+Open data
-Basic information
Entry | Database: PDB / ID: 7t6d | ||||||
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Title | CryoEM structure of the YejM/LapB complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / YejM / YciM / regulation / lipopolysaccharide synthesis / LpxC | ||||||
Function / homology | Function and homology information : / lipopolysaccharide metabolic process / regulation of lipid biosynthetic process / membrane => GO:0016020 / iron ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Mi, W. / Shu, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t6d.cif.gz | 230.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t6d.ent.gz | 164.2 KB | Display | PDB format |
PDBx/mmJSON format | 7t6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t6d_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7t6d_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7t6d_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 7t6d_validation.cif.gz | 65.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/7t6d ftp://data.pdbj.org/pub/pdb/validation_reports/t6/7t6d | HTTPS FTP |
-Related structure data
Related structure data | 25713MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 45546.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: lapB, lapB_1, lapB_2, yciM, A6519_003392, A8499_002320, A8W81_000860, A8X68_001918, A9X72_14480, AAG43_002492, ABE90_026530, ABT96_002964, ACN002_1742, ACN68_13760, ACU57_02830, ACW72_002916, ...Gene: lapB, lapB_1, lapB_2, yciM, A6519_003392, A8499_002320, A8W81_000860, A8X68_001918, A9X72_14480, AAG43_002492, ABE90_026530, ABT96_002964, ACN002_1742, ACN68_13760, ACU57_02830, ACW72_002916, AM270_04715, AM464_24460, AMK64_001197, AML23_13785, AO169_003132, AT335_001728, AT845_003561, AUQ29_06870, AW059_17045, B2D52_003072, B5N24_003363, B6L15_002768, B6R12_000713, B6R15_001447, B7C15_002578, B9T59_25470, BANRA_00913, BANRA_01922, BANRA_02272, BANRA_04238, BE930_07195, BF481_003525, BFL24_11350, BHF52_04915, BHS81_08140, BHS87_06805, BIZ41_06440, BJI68_16000, BK272_18185, BKD45_002476, BMC34_002615, BMT50_25160, BMT91_09485, BN17_11291, BOH76_12790, BON63_08380, BON65_11400, BON70_13430, BON72_10370, BON73_23360, BON76_22345, BON86_26965, BON87_00675, BON91_05790, BON93_04810, BON94_23115, BON95_24295, BON96_11840, BON98_20550, BTQ06_01755, BUE81_21790, BvCms2454_02783, BvCmsC61A_00867, BvCmsHHP019_01251, BvCmsHHP056_05185, BvCmsKKP005_01617, BvCmsKKP036_02977, BvCmsKKP057_02775, BvCmsKKP061_04930, BvCmsKSNP073_02552, BvCmsKSP011_00507, BvCmsKSP067_03395, BvCmsNSNP036_02647, BvCmsSIP082_03266, BVL39_21785, C2121_001848, C2U48_01890, C3F40_05575, C5F72_14800, C5N07_15420, C5Y87_08390, C6B13_16180, C6B22_15545, C6L19_000308, C6N50_002146, C7B02_10605, C9114_03730, C9160_12100, C9E67_15785, C9Z62_12310, CA593_21440, CBT22_000243, CCS08_27640, CCZ91_000907, CDL36_22330, CDL37_04200, CDL57_24010, CF32_002531, CG692_05225, CG831_002162, CIG67_22415, CLG78_002326, CN875_001332, CO706_02845, COD50_12455, CQP61_13055, CS116_002344, CT143_17675, D0X26_18180, D2183_20380, D3G36_18000, D3O91_23240, D3Y67_04030, D4U49_17205, D4V09_13060, D5H22_10790, D6T60_03370, D9D77_16425, D9E49_04245, D9F92_17650, D9H13_01425, D9H94_11055, D9J11_07075, D9K17_12190, DAH18_14065, DAH23_15505, DAH34_16510, DAH50_11685, DB282_08780, DEN89_18990, DEO15_14770, DIV22_30895, DM968_19040, DRW19_11270, DS732_11480, DS966_14175, DTL43_11095, DTL90_01335, DXB10_15580, DXB10_16775, DXT69_00360, DXT71_10990, DXT73_13915, E0I42_06310, E2112_02885, E2123_11980, E2127_03390, E2128_00455, E2129_00375, E3N34_18830, E4K51_14885, E4K54_14850, E5P52_03605, E5S34_10145, E5S35_09160, E5S38_11225, E5S43_08140, E5S47_06570, E5S52_03675, E5S61_07790, EAI46_04695, EAN77_13100, EBP16_17290, EC1094V2_2484, EC3234A_230c01430, EC95NR1_00326, ECs1853, ED648_03900, EGC08_11645, EH88_003316, EHD79_11840, EHH55_10950, EI021_13605, EI041_15605, EIA08_16130, EIA13_10710, EIZ93_19170, EKI52_01585, EL79_2487, EL80_2488, ELT21_12950, ELT31_16165, ELT33_13755, ELT49_21030, ELT58_08985, ELU83_12175, ELU95_16765, ELV08_11905, ELV10_01715, ELX76_20405, ELY05_10955, EO241_12655, EQO00_13740, ERS085358_00939, ERS085386_02975, ERS085406_00731, Esc0902E_14650, ETECE1373_02637, ETECE36_03510, EVY14_13400, EWK56_17840, ExPECSC038_05182, EXX13_01995, EYX47_09350, EYX55_08745, F6U69_15745, F9400_07670, F9407_04140, F9S76_06015, F9V07_00360, F9V24_11000, F9X20_015225, F9X20_15355, FC554_07815, FDM60_05915, FE587_04450, FEJ01_09950, FFF58_19650, FGG80_24000, FKO60_08750, FMP09_02050, FOI11_006585, FOI11_13555, FPI65_07590, FPS82_10375, FQE77_10850, FQF29_23035, FV293_10890, FY127_08365, G4A38_11915, G5603_19860, G5632_16960, G5696_03530, G6Z99_13635, G7635_000932, G9448_04240, GAJ26_07165, GBE29_13210, GF147_07410, GF646_08560, GF699_11645, GFY34_05975, GFZ60_14750, GIB53_11460, GKF86_18860, GKF89_20570, GKG12_03945, GLW94_11560, GNZ05_13290, GOP20_20825, GP662_03380, GQA06_04230, GQE42_15065, GQE64_13610, GQE87_12585, GQF58_06905, GQF59_08575, GQM06_04685, GQM10_06545, GQW07_00450, GQW76_09945, GRO95_01570, GRQ19_03720, GRW05_11530, GRW57_13825, GRW80_12460, GRW81_07680, GUB08_18980, H0O72_03640, H4P50_08895, H4P51_14150, HH411_001987, HH795_004427, HHG09_004014, HHH44_001843, HIE44_002503, HIF90_001390, HIR12_001593, HJN04_001209, HJO75_002524, HJS41_002779, HL425_08705, HL601_11520, HLZ20_07505, HLZ50_09210, HMJ82_13920, HMS79_05245, HMU48_18525, HMV41_16070, HMV95_10465, HNC38_13520, HNC52_13050, HND12_15785, HND24_14400, HNO08_14040, HNV65_09995, HNV94_15550, HNY50_11855, HNY54_14470, HV109_13370, HVV39_23985, HVV53_02660, HVW04_04200, HVW11_24340, HVY77_14595, HVZ33_13530, HVZ71_13670, HZ71_002608, I6H00_07305, I6H01_24000, I6H02_25750, JE86ST02C_16760, JE86ST05C_16890, NCTC10089_02682, NCTC10090_00861, NCTC10418_04179, NCTC10429_05120, NCTC10764_02333, NCTC10767_05193, NCTC10865_03455, NCTC11022_01072, NCTC11112_05334, NCTC11181_04717, NCTC13127_03637, NCTC13216_03875, NCTC4450_04325, NCTC7927_03033, NCTC8008_02211, NCTC8500_03093, NCTC8960_05553, NCTC8985_01499, NCTC9036_02890, NCTC9045_03196, NCTC9048_03637, NCTC9050_00806, NCTC9073_01700, NCTC9081_03892, NCTC9117_03545, NCTC9434_03952, NCTC9706_00177, NCTC9777_04051, NCTC9969_02938, PGD_01970, PU06_14205, RG28_16120, SAMEA3472043_03563, SAMEA3472056_02600, SAMEA3472080_01068, SAMEA3484427_01617, SAMEA3484429_01482, SAMEA3485101_02085, SAMEA3485110_04597, SAMEA3751407_01252, SAMEA3752386_00749, SAMEA3752557_02954, SAMEA3753064_00168, SAMEA3753290_01068, SAMEA3753300_03507, THOESC010_24410, TUM18780_23450, UN91_04670, WP2S18E08_26240, WP4S18E08_25230, WQ89_18230, WR15_00725 Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star pLysS / References: UniProt: C3TC27 #2: Protein | Mass: 67364.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: yejM, pbgA, yejM_2, A6583_09370, A6592_11615, A8499_001072, A8C65_16830, A8W81_001303, A9X72_08400, ACN002_2250, ACU57_09240, ADS93_002353, AM340_15765, AM464_02270, APX88_05005, AUQ29_19365, ...Gene: yejM, pbgA, yejM_2, A6583_09370, A6592_11615, A8499_001072, A8C65_16830, A8W81_001303, A9X72_08400, ACN002_2250, ACU57_09240, ADS93_002353, AM340_15765, AM464_02270, APX88_05005, AUQ29_19365, AW086_07975, AW118_16940, AWP47_24265, AZZ83_002338, B6R12_000845, B6R15_004238, B6R17_002480, B6R27_005186, B6R48_001484, B6R87_001451, B9T59_22870, BANRA_00752, BANRA_04871, BE930_28735, BER14_18270, BF271_000946, BFL24_16505, BG821_000075, BH692_09340, BHS87_12530, BIQ87_13040, BJI68_13215, BJJ90_08330, BK272_02805, BK373_07505, BM922_001699, BMC79_000422, BMT49_13905, BMT91_00115, BN17_14751, BO068_002744, BON72_16040, BON73_18350, BON76_17375, BON86_23915, BON87_08430, BON92_16815, BON93_21655, BON94_17700, BON96_18625, BON98_04460, BOY03_001080, BUE81_18280, BUE82_07615, BvCms2454_04584, BvCmsHHP019_05090, BvCmsSIP024_01508, BWI89_02190, BZL69_09245, C4952_001182, C4M78_17535, C5715_06575, C5F72_09155, C5Y87_12800, C6B13_00290, C6B22_01615, C7B02_03025, C9E67_09155, C9Z43_08610, C9Z68_16250, CA593_16265, CCS08_24350, CCV12_002491, CD42_001250, CDL36_01005, CDL37_14785, CDL57_04530, CG692_11165, CG831_003323, CQP61_10000, CT143_04215, D0X26_21125, D1912_29500, D2183_09840, D3822_12865, D3G36_02140, D3O91_01050, D3Y67_09165, D4U49_06490, D4V09_19965, D9F92_03905, D9H13_11200, D9J11_19635, D9J61_06525, DAH23_00425, DAH34_05185, DAH37_09170, DEN86_03840, DLW88_13930, DM968_07875, DNX30_05665, DS732_17010, DS966_01280, DTM10_09095, DTM45_08440, DU321_11480, DXB10_11805, E0N24_08640, E2119_00760, E2123_11275, E2127_01995, E2128_04195, E2129_08825, E3N34_20700, E4K51_00800, E4K54_03780, E5P52_00935, EA239_06720, EA435_00905, EC3234A_43c00110, ECs3080, EI021_01330, EI041_05800, EIA08_04310, ELT17_13065, ELT21_02385, ELT33_04940, ELT48_05200, ELT49_19620, ELT58_04240, ELT72_00755, ELV10_04545, ELV13_02810, ELV22_00720, ELV24_08035, ELX56_00815, ELX68_00770, ELX69_02045, ELX70_02545, ELX76_00500, ELX79_03840, ELX83_15305, ELY05_14680, ELY23_08830, ELY24_08630, ELY50_02880, EO241_01170, EPS76_06925, EQO00_09055, ERS085386_00298, ETECE925_01624, EWK56_07190, ExPECSC038_02216, EXX79_04640, F2N27_23515, F2N28_23660, F3N40_00740, F6U69_01695, F7F11_05890, F9386_09630, F9571_15145, F9S83_16100, F9V24_17745, FFF58_08555, FGG80_10995, FHR00_02145, FJQ51_21990, FKO60_02570, FMP09_00770, FNJ67_09010, FOI11_001990, FOI11_18055, FPI65_13810, FQF29_23785, FZN30_10900, G3565_00930, G3813_002500, G4A38_04620, G5603_04965, G6P89_08200, GF147_03470, GFY48_00705, GKF52_07460, GKG12_01680, GKZ24_12255, GLW94_00250, GNO40_04250, GP711_04060, GQE64_02255, GQE87_19270, GQW07_05465, GQW68_08245, GQW76_18825, GQW80_04770, GRC73_01825, GRO95_13145, GRQ19_15575, GRW05_06845, GRW80_02890, GRW81_01115, GTP88_01785, GUB92_18760, GUI33_19260, GW978_00750, GXU05_002919, GXV26_001787, H5C78_15085, HH411_001705, HH795_001884, HHG09_004071, HI055_001135, HIE29_002609, HIE44_001815, HIT56_002195, HJM92_004122, HJO75_003640, HJQ60_001849, HJS37_000913, HJS41_002956, HJU54_002487, HL425_00735, HL601_00640, HLU10_10190, HLU56_15835, HLV18_10515, HLZ20_01885, HmCms169_00898, HMJ82_13430, HMS79_06405, HMU06_05650, HMU48_06105, HMV95_16605, HMV95_25940, HNC30_04745, HNC36_11220, HNC38_05860, HNC52_14840, HNC59_05410, HNC66_16020, HNC99_03425, HND12_03865, HND24_03720, HNO08_17220, HNV94_03750, HNY50_05155, HNY54_04060, HPE39_17300, HVV39_02785, HVV53_07965, HVW04_24015, HVW43_25590, HVX16_08400, HVZ33_08545, HX136_08025, HZ71_001224, MJ49_19865, MS7163_02295, NCTC10082_04105, NCTC10089_01672, NCTC10764_00976, NCTC10767_02951, NCTC11022_02170, NCTC11126_04042, NCTC12950_01951, NCTC13127_02131, NCTC13216_04902, NCTC8008_01090, NCTC8500_01909, NCTC8959_02126, NCTC9001_02081, NCTC9044_05974, NCTC9045_01997, NCTC9048_01750, NCTC9073_01555, NCTC9081_05148, NCTC9434_01706, NCTC9702_01992, NCTC9706_04975, SAMEA3472064_00873, SAMEA3472080_00462, SAMEA3472112_02618, SAMEA3472117_02395, SAMEA3472120_00721, SAMEA3484427_01505, SAMEA3484429_01356, SAMEA3751407_04919, SAMEA3752312_00374, SAMEA3752386_04909, SAMEA3752557_00509, SAMEA3753064_00496, SAMEA3753290_01284, SAMEA3753300_00187, SM09_02308, WP2S18E08_17110, WP4S18E07_15720, WP4S18E08_15980, WQ89_02845 Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star pLysS / References: UniProt: C3T3G2 #3: Chemical | ChemComp-LPP / | #4: Chemical | ChemComp-PGV / ( | Has ligand of interest | Y | |
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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 |
-Sample preparation
Component | Name: complex of YejM and YciM / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 225.556 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8.84 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 / Movie frames/image: 82 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1181379 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: THROUGHOUT | ||||||||||||||||||||||||
Displacement parameters | Biso max: 137.57 Å2 / Biso mean: 49.2648 Å2 / Biso min: 20.65 Å2 |