6ZY3

Cryo-EM structure of MlaFEDB in complex with phospholipid

PDB DOI: https://doi.org/10.2210/pdb6ZY3/pdb
EM Map EMD-11548: 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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

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.

Macromolecule Content

Total Structure Weight: 255.92 kDa
Atom Count: 15,770
Modelled Residue Count: 2,071
Deposited Residue Count: 2,366
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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] 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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... 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P64602
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEE (Subject of Investigation/LOI) Query on PEE Download Ideal Coordinates CCD File SDF format, chain M [auth H] MOL2 format, chain M [auth H] mmCIF format, chain M [auth H]	M [auth H]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain M [auth H] Interactions & Density Focus chain M [auth H]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-25

Deposition Author(s):

Dong, C.J.

Dong, H.H.

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

Revision History (Full details and data files)

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 2.0: 2024-05-01
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary