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- PDB-7ph7: Nanodisc reconstituted MsbA in complex with nanobodies, spin-labe... -

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Basic information

Entry
Database: PDB / ID: 7ph7
TitleNanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position T68C
Components
  • ATP-binding transport protein multicopy suppressor of htrB
  • Nb_MsbA#1
KeywordsMEMBRANE PROTEIN / ABC transporter / nanobody / Gd-DOTA / lipid A
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, lipid A-core flippase, MsbA / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...ABC transporter, lipid A-core flippase, MsbA / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-88T / Chem-EIW / GADOLINIUM ATOM / ATP-binding transport protein MsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Vicugna pacos (alpaca)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsParey, K. / Januliene, D. / Galazzo, L. / Meier, G. / Vecchis, D. / Striednig, B. / Hilbi, H. / Schaefer, L.V. / Kuprov, I. / Bordignon, E. ...Parey, K. / Januliene, D. / Galazzo, L. / Meier, G. / Vecchis, D. / Striednig, B. / Hilbi, H. / Schaefer, L.V. / Kuprov, I. / Bordignon, E. / Seeger, M.A. / Moeller, A.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC944 Germany
German Research Foundation (DFG)SCHA 1574/6-1 Germany
German Research Foundation (DFG)EXC 2033 - 390677874 - RESOLV Germany
CitationJournal: Sci Adv / Year: 2022
Title: The ABC transporter MsbA adopts the wide inward-open conformation in cells.
Authors: Laura Galazzo / Gianmarco Meier / Dovile Januliene / Kristian Parey / Dario De Vecchis / Bianca Striednig / Hubert Hilbi / Lars V Schäfer / Ilya Kuprov / Arne Moeller / Enrica Bordignon / Markus A Seeger /
Abstract: Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their ...Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.
History
DepositionAug 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-binding transport protein multicopy suppressor of htrB
B: ATP-binding transport protein multicopy suppressor of htrB
C: Nb_MsbA#1
D: Nb_MsbA#1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7719
Polymers156,2014
Non-polymers3,5705
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area16300 Å2
ΔGint-124 kcal/mol
Surface area65670 Å2
MethodPISA

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Components

#1: Protein ATP-binding transport protein multicopy suppressor of htrB / Fused lipid transporter subunits of ABC superfamily: membrane component/ATP-binding component / ...Fused lipid transporter subunits of ABC superfamily: membrane component/ATP-binding component / Lipid A ABC exporter / fused ATPase and inner membrane subunits MsbA / Lipid A ABC transporter ATP-binding protein/permease MsbA / Lipid A export ATP-binding/permease MsbA / Lipid ABC transporter permease/ATP-binding protein / Lipid ABC transporter permease/ATPase / Lipid transporter ATP-binding/permease / MsbA_1 protein / Vga(B)_1_U82085


Mass: 65760.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: msbA, msbA_1, msbA_2, A6519_002657, A6583_03380, A8W81_004300, A9819_04800, A9X72_16400, ABE90_014965, ACN002_0966, ACN81_15380, ACU57_24985, AM270_11745, AM340_16275, AM464_22545, AML23_19245, ...Gene: msbA, msbA_1, msbA_2, A6519_002657, A6583_03380, A8W81_004300, A9819_04800, A9X72_16400, ABE90_014965, ACN002_0966, ACN81_15380, ACU57_24985, AM270_11745, AM340_16275, AM464_22545, AML23_19245, AT335_004069, AT845_000133, AUQ29_08145, AW118_05720, B6R17_000782, B6R27_001671, B6R48_004108, B6R87_004021, B7C15_003805, B9T59_23370, BANRA_01415, BANRA_01429, BANRA_01870, BANRA_04732, BB545_18890, BE930_09255, BER14_06940, BFL24_05720, BHF52_24880, BHS81_05720, BHS87_04865, BIZ41_01230, BJI68_12025, BJJ90_16965, BK272_01105, BK292_06360, BK375_14490, BMR21_05685, BMT50_27640, BMT91_04170, BN17_07751, BO068_002027, BOH76_14605, BON63_21995, BON65_05320, BON70_17525, BON72_03180, BON73_13825, BON76_25985, BON83_06085, BON86_09625, BON87_27260, BON92_08485, BON93_08135, BON94_25200, BON95_16785, BON98_06205, BTQ06_17225, BUE81_07620, BUE82_15395, BvCms2454_01012, BvCmsHHP019_00240, BvCmsHHP056_02753, BvCmsKKP036_03474, BvCmsKKP057_04444, BvCmsKKP061_04589, BvCmsKSNP073_02255, BvCmsKSP011_04133, BvCmsKSP067_04779, BvCmsKSP076_02409, BvCmsNSNP036_02201, BvCmsSIP082_02235, BVL39_23700, BXT93_13710, C2U48_04965, C3F40_07720, C4M78_08380, C5542_002813, C5F72_16745, C5N07_03265, C5Y87_10910, C6B13_07725, C6B22_10100, C6L19_001588, C6N50_003378, C7B02_01770, C9114_12150, C9160_08345, C9E67_20675, C9Z68_12550, CA593_23990, CCS08_03180, CDL36_06595, CDL37_15135, CDL57_07045, CF32_003389, CG692_03365, CG831_002276, CIG67_23400, CN875_000708, CO706_27405, COD50_05160, CQP61_10815, CR539_09135, CV83915_00690, CWS33_13120, CXJ73_002058, CY655_05185, D0X26_04540, D2183_24450, D3O91_14025, D3Y67_02540, D4V09_10155, D5H22_11140, D6T60_13225, D9D31_03340, D9D43_06690, D9D77_11865, D9E34_03365, D9F92_01915, D9H13_11555, D9H94_06915, D9J03_07670, D9J11_05210, D9K17_11210, DAH18_03035, DAH23_13205, DAH34_01125, DAH37_00585, DAH50_02210, DB282_07550, DD762_16175, DEN86_14305, DEN89_03425, DEN95_10710, DEO15_17500, DIV22_10835, DNX30_10425, DRW19_14025, DS732_09570, DTL43_10175, DTL90_05565, DXT69_23270, DXT71_05215, DXT73_09740, E0I42_08570, E0N24_23200, E0P28_13815, E2112_02115, E2119_08300, E2127_01135, E2128_05560, E2129_04820, E2135_02055, E4K51_09740, E4K54_00580, E5P52_13385, E5S34_05660, E5S35_04055, E5S38_09040, E5S43_05210, E5S47_11130, E5S52_11170, E5S61_08545, E5S62_04865, EAI46_02335, EAN77_14050, EC1094V2_2917, EC3234A_23c00180, EC95NR1_05191, ECs0997, EGC08_15830, EH88_002077, EHD79_04505, EHH55_13005, EI021_01080, EI041_12680, EIA08_02100, EIA13_09425, EIZ93_00575, EKI52_05875, EL79_2904, EL80_2842, ELT21_02010, ELT29_09755, ELT49_23725, ELV08_17635, ELV10_15150, ELV15_06100, ELV28_02850, ELX76_08675, ELX96_01205, ELY05_17895, ELY32_10925, ELY41_16195, ELY48_22120, EO241_05695, ERS139208_02792, ETECE36_03997, ETECE925_03058, EVY14_21410, ExPECSC038_03334, EXX13_00100, EYX47_00395, EYX55_20050, EYY34_02850, F2N31_11485, F3N40_21340, F6U69_03820, F9400_05025, F9407_17390, F9571_11380, F9B07_02055, F9S76_10820, F9V07_15065, F9V24_13720, F9X20_013070, F9X20_13170, FC554_21655, FDM60_03230, FFF58_05225, FGG80_22070, FMP09_04685, FOI11_008365, FOI11_11680, FPS82_01020, FQ021_09215, FQE77_03700, FQF29_10975, FV293_16625, FWK02_08630, FY127_20475, G4A38_14240, G5603_01415, G5696_09455, G7635_003895, G9448_05965, GAJ26_08300, GBE29_03250, GF646_03230, GF699_01980, GFY34_01280, GIB53_08740, GKF52_12915, GKF86_06495, GKF89_10460, GKG12_04785, GLW94_06610, GNZ05_08600, GOP20_01470, GP650_11715, GP662_17675, GP946_17935, GP979_00615, GQE42_02625, GQE64_04965, GQE87_02855, GQF58_12480, GQF59_12005, GQM04_13340, GQM09_13435, GQM10_19610, GQM13_15270, GQR15_15695, GQW76_08435, GQW80_18480, GRQ19_15240, GRW05_05270, GRW57_16455, GRW80_07070, GRW81_12285, GSY44_02515, GTP88_06305, GUB08_12365, GUB92_16760, GUC01_02505, H0O72_02105, H4P50_16515, H4P51_16365, HCF72_002462, HH411_000415, HH795_003376, HHG09_003242, HHH44_001077, HIE44_000973, HIR12_000741, HJM92_000296, HJN04_000401, HJO75_001041, HL425_03810, HL563_08835, HL601_14000, HLU10_14490, HLV18_14815, HLZ20_01105, HLZ50_00845, HmCms184_00694, HmCmsJML074_03039, HMJ82_16850, HMS79_05975, HMT08_20940, HMU48_16915, HMV95_03075, HNC36_01345, HNC38_15880, HNC52_01100, HNC59_18065, HNC99_19615, HND12_01880, HND24_12010, HNO08_02960, HNV65_06485, HNV94_02370, HNY50_12835, HNY54_05355, HPE39_08505, HV109_15490, HVV53_00230, HVW04_06410, HVW43_07760, HVY77_17160, HVZ33_15895, HVZ71_16085, HX136_16500, HZ71_000143, I6H00_09440, I6H01_22140, I6H02_23385, IA00_002659, JE86ST02C_10230, JE86ST05C_10770, NCTC10090_00491, NCTC10764_04605, NCTC10974_03682, NCTC11022_00376, NCTC11126_01170, NCTC11181_00391, NCTC11341_04668, NCTC13127_04478, NCTC13148_05927, NCTC13216_03514, NCTC4450_03952, NCTC8008_02844, NCTC8450_03697, NCTC8960_00595, NCTC8985_01994, NCTC9036_03317, NCTC9048_03196, NCTC9050_01167, NCTC9117_04053, NCTC9706_00592, NCTC9775_05686, NCTC9969_03388, ND22_004923, PGD_02377, PU06_09035, RG28_18920, SAMEA3472043_03213, SAMEA3472044_00113, SAMEA3472056_00386, SAMEA3472064_00296, SAMEA3472080_00651, SAMEA3472120_01782, SAMEA3484427_02830, SAMEA3484429_00081, SAMEA3485101_00393, SAMEA3485110_01711, SAMEA3751407_00423, SAMEA3752386_00337, SAMEA3753064_00778, SAMEA3753290_02602, SAMEA3753300_02847, SM09_01759, THOESC010_28510, TUM18780_27110, WP2S18E08_30120, WP4S18E08_28590, WQ89_23900, WR15_11915
Production host: Escherichia coli (E. coli) / References: UniProt: C3TGA2
#2: Protein Nb_MsbA#1


Mass: 12339.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Nanobody is labeled with GMO-GD at Cys68 / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-EIW / (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(3~{R})-3-nonanoyloxytetradecanoyl]oxy-5-[[(3~{R})-3-octanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{S},5~{S},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanylnonanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-oxan-2-yl]methoxy]-5-oxidanyl-oxane-2-carboxylic acid


Mass: 2206.503 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C102H186N2O44P2
#4: Chemical ChemComp-88T / (1~{R},4~{R},11~{S},14~{S},19~{Z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione


Mass: 524.524 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C22H32N6O9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli MsbA in complex with nanobody Nb_MsbA#1, labeled with Gd-DOTA at T68C
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 2.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
10cryoSPARCv3.0.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13cryoSPARCv3.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 247610 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00810846
ELECTRON MICROSCOPYf_angle_d0.90914644
ELECTRON MICROSCOPYf_dihedral_angle_d18.2661566
ELECTRON MICROSCOPYf_chiral_restr0.0521725
ELECTRON MICROSCOPYf_plane_restr0.0071844

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