6XJI

PmtCD ABC exporter at C1 symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Structural insight into the Staphylococcus aureus ATP-driven exporter of virulent peptide toxins

Zeytuni, N.Dickey, S.W.Hu, J.Chou, H.T.Worrall, L.J.Alexander, J.A.N.Carlson, M.L.Nosella, M.Duong, F.Yu, Z.Otto, M.Strynadka, N.C.J.

(2020) Sci Adv 6: eabb8219

  • DOI: 10.1126/sciadv.abb8219
  • Primary Citation of Related Structures:  
    6XFU, 6XJI, 6XJH, 6U2D

  • PubMed Abstract: 
  • Staphylococcus aureus is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs are amphipathic, membra ...

    Staphylococcus aureus is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs are amphipathic, membrane-destructive cytolytic peptides that are exported to the host-cell environment by a designated adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter, the PSM transporter (PmtABCD). Here, we demonstrate that the minimal Pmt unit necessary for PSM export is PmtCD and provide its first atomic characterization by single-particle cryo-EM and x-ray crystallography. We have captured the transporter in the ATP-bound state at near atomic resolution, revealing a type II ABC exporter fold, with an additional cytosolic domain. Comparison to a lower-resolution nucleotide-free map displaying an "open" conformation and putative hydrophobic inner chamber of a size able to accommodate the binding of two PSM peptides provides mechanistic insight and sets the foundation for therapeutic design.


    Organizational Affiliation

    High Resolution Macromolecular Cryo-Electron Microscopy facility, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenol-soluble modulin export ABC transporter permease subunit PmtDAB266Staphylococcus aureusMutation(s): 0 
Gene Names: D7S40_12560
Find proteins for A0A641A693 (Staphylococcus aureus)
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Go to UniProtKB:  A0A641A693
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ABC transporter ATP-binding proteinCD290Staphylococcus aureusMutation(s): 0 
Gene Names: 
ybhF_2pmtCybhF_1ybhF_3yxlF_3BN1321_320024BTN44_02050C7P97_04805CSC87_13000DD547_02044DQV53_11320E3A28_12735E3K14_10305EP54_10395EQ90_13985ERS072840_01916FA040_10030FVP29_15965G0V24_08340G0X12_10370G0Y02_11535G0Z18_07720G6Y10_09125GF545_12955GF559_09640GO677_03780GO746_12910GO788_10810GO793_05685GO803_12450GO805_15850GO821_11685GO894_01660GO915_01150GO942_00400HMPREF3211_02244NCTC10654_02103NCTC7878_02640NCTC9944_02076RK64_10625SAMEA1029528_01830SAMEA1029547_01960SAMEA1029553_01872SAMEA1469856_02290SAMEA1469884_02007SAMEA1531680_02230SAMEA1531701_02082SAMEA1964876_02068SAMEA1965205_02085SAMEA1966505_02066SAMEA1969349_01958SAMEA1969845_01938SAMEA1971706_01597SAMEA1972827_01913SAMEA2076212_01866SAMEA2076218_01932SAMEA2076220_02014SAMEA2076226_01811SAMEA2076463_01823SAMEA2076464_01930SAMEA2076470_01932SAMEA2076472_01753SAMEA2076478_01900SAMEA2076480_01920SAMEA2076481_01467SAMEA2076743_01970SAMEA2076745_01614SAMEA2076746_01870SAMEA2076747_01836SAMEA2076749_02062SAMEA2076751_01982SAMEA2076752_01904SAMEA2076755_01822SAMEA2076756_01934SAMEA2076758_01408SAMEA2076759_01859SAMEA2076761_01915SAMEA2076762_01823SAMEA2076763_01784SAMEA2076764_02091SAMEA2076765_01451SAMEA2077023_01977SAMEA2077025_01856SAMEA2077027_02045SAMEA2077029_01746SAMEA2077031_01324SAMEA2077034_01786SAMEA2077035_01916SAMEA2077039_01901SAMEA2077040_01788SAMEA2077041_01977SAMEA2077044_01944SAMEA2077045_01975SAMEA2077046_01887SAMEA2077293_01723SAMEA2077294_01827SAMEA2077295_02048SAMEA2077297_01939SAMEA2077300_01934SAMEA2077301_02026SAMEA2077302_01879SAMEA2077303_02008SAMEA2077307_01841SAMEA2077832_01965SAMEA2078252_01956SAMEA2078256_01753SAMEA2078307_01779SAMEA2078308_01714SAMEA2078553_02044SAMEA2078558_01905SAMEA2078560_00574SAMEA2078570_01344SAMEA2078572_01040SAMEA2078824_01866SAMEA2078837_02097SAMEA2079048_01951SAMEA2079051_01962SAMEA2079277_02115SAMEA2079291_02095SAMEA2079503_02028SAMEA2079507_01267SAMEA2079512_02011SAMEA2079517_01833SAMEA2079724_01791SAMEA2079727_02051SAMEA2079728_02023SAMEA2079732_01918SAMEA2079742_01950SAMEA2079946_01886SAMEA2079949_01853SAMEA2079951_01961SAMEA2079952_02016SAMEA2079957_02124SAMEA2079958_01897SAMEA2079960_02101SAMEA2079961_01871SAMEA2079968_01911SAMEA2080329_02036SAMEA2080330_01992SAMEA2080334_02019SAMEA2080433_02138SAMEA2080812_01832SAMEA2080898_02128SAMEA2080900_01016SAMEA2080904_02223SAMEA2080913_01859SAMEA2081043_02119SAMEA2081053_02035SAMEA2081054_02018SAMEA2081055_01945SAMEA2081060_01898SAMEA2081211_01271SAMEA2081213_01985SAMEA2081218_01903SAMEA2081341_01799SAMEA2081342_01874SAMEA2081349_01944SAMEA2081359_01873SAMEA2081362_01885SAMEA2081468_01756SAMEA2081474_01870SAMEA2081475_01830SAMEA2081476_01840SAMEA2081479_01917SAMEA2081480_01415SAMEA2081560_01741SAMEA2081561_02032SAMEA2081564_01958SAMEA2081567_01915SAMEA2081568_01922SAMEA2081569_01934SAMEA2081570_01929SAMEA2081571_01770SAMEA2081572_01818SAMEA2081573_01854SAMEA2081575_01948SAMEA2081577_01824SAMEA2081578_01820SAMEA2081579_02082SAMEA2081581_01802SAMEA2081582_00128SAMEA2081673_01898SAMEA2081674_01954SAMEA958766_02348SAMEA958770_01779SAMEA958772_01809SAMEA958778_02070SAMEA958779_02628SAMEA958785_01595SAMEA958793_02289SAMEA958798_01722SAMEA958804_02349SAMEA958810_02694SAMEA958836_01863SAMEA958838_02015SAMEA958845_02303SAMEA958846_02191SAMEA958848_02520SAMEA958855_02271SAMEA958858_02390SAMEA958870_01748SAMEA958898_02076SAMEA958906_02417SAMEA958924_02253SAMEA958925_02343SAMEA958951_02077SAMEA958953_01842SAMEA958961_02279SAMEA958979_01551SAMEA958987_01706SAMEA958995_01606SAST44_03940SAST45_02134

EC: 3.6.3
Find proteins for X5EJW5 (Staphylococcus aureus)
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download CCD File 
C, D
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaOperating grant

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release