL TMVALAKLWE AGKLDLDIPV QHYVPEFPEK EYEGEKVSVT TRLLISHLSG I RHYEKDIK ...String:
GPAAPAQSPA APDPEASPLA EPPQEQSLAP WSPQTPAPPC SRCFARAIES SRDLLHRIKD EVGAPGIVVG VSVDGKEVWS EGLGYADVE NRVPCKPETV MRIASISKSL TMVALAKLWE AGKLDLDIPV QHYVPEFPEK EYEGEKVSVT TRLLISHLSG I RHYEKDIK KVKEEKAYKA LKMMKENVAF EQEKEGKSNE KNDFTKFKTE QENEAKCRNS KPGKKKNDFE QGELYLREKF EN SIESLRL FKNDPLFFKP GSQFLYSTFG YTLLAAIVER ASGCKYLDYM QKIFHDLDML TTVQEENEPV IYNRARFYVY NKK KRLVNT PYVDNSYKWA GGGFLSTVGD LLKFGNAMLY GYQVGLFKNS NENLLPGYLK PETMVMMWTP VPNTEMSWDK EGKY AMAWG VVERKQTYGS CRKQRHYASH TGGAVGASSV LLVLPEELDT ETINNKVPPR GIIVSIICNM QSVGLNSTAL KIALE FDKD RSD

UniProtKB: Serine beta-lactamase-like protein LACTB, mitochondrial

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Macromolecule #2: ALA-ALA-B3S

MacromoleculeName: ALA-ALA-B3S / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 261.275 Da
SequenceString:
AA(B3S)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170111
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: RANDOM ASSIGNMENT

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