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Open data
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Basic information
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Title | CryoEM structure of the YejM/LapB complex | |||||||||
![]() | sharpened map with a B factor of -216 A2 | |||||||||
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![]() | YejM / YciM / regulation / lipopolysaccharide synthesis / LpxC / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() : / lipopolysaccharide metabolic process / regulation of lipid biosynthetic process / membrane => GO:0016020 / iron ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Mi W / Shu S | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli. Authors: Sheng Shu / Wei Mi / ![]() Abstract: Lipopolysaccharide (LPS) is an essential glycolipid and forms a protective permeability barrier for most Gram-negative bacteria. In E. coli, LPS levels are under feedback control, achieved by FtsH- ...Lipopolysaccharide (LPS) is an essential glycolipid and forms a protective permeability barrier for most Gram-negative bacteria. In E. coli, LPS levels are under feedback control, achieved by FtsH-mediated degradation of LpxC, which catalyzes the first committed step in LPS synthesis. FtsH is a membrane-bound AAA+ protease, and its protease activity toward LpxC is regulated by essential membrane proteins LapB and YejM. However, the regulatory mechanisms are elusive. We establish an in vitro assay to analyze the kinetics of LpxC degradation and demonstrate that LapB is an adaptor protein that utilizes its transmembrane helix to interact with FtsH and its cytoplasmic domains to recruit LpxC. Our YejM/LapB complex structure reveals that YejM is an anti-adaptor protein, competing with FtsH for LapB to inhibit LpxC degradation. Structural analysis unravels that LapB and LPS have overlapping binding sites in YejM. Thus, LPS levels control formation of the YejM/LapB complex to determine LpxC protein levels. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.6 KB 20.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.6 KB | Display | ![]() |
Images | ![]() | 77.8 KB | ||
Masks | ![]() | 27 MB | ![]() | |
Filedesc metadata | ![]() | 11.1 KB | ||
Others | ![]() ![]() ![]() | 13.4 MB 25.1 MB 25.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 735.1 KB | Display | ![]() |
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Full document | ![]() | 734.7 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t6dMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | sharpened map with a B factor of -216 A2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.346 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: original 3D reconstruction without sharpening
File | emd_25713_additional_1.map | ||||||||||||
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Annotation | original 3D reconstruction without sharpening | ||||||||||||
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-Half map: #2
File | emd_25713_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_25713_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : complex of YejM and YciM
Entire | Name: complex of YejM and YciM |
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Components |
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-Supramolecule #1: complex of YejM and YciM
Supramolecule | Name: complex of YejM and YciM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 225.556 kDa/nm |
-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: ![]() ![]() |
Molecular weight | Theoretical: 45.546953 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 DGLEHHHHHH UniProtKB: Lipopolysaccharide assembly protein B |
-Macromolecule #2: Inner membrane protein YejM
Macromolecule | Name: Inner membrane protein YejM / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 67.36468 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MVTHRQRYRE KVSQMVSWGH WFALFNILLS LVIGSRYLFI ADWPTTLAGR IYSYVSIIGH FSFLVFATYL LILFPLTFIV GSQRLMRFL SVILATAGMT LLLIDSEVFT RFHLHLNPIV WQLVINPDEN EMARDWQLMF ISVPVILLLE LVFATWSWQK L RSLTRRRR ...String: MVTHRQRYRE KVSQMVSWGH WFALFNILLS LVIGSRYLFI ADWPTTLAGR IYSYVSIIGH FSFLVFATYL LILFPLTFIV GSQRLMRFL SVILATAGMT LLLIDSEVFT RFHLHLNPIV WQLVINPDEN EMARDWQLMF ISVPVILLLE LVFATWSWQK L RSLTRRRR FARPLAAFLF IAFIASHVVY IWADANFYRP ITMQRANLPL SYPMTARRFL EKHGLLDAQE YQRRLIEQGN PD AVSVQYP LSELRYRDMG TGQNVLLITV DGLNYSRFEK QMPALAGFAE QNISFTRHMS SGNTTDNGIF GLFYGISPSY MDG ILSTRT PAALITALNQ QGYQLGLFSS DGFTSPLYRQ ALLSDFSMPS VRTQSDEQTA TQWINWLGRY AQEDNRWFSW VSFN GTNID DSNQQAFARK YSRAAGNVDD QINRVLNALR DSGKLDNTVV IITAGRGIPL SEEEETFDWS HGHLQVPLVI HWPGT PAQR INALTDHTDL MTTLMQRLLH VSTPASEYSQ GQDLFNPQRR HYWVTAADND TLAITTPKKT LVLNNNGKYR TYNLRG ERV KDEKPQLSLL LQVLTDEKRF IAN UniProtKB: Inner membrane protein YejM |
-Macromolecule #3: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
Macromolecule | Name: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE type: ligand / ID: 3 / Number of copies: 1 / Formula: LPP |
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Molecular weight | Theoretical: 648.891 Da |
Chemical component information | ![]() ChemComp-LPP: |
-Macromolecule #4: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
Macromolecule | Name: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE type: ligand / ID: 4 / Number of copies: 1 / Formula: PGV |
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Molecular weight | Theoretical: 749.007 Da |
Chemical component information | ![]() ChemComp-PGV: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL |
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Buffer | pH: 7.8 |
Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. |
Vitrification | Cryogen name: ETHANE |
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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) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 8.84 sec. / 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7t6d: |