6ZY2

Cryo-EM structure of apo MlaFEDB

• PDB DOI: https://doi.org/10.2210/pdb6ZY2/pdb
• EM Map EMD-11547: EMDB EMDataResource

• Classification: LIPID TRANSPORT
• Organism(s): Escherichia coli B185, Escherichia coli, Escherichia coli 909945-2, Escherichia coli 2.3916
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-30 Released: 2020-11-25 
• Deposition Author(s): Dong, C.J., Dong, H.H.
• Funding Organization(s): National Science Foundation (NSF, China), Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into outer membrane asymmetry maintenance in Gram-negative bacteria by MlaFEDB.

Tang, X., Chang, S., Qiao, W., Luo, Q., Chen, Y., Jia, Z., Coleman, J., Zhang, K., Wang, T., Zhang, Z., Zhang, C., Zhu, X., Wei, X., Dong, C., Zhang, X., Dong, H.

(2021) Nat Struct Mol Biol 28: 81-91

• PubMed: 33199922 
• DOI: https://doi.org/10.1038/s41594-020-00532-y
• Primary Citation of Related Structures:  
  6ZY2, 6ZY3, 6ZY4, 6ZY9


• PubMed Abstract: 
  

  The highly asymmetric outer membrane of Gram-negative bacteria functions in the defense against cytotoxic substances, such as antibiotics. The Mla pathway maintains outer membrane lipid asymmetry by transporting phospholipids between the inner and outer membranes. It comprises six Mla proteins, MlaFEDBCA, including the ABC transporter MlaFEDB, which functions via an unknown mechanism. Here we determine cryo-EM structures of Escherichia coli MlaFEDB in an apo state and bound to phospholipid, ADP or AMP-PNP to a resolution of 3.3-4.1 Å and establish a proteoliposome-based transport system that includes MlaFEDB, MlaC and MlaA-OmpF to monitor the transport direction of phospholipids. In vitro transport assays and in vivo membrane permeability assays combined with mutagenesis identify functional residues that not only recognize and transport phospholipids but also regulate the activity and structural stability of the MlaFEDB complex. Our results provide mechanistic insights into the Mla pathway, which could aid antimicrobial drug development.

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Organizational Affiliation: 

State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A5B2C2D2E1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 255.18 kDa 
• Atom Count: 15,718 
• Modelled Residue Count: 2,091 
• Deposited Residue Count: 2,366 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YrbD protein	A, B [auth D], C [auth I], D [auth J], E [auth K], F [auth L]	183	Escherichia coli B185	Mutation(s): 0  Gene Names: ECDG_03382

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component	G [auth B], H [auth C]	105	Escherichia coli	Mutation(s): 0  Gene Names:  mlaB, yrbB, A6581_13415, A6592_14225, A6V01_00625, A8C65_02170, A9P13_02945, A9R57_12600, A9X72_02835, AC067_23675, ACN002_3282, ACN68_12355, ACN81_18445, ACU57_14445, ACU90_11565, AM270_15510, AM446_04320, AM464_08585, AMK83_06340, AML07_19340, APT94_23200, APZ14_04295, ARC77_12405, AU473_05735, AUQ13_03075, AUS26_18260, AW106_13275, AWB10_02850, AWG90_020620, AWP75_14100, B9M99_10250, B9T59_16250, BANRA_01811, BANRA_03804, BANRA_03999, BANRA_04207, BB545_09780, BE963_06830, BER14_09135, BHJ80_21985, BHS81_19200, BHS87_17970, BIQ87_18040, BIU72_05405, BJJ90_02770, BK292_10220, BK296_13050, BK373_10175, BK375_18740, BK383_15965, BMA87_01295, BMT49_25595, BMT91_11610, BOH76_04915, BON63_14235, BON66_12205, BON69_26555, BON71_25170, BON72_13935, BON75_23145, BON76_05525, BON83_09240, BON86_01565, BON87_18195, BON92_11035, BON94_12335, BON95_22020, BON96_06355, BTQ04_16475, BTQ06_11870, BUE81_19690, BvCms2454_04822, BvCms28BK_03527, BvCms35BK_01543, BvCmsHHP001_01202, BvCmsHHP019_05314, BvCmsKKP061_00888, BvCmsKSNP073_02163, BvCmsKSNP081_00287, BvCmsKSP011_02050, BvCmsKSP024_00283, BvCmsKSP026_00502, BvCmsKSP045_01650, BvCmsKSP067_01464, BvCmsNSNP036_02151, BvCmsNSP006_04640, BvCmsNSP047_04118, BvCmsNSP072_03187, BvCmsOUP014_03632, BvCmsSINP011_04458, BvCmsSIP019_00407, BvCmsSIP044_00137, BVL39_10130, BW690_19360, BWI89_22070, BWP17_10155, BXT93_02550, BZL31_05925, BZL69_07715, C2M16_04215, C5715_22795, C5N07_18070, C5P01_18835, C6669_12020, C7235_03225, C7B02_15875, C7B08_03565, C7B18_13830, C9098_07790, C9114_15455, C9141_00390, C9160_02340, C9162_04110, C9201_13875, C9306_00415, C9E25_11270, C9E67_03375, C9Z03_07490, C9Z28_00385, C9Z29_07190, C9Z37_14660, C9Z39_14275, C9Z43_00380, C9Z68_06245, C9Z69_11175, C9Z70_06765, C9Z78_03315, C9Z89_09065, CA593_10345, CDL37_12215, CF006_16665, CG692_07300, CI641_009255, CI693_03675, CI694_20835, CIG45_16045, CJU63_19140, CJU64_19020, CMR93_08835, CO706_14630, COD30_12915, COD46_10760, CQP61_03650, CR538_03070, CR539_21250, CRD98_04715, CRE06_06830, CRM83_23500, CRX46_03745, CVH05_10780, CWM24_22870, CWS33_08375, D0X26_09090, D2184_10505, D2185_00445, D2188_02580, D3821_08325, D3822_14575, D3O91_07625, D3P01_09160, D3Y67_18290, D4011_13725, D4074_02435, D4628_02655, D4636_02890, D4638_00790, D4660_02830, D4718_09085, D4L91_11950, D4M06_11225, D4U85_14330, D5H35_09780, D5I97_10670, D6004_08125, D6C36_14160, D6D43_15510, D6T60_15390, D6T98_02410, D6W00_14015, D6X36_05360, D6X63_01430, D6X76_04335, D7K33_12855, D7K63_12220, D7K66_04495, D7W70_15855, D7Z75_02945, D8Y65_13475, D9610_07810, D9C99_05120, D9D20_06275, D9D31_14515, D9D43_03615, D9D44_04410, D9E19_10400, D9E34_11740, D9E49_09595, D9F17_07200, D9F32_01240, D9F87_05870, D9G29_07025, D9G48_11290, D9G69_01100, D9G95_17085, D9H53_01195, D9H68_07560, D9I18_07175, D9I88_07240, D9J03_05150, D9J11_01130, D9J44_07850, D9J52_07915, D9J58_06110, D9J60_11185, D9J63_16910, D9J78_05130, D9K02_06080, D9K48_12255, D9L89_05370, D9S45_00255, D9X77_02330, D9X97_03120, D9Z28_03370, DAH18_20610, DAH26_17315, DAH30_12875, DAH32_13975, DAH34_01980, DAH37_04255, DAH43_16780, DBQ99_04040, DD762_13125, DEN86_08060, DEN89_09405, DEN97_16135, DEO04_19605, DEO19_06430, DIV22_02975, DJ503_19040, DK132_07375, DL257_05650, DL292_05795, DL326_06060, DL455_12700, DL479_06590, DL530_10055, DL705_01300, DL800_23275, DLT82_02655, DLU50_08550, DLU67_08375, DLU82_10330, DLW60_07490, DLW88_04795, DLY41_08155, DM102_15165, DM155_07645, DM267_03265, DM280_09055, DM296_04835, DM382_07360, DM820_04625, DM962_02640, DM973_04650, DMI04_04270, DMI53_12715, DMO02_15405, DMY83_09920, DN660_01330, DN700_04595, DN703_01080, DN808_01890, DNB37_13705, DNC98_07160, DND16_06535, DND79_01330, DNI21_03635, DNJ62_12070, DNK12_02835, DNQ45_01620, DNW42_05405, DNX19_05580, DNX30_11365, DOE35_12610, DOS18_13030, DOT81_04255, DOU81_12375, DOY22_14085, DOY56_12245, DOY61_04695, DOY67_01285, DP265_06555, DP277_10105, DQE83_16545, DQE91_01265, DQF36_08635, DQF57_03615, DQF71_07160, DQF72_06460, DQG35_02830, DQO13_01295, DQP61_01770, DRP48_13910, DRW19_01295, DS143_06770, DS721_11090, DS732_23695, DT034_01270, DTL43_04295, DTM10_06985, DTM45_14510, DTZ20_12090, DU309_11135, DU321_08670, DVB38_07395, DXT69_05520, DXT71_00440, DXX80_009590, E0I42_14340, E0K84_17700, E0L12_03915, E2119_05870, E2127_02575, E2128_02495, E2129_05760, E2134_15595, E2135_08080, E2855_04145, E2863_03970, E4K55_06660, E4K61_09280, E5P22_07075, E5P28_12910, E5P37_13135, E5S42_17100, E5S46_15725, E5S47_16890, E5S58_02935, E5S61_19420, EA214_08600, EA223_04825, EA225_07080, EA233_06175, EAI42_05495, EAI52_09890, EAM59_01020, EAN70_10745, EAX79_13230, EB476_09250, EB509_07200, EB510_12405, EB515_07025, EBA84_05830, EBJ06_06135, EBM08_05455, EC1094V2_454, EC3234A_53c00700, EC3426_04342, EC95NR1_02575, ECTO6_00563, ED225_04270, ED307_11785, ED600_09400, ED607_10425, ED611_04280, ED903_04655, ED944_07260, EEA45_06940, EEP23_06300, EF082_03990, EF173_17005, EG075_10110, EG599_06165, EG796_01190, EG808_04845, EGC26_04915, EGU87_04215, EH186_08760, EH412_00995, EHD45_17860, EHD63_05275, EHD79_13055, EHJ36_00995, EHJ66_06090, EHV81_00555, EHV90_06170, EHW09_05600, EHX09_11795, EI021_04065, EI028_15050, EI032_12380, EI041_02000, EIZ86_06785, EIZ93_11790, EJ366_25995, EJC75_15225, EKI52_18235, EL75_0496, EL79_0518, EL80_0509, ELT20_05045, ELU85_06925, ELV05_02275, ELV08_02985, ELV15_01830, ELV28_06345, EPT01_00415, EQ820_11545, EQ823_05050, EQ830_04520, ERL57_13435, ERS085365_00538, ERS085366_00551, ERS085374_01930, ERS085379_00371, ERS085383_00695, ERS085404_02185, ERS085406_02933, ERS085416_00356, ERS139211_02331, ERS150873_02331, ERS150876_01029, EST51_02745, EVY14_07725, EXM29_19995, ExPECSC019_00712, ExPECSC038_02702, EXX71_13400, EXX78_16730, EYD11_02645, EYX82_02455, EYY34_10615, F1E19_20375, F7F00_12170, F7F11_09035, F7F18_01205, F7F23_11445, F7F26_00405, F7F29_05115, F7G01_13980, F7G03_16150, F9Z74_11630, FAF34_018885, FE846_13735, FKO60_06240, FNJ69_14865, FNJ83_20565, FORC82_0569, FQ022_08190, FQ915_12490, FQR64_03035, FQZ46_16130, FTV92_21230, FV293_08375, FVB16_04440, FWK02_19645, FY127_07380, FZ043_22035, GHR40_07595, GII67_12750, GIY13_09305, GIY19_08335, GJ11_20810, GJD97_02885, GKE15_04665, GKE22_12205, GKE24_04655, GKE26_04130, GKE29_02675, GKE31_04620, GKE39_10535, GKE46_11210, GKE58_04575, GKE60_04100, GKE64_10535, GKE77_05005, GKE87_00910, GKE93_06185, GKF00_03235, GKF03_05520, GKF28_12045, GKF34_04640, GKF47_04635, GKF74_09220, GKF86_04260, GKF89_14375, GKG12_08325, GN312_06640, GNZ00_05080, GNZ02_01290, GNZ03_06110, GP654_17710, GP661_13045, GP664_12080, GP666_12960, GP689_13875, GP712_11385, GP935_13340, GP946_08670, GP950_18225, GQE30_02570, GQE34_13735, GQE51_04670, GQE64_09725, GQE68_06200, GQE88_20265, GQE93_14850, GQM06_05785, GQM09_11065, GQM13_09420, GQM17_12885, GQN16_09500, GRW42_15935, GRW80_12045, HmCmsJML074_04878, HmCmsJML079_04444, HmCmsJML204_02250, HMPREF3040_00351, HW43_20915, MJ49_14345, NCTC10082_02946, NCTC10090_03637, NCTC10418_00837, NCTC10764_03982, NCTC10766_02903, NCTC10865_00786, NCTC10963_00565, NCTC10974_00682, NCTC11022_03358, NCTC11341_01768, NCTC12650_00838, NCTC12950_00597, NCTC13127_00906, NCTC13216_01244, NCTC7922_03906, NCTC7927_00668, NCTC8179_06070, NCTC8500_00486, NCTC8622_00353, NCTC8960_03188, NCTC8985_05122, NCTC9007_04416, NCTC9044_01237, NCTC9050_03718, NCTC9055_02489, NCTC9062_02576, NCTC9077_00732, NCTC9111_00974, NCTC9117_00877, NCTC9701_00685, NCTC9702_00649, NCTC9703_05076, NCTC9706_02844, NCTC9777_02009, PGD_03924, RG28_21075, RK56_014610, RX35_04279, SAMEA3472043_01825, SAMEA3472047_01897, SAMEA3472055_00376, SAMEA3472070_01148, SAMEA3472080_00969, SAMEA3472090_00572, SAMEA3472110_01519, SAMEA3472112_01503, SAMEA3472114_00459, SAMEA3472147_01902, SAMEA3484427_00584, SAMEA3484429_00758, SAMEA3484434_03617, SAMEA3752372_01803, SAMEA3752553_01163, SAMEA3752557_01851, SAMEA3752559_03249, SAMEA3752620_02365, SAMEA3753064_02960, SAMEA3753164_02324, SAMEA3753290_00124, SAMEA3753300_02107, SK85_03504, UC41_09935, UN86_15380, WQ89_06640, WR15_24440, YDC107_1864
UniProt
Find proteins for P64602 (Escherichia coli (strain K12)) Explore P64602  Go to UniProtKB:  P64602

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Toluene tolerance protein Ttg2A	I [auth F], J [auth G]	269	Escherichia coli 909945-2	Mutation(s): 0  Gene Names: HMPREF1620_02486

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	K [auth E], L [auth H]	260	Escherichia coli 2.3916	Mutation(s): 0  Gene Names: EC23916_1052

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Dong, C.J., Dong, H.H.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	2017YFA0504803, 2018YFA0507700, 2017YFC0840100, 2017YFC00840101,31900039,81971974
Wellcome Trust	United Kingdom	WT106121MA

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2021-01-20
  Changes: Database references
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references