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- EMDB-47796: Pseudomonas aeruginosa MexY -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47796
TitlePseudomonas aeruginosa MexY
Map data
Sample
  • Complex: MexY
    • Protein or peptide: Efflux pump membrane transporter
KeywordsPseudomonsa aeruginosa / MexY / RND / Efflux / MEMBRANE PROTEIN
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / response to toxic substance / plasma membrane / Efflux pump membrane transporter
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsGregor WD / Maharjan R / Zhang Z / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI145069 United States
CitationJournal: To Be Published
Title: Pseudomonas aeruginosa MexY
Authors: Gregor WD / Maharjan R / Zhang Z / Yu EW
History
DepositionNov 8, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47796.png

Downloads & links

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Map

FileDownload / File: emd_47796.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3587196 - 0.68962556
Average (Standard dev.)-0.00021524368 (±0.028674109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47796_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47796_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MexY

EntireName: MexY
Components
  • Complex: MexY
    • Protein or peptide: Efflux pump membrane transporter

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Supramolecule #1: MexY

SupramoleculeName: MexY / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Efflux pump membrane transporter

MacromoleculeName: Efflux pump membrane transporter / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 111.287914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MARFFIDRPV FAWVISLLIV LAGVLAIRFL PVAQYPDIAP PVVNVSASYP GASAKVVEEA VTAIIEREMN GAPGLLYTKA TSSTGQASL TLTFRQGVNA DLAAVEVQNR LKIVESRLPE SVRRDGIYVE KAADSIQLIV TLTSSSGRYD AMELGEIASS N VLQALRRV ...String:
MARFFIDRPV FAWVISLLIV LAGVLAIRFL PVAQYPDIAP PVVNVSASYP GASAKVVEEA VTAIIEREMN GAPGLLYTKA TSSTGQASL TLTFRQGVNA DLAAVEVQNR LKIVESRLPE SVRRDGIYVE KAADSIQLIV TLTSSSGRYD AMELGEIASS N VLQALRRV EGVGKVETWG AEYAMRIWPD PAKLTSMNLS ASDLVNAVRR HNARLTVGDI GNLGVPDSAP ISATVKVDDT LV TPEQFGE IPLRIRADGG AIRLRDVARV EFGQSEYGFV SRVNQMTATG LAVKMAPGSN AVATAKRIRA TLDELSRYFP EGV SYNIPY DTSAFVEISI RKVVSTLLEA MLLVFAVMYL FMQNFRATLI PTLVVPVALL GTFTVMLGLG FSINVLTMFG MVLA IGILV DDAIIVVENV ERLMAEEGLS PHDATVKAMR QISGAIVGIT VVLVSVFVPM AFFSGAVGNI YRQFAVTLAV SIGFS AFLA LSLTPALCAT LLRPIDADHH EKRGFFGWFN RAFLRLTGRY RNAVAGILAR PIRWMLVYAL VIGVVALLFV RLPQAF LPE EDQGDFMIMV MQPEGTPMAE TMANVGDVER YLAEHEPVAY AYAVGGFSLY GDGTSSAMIF ATLKDWSERR EASQHVG AI VERINQRFAG LPNRTVYAMN SPPLPDLGST SGFDFRLQDR GGVGYEALVK ARDQLLARAA EDPRLANVMF AGQGEAPQ I RLDIDRRKAE TLGVSMDEIN TTLAVMFGSD YIGDFMHGSQ VRKVVVQADG AKRLGIDDIG RLHVRNEQGE MVPLATFAK AAWTLGPPQL TRYNGYPSFN LEGQAAPGYS SGEAMQAMEQ LMQGLPEGIA HEWSGQSFEE RLSGAQAPAL FALSVLIVFL ALAALYESW SIPLAVILVV PLGVLGALLG VSLRGLPNDI YFKVGLITII GLSAKNAILI IEVAKDHYQE GMSLLQATLE A ARLRLRPI VMTSLAFGFG VVPLALSSGA GSGAQVAIGT GVLGGIVTAT VLAVFLVPLF FLVVGRLFRL RKA

UniProtKB: Efflux pump membrane transporter

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris HCl
100.0 mMsodium chlorideNaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 37.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2124205
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8886
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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