7B5P | pdb_00007b5p

AcrB in cycloalkane amphipol

• PDB DOI: https://doi.org/10.2210/pdb7B5P/pdb
• EM Map EMD-12043: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-12-05 Released: 2021-12-08 
• Deposition Author(s): Higgins, A.J., Flynn, A.J., Muench, S.P.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cycloalkane-modified amphiphilic polymers provide direct extraction of membrane proteins for CryoEM analysis.

Higgins, A.J., Flynn, A.J., Marconnet, A., Musgrove, L.J., Postis, V.L.G., Lippiat, J.D., Chung, C.W., Ceska, T., Zoonens, M., Sobott, F., Muench, S.P.

(2021) Commun Biol 4: 1337-1337

• PubMed: 34824357 
• DOI: https://doi.org/10.1038/s42003-021-02834-3
• Primary Citation of Related Structures:  
  7B5P


• PubMed Abstract: 
  

  Membrane proteins are essential for cellular growth, signalling and homeostasis, making up a large proportion of therapeutic targets. However, the necessity for a solubilising agent to extract them from the membrane creates challenges in their structural and functional study. Although amphipols have been very effective for single-particle electron cryo-microscopy (cryoEM) and mass spectrometry, they rely on initial detergent extraction before exchange into the amphipol environment. Therefore, circumventing this pre-requirement would be a big advantage. Here we use an alternative type of amphipol: a cycloalkane-modified amphiphile polymer (CyclAPol) to extract Escherichia coli AcrB directly from the membrane and demonstrate that the protein can be isolated in a one-step purification with the resultant cryoEM structure achieving 3.2 Å resolution. Together this work shows that cycloalkane amphipols provide a powerful approach for the study of membrane proteins, allowing native extraction and high-resolution structure determination by cryoEM.

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Organizational Affiliation: 
• School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
Université de Paris, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, F-75005, Paris, France.
Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le dévelopement de la recherche scientifique, F-75005, Paris, France.
Wellcome Centre for Anti-Infectives Research, Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 5EH, UK.
GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK.
UCB Pharma, Slough, SL1 3WE, UK.
Université de Paris, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, F-75005, Paris, France. [e-mail].
Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le dévelopement de la recherche scientifique, F-75005, Paris, France. [e-mail].
School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. [e-mail].
School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 341.76 kDa 
• Atom Count: 22,527 
• Modeled Residue Count: 3,013 
• Deposited Residue Count: 3,153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Efflux pump membrane transporter	A [auth B], B [auth C], C [auth A]	1,051	Escherichia coli	Mutation(s): 0  Gene Names:  acrB_1, acrB, acrB_2, acrB_3, acrB_4, acrB_5, acrB_6, A8C65_09270, A9819_02265, A9X72_18695, AC789_1c04620, ACN002_0478, ACN68_10695, ACN81_24630, ACU57_11680, ACU90_20590, AM270_01980, AM464_19305, AMK83_09190, AML35_17310, AUQ13_18190, AW059_13640, AWB10_19050, AWG78_005565, B6V57_02435, BANRA_00889, BANRA_00999, BB545_15910, BEN53_04520, BHF03_18080, BHF46_21335, BHS81_02950, BHS87_02495, BIQ87_02540, BIZ41_13825, BJJ90_19940, BK248_01725, BK292_14280, BK296_16050, BK334_05580, BK373_00965, BK383_14595, BMA87_04530, BMT49_03610, BMT91_04935, BN17_02651, BOH76_16460, BON63_11900, BON65_19130, BON66_08715, BON69_11225, BON71_10040, BON72_14720, BON75_11085, BON76_24190, BON86_26060, BON94_15210, BON95_06075, BON98_18530, BTQ06_00925, BUE81_06435, BvCms12BK_04863, BvCms2454_01835, BvCms28BK_00632, BvCmsC61A_03075, BvCmsHHP019_03148, BvCmsHHP056_01479, BvCmsKKP061_00163, BvCmsKSNP073_04604, BvCmsKSNP081_04683, BvCmsKSNP120_04201, BvCmsKSP011_05014, BvCmsKSP024_04861, BvCmsKSP026_02627, BvCmsKSP045_04703, BvCmsKSP058_04933, BvCmsKSP067_05122, BvCmsKSP076_04688, BvCmsNSNP036_04234, BvCmsNSP006_01210, BvCmsNSP007_00776, BvCmsNSP047_01693, BvCmsNSP072_02397, BvCmsOUP014_01037, BvCmsSINP011_02642, BvCmsSINP022_01605, BvCmsSIP019_03696, BvCmsSIP044_00930, BW690_06940, BWI89_12175, BXT93_07785, BZL31_19295, C2U48_07740, C4K41_07725, C4M78_18085, C5F73_09745, C5N07_13110, C5P01_15940, C5P44_16955, C6669_02375, C6B13_10325, C7B02_04170, C7B06_13000, C7B07_14810, C9114_13235, C9141_12200, C9160_00185, C9162_13005, C9201_04165, C9E25_04215, C9Z03_06210, C9Z23_00255, C9Z28_08635, C9Z37_05005, C9Z39_05195, C9Z43_06095, C9Z69_16095, C9Z70_09245, CA593_00820, CDC27_01240, CDL37_08810, CF006_06195, CG692_04680, CI693_16095, CI694_14685, CIG45_11530, CJU63_02500, CJU64_02490, CMR93_03420, CO706_24730, COD46_04485, CR538_19130, CR539_06565, CRD98_02045, CRJUMX01_650090, CRM83_13415, CT146_16100, CV83915_01104, CWS33_13665, D0X26_07790, D2184_11155, D2185_12425, D3C88_31425, D3O91_18365, D4023_06520, D4628_13155, D4636_06025, D4638_05215, D4718_02720, D4V08_10150, D6T60_09670, D6T98_07735, D6W00_12590, D6X36_16210, D7W70_07875, D7Z75_05690, D9C99_07900, D9D20_11125, D9D44_10685, D9E13_00485, D9E19_02400, D9E35_07135, D9E73_21575, D9F17_03155, D9F32_03530, D9F87_10685, D9G11_17580, D9G29_00450, D9G42_13565, D9G69_10585, D9G95_10390, D9H36_07220, D9H68_03680, D9H70_06065, D9H94_07380, D9I18_05035, D9I87_03680, D9I97_02625, D9J11_02570, D9J44_06200, D9J52_11760, D9J63_03815, D9K02_03900, D9K54_20470, D9Z28_24640, DAH18_15350, DAH30_15550, DAH34_12755, DAH37_04875, DB359_14850, DBQ99_19255, DEN89_14865, DEN97_16890, DEO04_04920, DEO19_17525, DEO20_17510, DJ487_10315, DJ503_01450, DK132_02395, DL292_07005, DL326_11785, DL479_02540, DL545_18765, DL705_13145, DLU50_07900, DLU67_10935, DLU82_01970, DLW88_19215, DLX40_09005, DLY41_06715, DLY44_14465, DM129_08550, DM267_01255, DM296_06955, DM382_09705, DM820_06155, DM973_09850, DMY83_13165, DN627_04140, DN660_06030, DN700_07110, DN808_01530, DNC98_06145, DND79_04450, DNI21_09935, DNR35_00855, DNW42_12745, DNX19_03500, DOY61_02460, DOY67_09480, DP258_04725, DP265_04400, DP277_07910, DQE91_07055, DQF36_01200, DQF57_08040, DQF72_04240, DQO13_05880, DQP61_17770, DRW19_06780, DS732_07285, DT034_10130, DTL43_07030, DTL90_18880, DTM10_06440, DU333_14630, DW236_16180, DWB25_18810, DXT69_07740, DXT71_02600, DXT73_02225, E0I42_07045, E0K84_10260, E2112_11465, E2114_15395, E2115_11930, E2119_01370, E2127_09005, E2128_08320, E2129_12030, E2134_12580, E2135_12650, E2148_08850, E4A44_12425, E4K51_12425, E4K55_09900, E4K60_11595, E5P22_01620, E5P24_11315, E5P28_18315, E5P37_02890, E5S42_13425, E5S56_04760, EA184_13145, EA189_17430, EA218_08750, EA223_15405, EA231_12325, EA239_15375, EA250_11755, EA429_15685, EAI46_01035, EAI52_03305, EAN77_07570, EAX79_06460, EB476_04025, EB525_RS00175, EC1094V2_3386, EC3426_01300, EC382_09135, ECONIH1_02500, ECTO6_03638, ED178_10910, ED307_06795, ED648_02095, EEP23_01410, EG075_08750, EG796_01740, EH186_13990, EHD79_03845, EI021_20720, EI028_12150, EI032_07905, EI041_08500, EIA08_09625, EIA21_12180, EJC75_24510, EL75_3290, EL79_3385, EL80_3339, ELT20_07985, ELT58_12170, ELV08_01140, ELY05_12005, EO241_14205, EPT01_06710, EPU41_02295, EQ825_17705, ERS085365_02371, ERS085366_03391, ERS085374_02303, ERS085379_01141, ERS139211_01948, ERS150873_01787, ExPECSC019_00381, ExPECSC038_03243, EXX06_12030, EXX13_09300, EXX23_10330, EXX24_02235, EXX53_07265, EXX55_11505, EXX71_19130, EXX78_05470, EXX87_11195, EYD11_17095, EYX82_01500, EYX99_02255, EYY27_15910, EYY78_02330, F1E13_02930, F1E19_02810, F7F11_07205, F7F18_02645, F7F29_13450, F7F56_10820, F9040_08845, F9225_13995, F9X20_11065, F9Z53_11120, F9Z74_08955, FORC82_3586, FQ022_06350, FQ915_11580, FQR64_17285, FQU83_20500, FQZ46_14155, FRV13_04215, FV293_05765, FV438_08525, FZ043_05490, FZN06_02310, FZN30_08470, G3V64_03945, G5603_08575, G5608_10915, G5616_17800, G5632_14455, G5686_06550, G5688_07040, GHR40_21640, GII67_09125, GII91_03825, GKF21_12125, GKF28_11295, GKF34_11195, GKF39_01530, GKF47_11385, GKF52_13635, GKF74_01825, GKF86_04555, GKF89_04410, GKG12_03295, GNZ03_09590, GNZ05_01310, GP650_17935, GP654_09140, GP666_11010, GP671_13130, GP678_16470, GP689_14290, GP698_14015, GP700_10545, GP720_06095, GP727_13610, GP892_11190, GP912_14175, GP935_15175, GP945_16670, GP946_00315, GP950_13345, GQA06_04590, GQA23_11080, GQA63_01155, GQA64_12425, GQE22_08970, GQE30_17545, GQE33_07470, GQE34_01120, GQE42_04545, GQE51_10380, GQE58_13150, GQE64_19110, GQE87_01345, GQE93_05675, GQF59_01155, GQL64_11830, GQM10_04910, GQM17_15105, GQM18_02835, GQM28_04965, GQN16_06365, GQN24_05120, GQY14_07730, GRW05_06170, GRW12_18865, GRW27_17010, GRW30_01790, GRW42_02940, GRW80_13135, GRW81_04465, GUB85_11530, GUB91_14860, GUB95_14530, GUC01_07830, GUC12_14650, GZS12_17565, HmCms184_01943, HmCmsJML079_00721, HmCmsJML146_03063, HmCmsJML204_02413, HW43_05935, MJ49_04125, MS6198_04670, MS8345_00466, NCTC10418_05566, NCTC10766_05800, NCTC10865_04672, NCTC10963_03279, NCTC11126_00116, NCTC11181_01060, NCTC12650_04129, NCTC13148_06601, NCTC13216_02965, NCTC13846_03608, NCTC9007_00190, NCTC9036_03767, NCTC9045_04279, NCTC9055_00632, NCTC9058_03192, NCTC9062_04550, NCTC9111_03904, NCTC9117_04708, NCTC9119_03922, NCTC9434_02883, NCTC9706_01042, NCTC9969_03956, PGD_02849, PU06_12600, RG28_02520, RK56_026290, RX35_02133, SAMEA3472043_02753, SAMEA3472044_00392, SAMEA3472047_02966, SAMEA3472055_02089, SAMEA3472056_03557, SAMEA3472070_02210, SAMEA3472080_01739, SAMEA3472090_01741, SAMEA3472108_01933, SAMEA3472114_01186, SAMEA3484427_03472, SAMEA3484429_01960, SAMEA3485101_03912, SAMEA3752553_00212, SAMEA3752557_00298, SAMEA3752559_02826, SAMEA3752620_00857, SAMEA3753064_01307, SAMEA3753097_00439, SAMEA3753164_00290, SAMEA3753290_01796, SAMEA3753300_00529, SK85_00486, UN86_09270, UN91_18355, WQ89_01050, WR15_04005 Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 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: 2021-12-08 
Deposition Author(s): Higgins, A.J., Flynn, A.J., Muench, S.P.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R018561/1/

Revision History  

• Version 1.0: 2021-12-08
  Type: Initial release
  
• Version 1.1: 2024-07-10
  Changes: Data collection
• Version 1.2: 2025-07-02
  Changes: Data collection, Structure summary