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 OPM PDBTM MemProtMD mpstruc

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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-021-02834-3
Primary Citation 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.

Organizational Affiliation

School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.

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

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| 3D Structure

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... 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31224
Sequence Annotations Expand
Reference Sequence