7T6D | pdb_00007t6d

CryoEM structure of the YejM/LapB complex

PDB DOI: https://doi.org/10.2210/pdb7T6D/pdb
EM Map EMD-25713: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2021-12-13 Released: 2022-08-17
Deposition Author(s): Mi, W., Shu, S.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli.

Shu, S., Mi, W.

(2022) Nat Commun 13: 4576-4576

PubMed: 35931690 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-32277-1
Primary Citation of Related Structures:
7T6D

PubMed 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-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.

Organizational Affiliation

Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.

Macromolecule Content

Total Structure Weight: 227.22 kDa
Atom Count: 7,566
Modelled Residue Count: 1,181
Deposited Residue Count: 1,964
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipopolysaccharide assembly protein B	A, B	396	Escherichia coli	Mutation(s): 0 Gene Names: lapB, lapB_1, lapB_2, yciM, A6519_003392, A8499_002320, A8W81_000860, A8X68_001918, A9X72_14480, AAG43_002492... 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 Membrane Entity: Yes
UniProt
Find proteins for P0AB58 (Escherichia coli (strain K12)) Explore P0AB58 Go to UniProtKB: P0AB58
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AB58
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inner membrane protein YejM	C, D	586	Escherichia coli	Mutation(s): 0 Gene Names: yejM, pbgA, yejM_2, A6583_09370, A6592_11615, A8499_001072, A8C65_16830, A8W81_001303, A9X72_08400, ACN002_2250... 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 Membrane Entity: Yes
UniProt
Find proteins for P0AD27 (Escherichia coli (strain K12)) Explore P0AD27 Go to UniProtKB: P0AD27
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AD27
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGV (Subject of Investigation/LOI) Query on PGV Download Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
LPP (Subject of Investigation/LOI) Query on LPP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE C₃₅ H₆₉ O₈ P PORPENFLTBBHSG-MGBGTMOVSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]