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- PDB-8vlw: TolQ-TolR inner membrane protein complex from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 8vlw
TitleTolQ-TolR inner membrane protein complex from Acinetobacter baumannii
Components
  • Tol-Pal system protein TolQ
  • Tol-Pal system protein TolR
KeywordsMEMBRANE PROTEIN / inner membrane protein complex / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


bacteriocin transport / protein import / transmembrane transporter activity / protein transport / cell division / plasma membrane
Similarity search - Function
Tol-Pal system, TolQ / Tol-Pal system protein TolR / : / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family
Similarity search - Domain/homology
Tol-Pal system protein TolR / Tol-Pal system protein TolQ
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsGuo, Y. / Borek, D. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2024
Title: Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogen .
Authors: Elina Karimullina / Yirui Guo / Hanif M Khan / Tabitha Emde / Bradley Quade / Rosa Di Leo / Zbyszek Otwinowski / D Tieleman Peter / Dominika Borek / Alexei Savchenko
Abstract: Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold the integrity of their cell envelope, an indispensable aspect for both division and survival. ...Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold the integrity of their cell envelope, an indispensable aspect for both division and survival. The IM TolQ-TolR complex is the essential part of the Tol-Pal system, serving as a conduit for PMF energy transfer to the outer membrane. Here we present cryo-EM reconstructions of TolQ in apo and TolR- bound forms at atomic resolution. The apo TolQ configuration manifests as a symmetric pentameric pore, featuring a trans-membrane funnel leading towards a cytoplasmic chamber. In contrast, the TolQ-TolR complex assumes a proton non-permeable stance, characterized by the TolQ pentamer's flexure to accommodate the TolR dimer, where two protomers undergo a translation-based relationship. Our structure-guided analysis and simulations support the rotor-stator mechanism of action, wherein the rotation of the TolQ pentamer harmonizes with the TolR protomers' interplay. These findings broaden our mechanistic comprehension of molecular stator units empowering critical functions within the Gram-negative bacterial cell envelope.
TEASER: Apo TolQ and TolQ-TolR structures depict structural rearrangements required for cell envelope organization in bacterial cell division.
History
DepositionJan 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tol-Pal system protein TolQ
E: Tol-Pal system protein TolQ
D: Tol-Pal system protein TolQ
C: Tol-Pal system protein TolQ
B: Tol-Pal system protein TolQ
F: Tol-Pal system protein TolR
G: Tol-Pal system protein TolR


Theoretical massNumber of molelcules
Total (without water)129,5077
Polymers129,5077
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
32A
42D
53A
63C
74A
84B
95E
105D
116E
126C
137E
147B
158D
168C
179D
189B
1910C
2010B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRVALVALAA8 - 2252 - 219
221THRTHRVALVALEB8 - 2252 - 219
332THRTHRVALVALAA8 - 2252 - 219
442THRTHRVALVALDC8 - 2252 - 219
553SERSERGLYGLYAA7 - 2261 - 220
663SERSERGLYGLYCD7 - 2261 - 220
774THRTHRVALVALAA8 - 2252 - 219
884THRTHRVALVALBE8 - 2252 - 219
995THRTHRGLYGLYEB8 - 2262 - 220
10105THRTHRGLYGLYDC8 - 2262 - 220
11116THRTHRVALVALEB8 - 2252 - 219
12126THRTHRVALVALCD8 - 2252 - 219
13137THRTHRGLYGLYEB8 - 2262 - 220
14147THRTHRGLYGLYBE8 - 2262 - 220
15158THRTHRVALVALDC8 - 2252 - 219
16168THRTHRVALVALCD8 - 2252 - 219
17179THRTHRGLYGLYDC8 - 2262 - 220
18189THRTHRGLYGLYBE8 - 2262 - 220
191910THRTHRVALVALCD8 - 2252 - 219
202010THRTHRVALVALBE8 - 2252 - 219

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20

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Components

#1: Protein
Tol-Pal system protein TolQ


Mass: 24112.875 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: tolQ, tolQ_1, tolQ_2, tolQ_4, A0141_RS10830, A7M90_09765, Aba9201_08940, ABR2091_2796, ABUW_0996, APD31_00525, APD33_17580, AUO97_01865, AW828_RS03605, AYR68_13685, B7L45_04995, BAA1790NC_0859, ...Gene: tolQ, tolQ_1, tolQ_2, tolQ_4, A0141_RS10830, A7M90_09765, Aba9201_08940, ABR2091_2796, ABUW_0996, APD31_00525, APD33_17580, AUO97_01865, AW828_RS03605, AYR68_13685, B7L45_04995, BAA1790NC_0859, C2U32_09640, C5U03_03335, CBL15_04350, CSB70_2719, CTZ19_04585, CV951_008080, D3X61_12465, D8O08_005770, DLI71_16240, DOL94_08825, DVA69_12350, E1A86_14605, E1A87_10600, EA686_06225, EA720_015070, EGM95_04675, F2P40_13060, F4T85_01675, F4U07_01760, FD896_04670, FDN00_16055, FE003_04410, FJU42_05940, FJU76_00580, GNY86_14120, GO909_05480, GSE42_15235, GUK62_07315, H0529_00070, HBK86_13640, HBM78_04335, HIN86_04650, I8Q59_19560, IAG11_03545, IHV20_13560, IMO23_13480, ITE13_00470, JHZ39_000281, NCTC13305_03361, NCTC13421_00953, SAMEA104305208_03115, SAMEA104305318_01018, SAMEA104305340_01728, SAMEA104305385_00524, SAMEA4394745_01250
Production host: Escherichia coli (E. coli) / References: UniProt: V5VAS0
#2: Protein/peptide Tol-Pal system protein TolR


Mass: 4471.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: tolR, C2U32_09645, JHZ39_000282 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I8CU89
Has protein modificationN

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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: TolQ-TolR inner membrane protein complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C43(DE3)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: PROPANE

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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: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224768 / Symmetry type: POINT
RefinementResolution: 3.34→3.34 Å / Cor.coef. Fo:Fc: 0.902 / WRfactor Rwork: 0.396 / SU B: 30.129 / SU ML: 0.455 / Average fsc overall: 0.7004 / Average fsc work: 0.7004 / ESU R: 0.816
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3955 60493 -
all0.396 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 93.999 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0140.0139268
ELECTRON MICROSCOPYr_bond_other_d00.0159132
ELECTRON MICROSCOPYr_ext_dist_refined_d0.110.0134145
ELECTRON MICROSCOPYr_angle_refined_deg1.6931.6212548
ELECTRON MICROSCOPYr_angle_other_deg1.7641.56820928
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.41651168
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.28122.482411
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.348151612
ELECTRON MICROSCOPYr_dihedral_angle_4_deg22.8381543
ELECTRON MICROSCOPYr_chiral_restr0.1120.21241
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0210379
ELECTRON MICROSCOPYr_gen_planes_other0.0030.022139
ELECTRON MICROSCOPYr_nbd_refined0.2160.25488
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1920.218734
ELECTRON MICROSCOPYr_nbtor_refined0.1860.210288
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0840.29324
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.2310.2218
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0850.214
ELECTRON MICROSCOPYr_mcbond_it2.2939.8684690
ELECTRON MICROSCOPYr_mcbond_other2.2939.8674689
ELECTRON MICROSCOPYr_mcangle_it4.14314.7925852
ELECTRON MICROSCOPYr_mcangle_other4.14214.7945853
ELECTRON MICROSCOPYr_scbond_it2.09710.3144578
ELECTRON MICROSCOPYr_scbond_other2.09710.3144578
ELECTRON MICROSCOPYr_scangle_it3.93115.316696
ELECTRON MICROSCOPYr_scangle_other3.93115.3116697
ELECTRON MICROSCOPYr_lrange_it11.513191.27239928
ELECTRON MICROSCOPYr_lrange_other11.514191.25839927
ELECTRON MICROSCOPYr_ncsr_local_group_10.20.0512446
ELECTRON MICROSCOPYr_ncsr_local_group_20.2040.0512508
ELECTRON MICROSCOPYr_ncsr_local_group_30.2150.0512424
ELECTRON MICROSCOPYr_ncsr_local_group_40.1930.0512590
ELECTRON MICROSCOPYr_ncsr_local_group_50.2130.0512244
ELECTRON MICROSCOPYr_ncsr_local_group_60.2020.0512518
ELECTRON MICROSCOPYr_ncsr_local_group_70.1950.0512504
ELECTRON MICROSCOPYr_ncsr_local_group_80.2140.0512216
ELECTRON MICROSCOPYr_ncsr_local_group_90.1940.0512492
ELECTRON MICROSCOPYr_ncsr_local_group_100.2020.0512326
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AELECTRON MICROSCOPYLocal ncs0.200380.05005
12EELECTRON MICROSCOPYLocal ncs0.200380.05005
23AELECTRON MICROSCOPYLocal ncs0.203730.05005
24DELECTRON MICROSCOPYLocal ncs0.203730.05005
35AELECTRON MICROSCOPYLocal ncs0.214570.05005
36CELECTRON MICROSCOPYLocal ncs0.214570.05005
47AELECTRON MICROSCOPYLocal ncs0.193430.05005
48BELECTRON MICROSCOPYLocal ncs0.193430.05005
59EELECTRON MICROSCOPYLocal ncs0.212610.05005
510DELECTRON MICROSCOPYLocal ncs0.212610.05005
611EELECTRON MICROSCOPYLocal ncs0.201670.05006
612CELECTRON MICROSCOPYLocal ncs0.201670.05006
713EELECTRON MICROSCOPYLocal ncs0.195110.05005
714BELECTRON MICROSCOPYLocal ncs0.195110.05005
815DELECTRON MICROSCOPYLocal ncs0.213790.05005
816CELECTRON MICROSCOPYLocal ncs0.213790.05005
917DELECTRON MICROSCOPYLocal ncs0.194230.05005
918BELECTRON MICROSCOPYLocal ncs0.194230.05005
1019CELECTRON MICROSCOPYLocal ncs0.202010.05005
1020BELECTRON MICROSCOPYLocal ncs0.202010.05005
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.36-3.4471.8544541.8544540.1511.85
3.447-3.5421.81243771.81243770.2691.812
3.542-3.6441.37542621.37542620.4221.375
3.644-3.7560.8541070.8541070.5720.85
3.756-3.8790.52439650.52439650.6820.524
3.879-4.0150.40939000.40939000.7540.409
4.015-4.1670.38737340.38737340.790.387
4.167-4.3370.38435830.38435830.8480.384
4.337-4.5290.40134130.40134130.8810.401
4.529-4.750.40733140.40733140.8950.407
4.75-5.0070.39830670.39830670.8980.398
5.007-5.310.36829710.36829710.8910.368
5.31-5.6760.34127820.34127820.8620.341
5.676-6.1290.33525970.33525970.8390.335
6.129-6.7130.35723880.35723880.830.357
6.713-7.5020.35821370.35821370.8180.358
7.502-8.6570.32519170.32519170.8810.325
8.657-10.590.25515890.25515890.9390.255
10.59-14.9220.19512440.19512440.9640.195
14.922-123.4320.3846920.3846920.9760.384

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