+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42897 | |||||||||
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Title | LapB cytoplasmic domain in complex with LpxC | |||||||||
Map data | ||||||||||
Sample |
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Keywords | adaptor / complex / deacetylase / LPS / LpxC / LapB(YciM) / PROTEIN BINDING | |||||||||
Function / homology | Function and homology information lipopolysaccharide metabolic process / UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / regulation of lipid biosynthetic process / lipid A biosynthetic process / cytoplasmic side of plasma membrane / iron ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli CFT073 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Mi W / Shu S | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Dual function of LapB (YciM) in regulating lipopolysaccharide synthesis. Authors: Sheng Shu / Yuko Tsutsui / Rajkanwar Nathawat / Wei Mi / Abstract: Levels of lipopolysaccharide (LPS), an essential glycolipid on the surface of most gram-negative bacteria, are tightly controlled-making LPS synthesis a promising target for developing new ...Levels of lipopolysaccharide (LPS), an essential glycolipid on the surface of most gram-negative bacteria, are tightly controlled-making LPS synthesis a promising target for developing new antibiotics. adaptor protein LapB (YciM) plays an important role in regulating LPS synthesis by promoting degradation of LpxC, a deacetylase that catalyzes the first committed step in LPS synthesis. Under conditions where LPS is abundant, LapB recruits LpxC to the AAA+ protease FtsH for degradation. LapB achieves this by simultaneously interacting with FtsH through its transmembrane helix and LpxC through its cytoplasmic domain. Here, we describe a cryo-EM structure of the complex formed between LpxC and the cytoplasmic domain of LapB (LapB). The structure reveals how LapB exploits both its tetratricopeptide repeat (TPR) motifs and rubredoxin domain to interact with LpxC. Through both in vitro and in vivo analysis, we show that mutations at the LapB/LpxC interface prevent LpxC degradation. Unexpectedly, binding to LapB also inhibits the enzymatic activity of LpxC through allosteric effects reminiscent of LpxC activation by MurA in Our findings argue that LapB regulates LPS synthesis in two steps: In the first step, LapB inhibits the activity of LpxC, and in the second step, it commits LpxC to degradation by FtsH. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42897.map.gz | 33.3 MB | EMDB map data format | |
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Header (meta data) | emd-42897-v30.xml emd-42897.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42897_fsc.xml | 7 KB | Display | FSC data file |
Images | emd_42897.png | 47.6 KB | ||
Filedesc metadata | emd-42897.cif.gz | 6.4 KB | ||
Others | emd_42897_half_map_1.map.gz emd_42897_half_map_2.map.gz | 32.8 MB 32.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42897 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42897 | HTTPS FTP |
-Validation report
Summary document | emd_42897_validation.pdf.gz | 784.1 KB | Display | EMDB validaton report |
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Full document | emd_42897_full_validation.pdf.gz | 783.7 KB | Display | |
Data in XML | emd_42897_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | emd_42897_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42897 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42897 | HTTPS FTP |
-Related structure data
Related structure data | 8v24MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_42897.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.068 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_42897_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_42897_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : LapB/LpxC
Entire | Name: LapB/LpxC |
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Components |
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-Supramolecule #1: LapB/LpxC
Supramolecule | Name: LapB/LpxC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli CFT073 (bacteria) |
-Macromolecule #1: Lipopolysaccharide assembly protein B
Macromolecule | Name: Lipopolysaccharide assembly protein B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli CFT073 (bacteria) / Strain: CFT073 / ATCC 700928 / UPEC |
Molecular weight | Theoretical: 44.588969 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MLELLFLLLP VAAAYGWYMG RRSAQQNKQD EANRLSRDYV AGVNFLLSNQ QDKAVDLFLD MLKEDTGTVE AHLTLGNLFR SRGEVDRAI RIHQTLMESA SLTYEQRLLA IQQLGRDYMA AGLYDRAEDM FNQLTDETDF RIGALQQLLQ IYQATSEWQK A IDVAERLV ...String: MLELLFLLLP VAAAYGWYMG RRSAQQNKQD EANRLSRDYV AGVNFLLSNQ QDKAVDLFLD MLKEDTGTVE AHLTLGNLFR SRGEVDRAI RIHQTLMESA SLTYEQRLLA IQQLGRDYMA AGLYDRAEDM FNQLTDETDF RIGALQQLLQ IYQATSEWQK A IDVAERLV KLGKDKQRVE IAHFYCELAL QHMASDDLDR AMTLLKKGAA ADKNSARVSI MMGRVFMAKG EYAKAVESLQ RV ISQDREL VSETLEMLQT CYQQLGKTAE WAEFLQRAVE ENTGADAELM LADIIEARDG SEAAQVYITR QLQRHPTMRV FHK LMDYHL NEAEEGRAKE SLMVLRDMVG EKVRSKPRYR CQKCGFTAYT LYWHCPSCRA WSTIKPIRGL DGL UniProtKB: Lipopolysaccharide assembly protein B |
-Macromolecule #2: UDP-3-O-acyl-N-acetylglucosamine deacetylase
Macromolecule | Name: UDP-3-O-acyl-N-acetylglucosamine deacetylase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli CFT073 (bacteria) / Strain: CFT073 / ATCC 700928 / UPEC |
Molecular weight | Theoretical: 33.995871 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MIKQRTLKRI VQATGVGLHT GKKVTLTLRP APANTGVIYR RTDLNPPVDF PADAKSVRDT MLCTCLVNEH DVRISTVEHL NAALAGLGI DNIVIEVNAP EIPIMDGSAA PFVYLLLDAG IDELNCAKKF VRIKETVRVE DGDKWAEFKP YNGFSLDFTI D FNHPAIDS ...String: MIKQRTLKRI VQATGVGLHT GKKVTLTLRP APANTGVIYR RTDLNPPVDF PADAKSVRDT MLCTCLVNEH DVRISTVEHL NAALAGLGI DNIVIEVNAP EIPIMDGSAA PFVYLLLDAG IDELNCAKKF VRIKETVRVE DGDKWAEFKP YNGFSLDFTI D FNHPAIDS SNQRYAMNFS ADAFMRQISR ARTFGFMRDI EYLQSRGLCL GGSFDCAIVV DDYRVLNEDG LRFEDEFVRH KM LDAIGDL FMCGHNIIGA FTAYKSGHAL NNKLLQAVLA KQEAWEYVTF QDDAELPLAF KAPSAVLA UniProtKB: UDP-3-O-acyl-N-acetylglucosamine deacetylase |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-glucosamine
Macromolecule | Name: uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-glucosamine type: ligand / ID: 4 / Number of copies: 2 / Formula: 24G |
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Molecular weight | Theoretical: 791.672 Da |
Chemical component information | ChemComp-24G: |
-Macromolecule #5: ACETATE ION
Macromolecule | Name: ACETATE ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ACT |
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Molecular weight | Theoretical: 59.044 Da |
Chemical component information | ChemComp-ACT: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.8 |
Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 2.6 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |