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- EMDB-25400: Multidrug efflux pump subunit AcrB -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-25400
TitleMultidrug efflux pump subunit AcrB
Map data
Sample
  • Complex: Multidrug efflux pump subunit AcrB
    • Protein or peptide: Multidrug efflux pump subunit AcrB
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.69 Å
AuthorsTrinh TKH / Catalano C / Guo Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132329 United States
CitationJournal: To Be Published
Title: Multidrug efflux pump subunit AcrB
Authors: Trinh TKH / Catalano C / Guo Y
History
DepositionNov 8, 2021-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25400.png

Downloads & links

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Map

FileDownload / File: emd_25400.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8256 Å
Density
Contour LevelBy AUTHOR: 0.305
Minimum - Maximum-1.217363 - 1.8516966
Average (Standard dev.)0.003064855 (±0.05483498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.216 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Multidrug efflux pump subunit AcrB

EntireName: Multidrug efflux pump subunit AcrB
Components
  • Complex: Multidrug efflux pump subunit AcrB
    • Protein or peptide: Multidrug efflux pump subunit AcrB

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Supramolecule #1: Multidrug efflux pump subunit AcrB

SupramoleculeName: Multidrug efflux pump subunit AcrB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Macromolecule #1: Multidrug efflux pump subunit AcrB

MacromoleculeName: Multidrug efflux pump subunit AcrB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MPNFFIDRPI FAWVIAIIIM LAGGLAILKL PVAQYPTIAP PAVTISASYP GADAKTVQDT VTQVIEQNM NGIDNLMYMS SNSDSTGTVQ ITLTFESGTD ADIAQVQVQN KLQLAMPLLP Q EVQQQGVS VEKSSSSFLM VVGVINTDGT MTQEDISDYV AANMKDAISR ...String:
MPNFFIDRPI FAWVIAIIIM LAGGLAILKL PVAQYPTIAP PAVTISASYP GADAKTVQDT VTQVIEQNM NGIDNLMYMS SNSDSTGTVQ ITLTFESGTD ADIAQVQVQN KLQLAMPLLP Q EVQQQGVS VEKSSSSFLM VVGVINTDGT MTQEDISDYV AANMKDAISR TSGVGDVQLF GS QYAMRIW MNPNELNKFQ LTPVDVITAI KAQNAQVAAG QLGGTPPVKG QQLNASIIAQ TRL TSTEEF GKILLKVNQD GSRVLLRDVA KIELGGENYD IIAEFNGQPA SGLGIKLATG ANAL DTAAA IRAELAKMEP FFPSGLKIVY PYDTTPFVKI SIHEVVKTLV EAIILVFLVM YLFLQ NFRA TLIPTIAVPV VLLGTFAVLA AFGFSINTLT MFGMVLAIGL LVDDAIVVVE NVERVM AEE GLPPKEATRK SMGQIQGALV GIAMVLSAVF VPMAFFGGST GAIYRQFSIT IVSAMAL SV LVALILTPAL CATMLKPIAK GDHGEGKKGF FGWFNRMFEK STHHYTDSVG GILRSTGR Y LVLYLIIVVG MAYLFVRLPS SFLPDEDQGV FMTMVQLPAG ATQERTQKVL NEVTHYYLT KEKNNVESVF AVNGFGFAGR GQNTGIAFVS LKDWADRPGE ENKVEAITMR ATRAFSQIKD AMVFAFNLP AIVELGTATG FDFELIDQAG LGHEKLTQAR NQLLAEAAKH PDMLTSVRPN G LEDTPQFK IDIDQEKAQA LGVSINDINT TLGAAWGGSY VNDFIDRGRV KKVYVMSEAK YR MLPDDIG DWYVRAADGQ MVPFSAFSSS RWEYGSPRLE RYNGLPSMEI LGQAAPGKST GEA MELMEQ LASKLPTGVG YDWTGMSYQE RLSGNQAPSL YAISLIVVFL CLAALYESWS IPFS VMLVV PLGVIGALLA ATFRGLTNDV YFQVGLLTTI GLSAKNAILI VEFAKDLMDK EGKGL IEAT LDAVRMRLRP ILMTSLAFIL GVMPLVISTG AGSGAQNAVG TGVMGGMVTA TVLAIF FVP VFFVVVRRRF SRKNEDIEHS HTVDHH

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
StainingType: NEGATIVE / Material: 2% uranyl acetate
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 44.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86011
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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