6ZY3

Cryo-EM structure of MlaFEDB in complex with phospholipid


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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YrbD protein183Escherichia coli B185Mutation(s): 0 
Gene Names: ECDG_03382
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS componentG [auth B],
H [auth C]
105Escherichia coliMutation(s): 0 
Gene Names: 
mlaByrbBA6581_13415A6592_14225A6V01_00625A8C65_02170A9P13_02945A9R57_12600A9X72_02835AC067_23675ACN002_3282ACN68_12355ACN81_18445ACU57_14445ACU90_11565AM270_15510AM446_04320AM464_08585AMK83_06340AML07_19340APT94_23200APZ14_04295ARC77_12405AU473_05735AUQ13_03075AUS26_18260AW106_13275AWB10_02850AWG90_020620AWP75_14100B9M99_10250B9T59_16250BANRA_01811BANRA_03804BANRA_03999BANRA_04207BB545_09780BE963_06830BER14_09135BHJ80_21985BHS81_19200BHS87_17970BIQ87_18040BIU72_05405BJJ90_02770BK292_10220BK296_13050BK373_10175BK375_18740BK383_15965BMA87_01295BMT49_25595BMT91_11610BOH76_04915BON63_14235BON66_12205BON69_26555BON71_25170BON72_13935BON75_23145BON76_05525BON83_09240BON86_01565BON87_18195BON92_11035BON94_12335BON95_22020BON96_06355BTQ04_16475BTQ06_11870BUE81_19690BvCms2454_04822BvCms28BK_03527BvCms35BK_01543BvCmsHHP001_01202BvCmsHHP019_05314BvCmsKKP061_00888BvCmsKSNP073_02163BvCmsKSNP081_00287BvCmsKSP011_02050BvCmsKSP024_00283BvCmsKSP026_00502BvCmsKSP045_01650BvCmsKSP067_01464BvCmsNSNP036_02151BvCmsNSP006_04640BvCmsNSP047_04118BvCmsNSP072_03187BvCmsOUP014_03632BvCmsSINP011_04458BvCmsSIP019_00407BvCmsSIP044_00137BVL39_10130BW690_19360BWI89_22070BWP17_10155BXT93_02550BZL31_05925BZL69_07715C2M16_04215C5715_22795C5N07_18070C5P01_18835C6669_12020C7235_03225C7B02_15875C7B08_03565C7B18_13830C9098_07790C9114_15455C9141_00390C9160_02340C9162_04110C9201_13875C9306_00415C9E25_11270C9E67_03375C9Z03_07490C9Z28_00385C9Z29_07190C9Z37_14660C9Z39_14275C9Z43_00380C9Z68_06245C9Z69_11175C9Z70_06765C9Z78_03315C9Z89_09065CA593_10345CDL37_12215CF006_16665CG692_07300CI641_009255CI693_03675CI694_20835CIG45_16045CJU63_19140CJU64_19020CMR93_08835CO706_14630COD30_12915COD46_10760CQP61_03650CR538_03070CR539_21250CRD98_04715CRE06_06830CRM83_23500CRX46_03745CVH05_10780CWM24_22870CWS33_08375D0X26_09090D2184_10505D2185_00445D2188_02580D3821_08325D3822_14575D3O91_07625D3P01_09160D3Y67_18290D4011_13725D4074_02435D4628_02655D4636_02890D4638_00790D4660_02830D4718_09085D4L91_11950D4M06_11225D4U85_14330D5H35_09780D5I97_10670D6004_08125D6C36_14160D6D43_15510D6T60_15390D6T98_02410D6W00_14015D6X36_05360D6X63_01430D6X76_04335D7K33_12855D7K63_12220D7K66_04495D7W70_15855D7Z75_02945D8Y65_13475D9610_07810D9C99_05120D9D20_06275D9D31_14515D9D43_03615D9D44_04410D9E19_10400D9E34_11740D9E49_09595D9F17_07200D9F32_01240D9F87_05870D9G29_07025D9G48_11290D9G69_01100D9G95_17085D9H53_01195D9H68_07560D9I18_07175D9I88_07240D9J03_05150D9J11_01130D9J44_07850D9J52_07915D9J58_06110D9J60_11185D9J63_16910D9J78_05130D9K02_06080D9K48_12255D9L89_05370D9S45_00255D9X77_02330D9X97_03120D9Z28_03370DAH18_20610DAH26_17315DAH30_12875DAH32_13975DAH34_01980DAH37_04255DAH43_16780DBQ99_04040DD762_13125DEN86_08060DEN89_09405DEN97_16135DEO04_19605DEO19_06430DIV22_02975DJ503_19040DK132_07375DL257_05650DL292_05795DL326_06060DL455_12700DL479_06590DL530_10055DL705_01300DL800_23275DLT82_02655DLU50_08550DLU67_08375DLU82_10330DLW60_07490DLW88_04795DLY41_08155DM102_15165DM155_07645DM267_03265DM280_09055DM296_04835DM382_07360DM820_04625DM962_02640DM973_04650DMI04_04270DMI53_12715DMO02_15405DMY83_09920DN660_01330DN700_04595DN703_01080DN808_01890DNB37_13705DNC98_07160DND16_06535DND79_01330DNI21_03635DNJ62_12070DNK12_02835DNQ45_01620DNW42_05405DNX19_05580DNX30_11365DOE35_12610DOS18_13030DOT81_04255DOU81_12375DOY22_14085DOY56_12245DOY61_04695DOY67_01285DP265_06555DP277_10105DQE83_16545DQE91_01265DQF36_08635DQF57_03615DQF71_07160DQF72_06460DQG35_02830DQO13_01295DQP61_01770DRP48_13910DRW19_01295DS143_06770DS721_11090DS732_23695DT034_01270DTL43_04295DTM10_06985DTM45_14510DTZ20_12090DU309_11135DU321_08670DVB38_07395DXT69_05520DXT71_00440DXX80_009590E0I42_14340E0K84_17700E0L12_03915E2119_05870E2127_02575E2128_02495E2129_05760E2134_15595E2135_08080E2855_04145E2863_03970E4K55_06660E4K61_09280E5P22_07075E5P28_12910E5P37_13135E5S42_17100E5S46_15725E5S47_16890E5S58_02935E5S61_19420EA214_08600EA223_04825EA225_07080EA233_06175EAI42_05495EAI52_09890EAM59_01020EAN70_10745EAX79_13230EB476_09250EB509_07200EB510_12405EB515_07025EBA84_05830EBJ06_06135EBM08_05455EC1094V2_454EC3234A_53c00700EC3426_04342EC95NR1_02575ECTO6_00563ED225_04270ED307_11785ED600_09400ED607_10425ED611_04280ED903_04655ED944_07260EEA45_06940EEP23_06300EF082_03990EF173_17005EG075_10110EG599_06165EG796_01190EG808_04845EGC26_04915EGU87_04215EH186_08760EH412_00995EHD45_17860EHD63_05275EHD79_13055EHJ36_00995EHJ66_06090EHV81_00555EHV90_06170EHW09_05600EHX09_11795EI021_04065EI028_15050EI032_12380EI041_02000EIZ86_06785EIZ93_11790EJ366_25995EJC75_15225EKI52_18235EL75_0496EL79_0518EL80_0509ELT20_05045ELU85_06925ELV05_02275ELV08_02985ELV15_01830ELV28_06345EPT01_00415EQ820_11545EQ823_05050EQ830_04520ERL57_13435ERS085365_00538ERS085366_00551ERS085374_01930ERS085379_00371ERS085383_00695ERS085404_02185ERS085406_02933ERS085416_00356ERS139211_02331ERS150873_02331ERS150876_01029EST51_02745EVY14_07725EXM29_19995ExPECSC019_00712ExPECSC038_02702EXX71_13400EXX78_16730EYD11_02645EYX82_02455EYY34_10615F1E19_20375F7F00_12170F7F11_09035F7F18_01205F7F23_11445F7F26_00405F7F29_05115F7G01_13980F7G03_16150F9Z74_11630FAF34_018885FE846_13735FKO60_06240FNJ69_14865FNJ83_20565FORC82_0569FQ022_08190FQ915_12490FQR64_03035FQZ46_16130FTV92_21230FV293_08375FVB16_04440FWK02_19645FY127_07380FZ043_22035GHR40_07595GII67_12750GIY13_09305GIY19_08335GJ11_20810GJD97_02885GKE15_04665GKE22_12205GKE24_04655GKE26_04130GKE29_02675GKE31_04620GKE39_10535GKE46_11210GKE58_04575GKE60_04100GKE64_10535GKE77_05005GKE87_00910GKE93_06185GKF00_03235GKF03_05520GKF28_12045GKF34_04640GKF47_04635GKF74_09220GKF86_04260GKF89_14375GKG12_08325GN312_06640GNZ00_05080GNZ02_01290GNZ03_06110GP654_17710GP661_13045GP664_12080GP666_12960GP689_13875GP712_11385GP935_13340GP946_08670GP950_18225GQE30_02570GQE34_13735GQE51_04670GQE64_09725GQE68_06200GQE88_20265GQE93_14850GQM06_05785GQM09_11065GQM13_09420GQM17_12885GQN16_09500GRW42_15935GRW80_12045HmCmsJML074_04878HmCmsJML079_04444HmCmsJML204_02250HMPREF3040_00351HW43_20915MJ49_14345NCTC10082_02946NCTC10090_03637NCTC10418_00837NCTC10764_03982NCTC10766_02903NCTC10865_00786NCTC10963_00565NCTC10974_00682NCTC11022_03358NCTC11341_01768NCTC12650_00838NCTC12950_00597NCTC13127_00906NCTC13216_01244NCTC7922_03906NCTC7927_00668NCTC8179_06070NCTC8500_00486NCTC8622_00353NCTC8960_03188NCTC8985_05122NCTC9007_04416NCTC9044_01237NCTC9050_03718NCTC9055_02489NCTC9062_02576NCTC9077_00732NCTC9111_00974NCTC9117_00877NCTC9701_00685NCTC9702_00649NCTC9703_05076NCTC9706_02844NCTC9777_02009PGD_03924RG28_21075RK56_014610RX35_04279SAMEA3472043_01825SAMEA3472047_01897SAMEA3472055_00376SAMEA3472070_01148SAMEA3472080_00969SAMEA3472090_00572SAMEA3472110_01519SAMEA3472112_01503SAMEA3472114_00459SAMEA3472147_01902SAMEA3484427_00584SAMEA3484429_00758SAMEA3484434_03617SAMEA3752372_01803SAMEA3752553_01163SAMEA3752557_01851SAMEA3752559_03249SAMEA3752620_02365SAMEA3753064_02960SAMEA3753164_02324SAMEA3753290_00124SAMEA3753300_02107SK85_03504UC41_09935UN86_15380WQ89_06640WR15_24440YDC107_1864

UniProt
Find proteins for P64602 (Escherichia coli (strain K12))
Explore P64602 
Go to UniProtKB:  P64602
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP64602
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Toluene tolerance protein Ttg2AI [auth F],
J [auth G]
269Escherichia coli 909945-2Mutation(s): 0 
Gene Names: HMPREF1620_02486
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinK [auth E],
L [auth H]
260Escherichia coli 2.3916Mutation(s): 0 
Gene Names: EC23916_1052
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEE (Subject of Investigation/LOI)
Query on PEE

Download Ideal Coordinates CCD File 
M [auth H]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China2017YFA0504803, 2018YFA0507700, 2017YFC0840100, 2017YFC00840101,31900039,81971974
Wellcome TrustUnited KingdomWT106121MA

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