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- EMDB-61115: Cryo-EM structure of TMexCD1-TOprJ1 in complex with 1-(1-naphthyl... -

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Basic information

Entry
Database: EMDB / ID: EMD-61115
TitleCryo-EM structure of TMexCD1-TOprJ1 in complex with 1-(1-naphthylmethyl)piperazine
Map data
Sample
  • Complex: TMexCD1-TOprJ1
    • Protein or peptide: RND efflux system, OprJ-like protein
    • Protein or peptide: RND efflux system, MexC-like protein
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: 1-(naphthalen-1-ylmethyl)piperazine
Keywordsefflux pump / transporter / antibiotics / antimicrobial resistance / TRANSPORT PROTEIN
Function / homology
Function and homology information


efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / response to toxic substance / cell outer membrane / response to antibiotic / plasma membrane
Similarity search - Function
: / RND efflux system, outer membrane lipoprotein, NodT / : / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Outer membrane efflux protein / Outer membrane efflux protein ...: / RND efflux system, outer membrane lipoprotein, NodT / : / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Outer membrane efflux protein / Outer membrane efflux protein / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
RND efflux system, MexC-like protein / Efflux pump membrane transporter / RND efflux system, OprJ-like protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsShi Y / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of TMexCD1-TOprJ1
Authors: Shi Y / Feng Y
History
DepositionAug 8, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61115.png

Downloads & links

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Map

FileDownload / File: emd_61115.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 600 pix.
= 558. Å		0.93 Å/pix.
x 600 pix.
= 558. Å		0.93 Å/pix.
x 600 pix.
= 558. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.77756035 - 1.284707
Average (Standard dev.)0.0018314603 (±0.030300187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 558.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61115_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_61115_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 : TMexCD1-TOprJ1

EntireName: TMexCD1-TOprJ1
Components
  • Complex: TMexCD1-TOprJ1
    • Protein or peptide: RND efflux system, OprJ-like protein
    • Protein or peptide: RND efflux system, MexC-like protein
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: 1-(naphthalen-1-ylmethyl)piperazine

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Supramolecule #1: TMexCD1-TOprJ1

SupramoleculeName: TMexCD1-TOprJ1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Klebsiella pneumoniae (bacteria)

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Macromolecule #1: RND efflux system, OprJ-like protein

MacromoleculeName: RND efflux system, OprJ-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 52.397453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSHFMLRRA LLPLAIAALA GCSLAPTYER PQAPVASHWQ AADAEGARAQ ALDWQTFIVD ADLRRAVDTA LSNNRSLRQA LLDIEAARA QYRIQRADRL PSINANASGN RQRLPADLSQ TGRSEVTSNY QVGLGLAEYE VDLFGRVRNL SEAALETYLA T EEATRATQ ...String:
MTSHFMLRRA LLPLAIAALA GCSLAPTYER PQAPVASHWQ AADAEGARAQ ALDWQTFIVD ADLRRAVDTA LSNNRSLRQA LLDIEAARA QYRIQRADRL PSINANASGN RQRLPADLSQ TGRSEVTSNY QVGLGLAEYE VDLFGRVRNL SEAALETYLA T EEATRATQ ISLVAEVIQA YLTRDGALRR MALVEQTLDS RMASLELVSQ RRAAGAATAL DYQEAVGLAE QARAERESTE RQ LRQADNA LVLLLGTPDA ARLLPATPRD DLMVLQDIAP GTSSELIERR PDILASEHRL KARNADIGAA RAAFFPRISL TGS VGSSSA ELSGLFDGGS RAWSFAPTLS LPIFAGGRNR ANLDLAEVRQ DAAVADYEGT IQTAFREVAD ALAATDTLRR EEAA RQALA GSSEAAMALA KARYEGGVDD YLRYLDAQRS TFSNQTTLIQ ISTERQIALV DLFRSLGGGW GQTEPMAGIG AEHHH HHH

UniProtKB: RND efflux system, OprJ-like protein

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Macromolecule #2: RND efflux system, MexC-like protein

MacromoleculeName: RND efflux system, MexC-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 42.678289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKFREWITF SVISCLVAVT LVGCDKPEEQ REEAPAREVD VLSVKTEPFT VFAELPGRIE PVRVAEVRAR VAGIVLKRTF EEGADVKAG DVLFQIDPAP FKAALSRAQG ELARAEAQLF QAQAMVRRYE PLVKIDAVSQ QDFDNAMAAL QSAQADKRSA Q ANVETARL ...String:
MNKFREWITF SVISCLVAVT LVGCDKPEEQ REEAPAREVD VLSVKTEPFT VFAELPGRIE PVRVAEVRAR VAGIVLKRTF EEGADVKAG DVLFQIDPAP FKAALSRAQG ELARAEAQLF QAQAMVRRYE PLVKIDAVSQ QDFDNAMAAL QSAQADKRSA Q ANVETARL DLGYAEVRAP IAGRIGRAQV TEGALVGQGE ATLLARIQQL DPVYADFTQP AADALRLRAA IAEGKVAGAS DQ PLSLRVD GTDIERKGTL LFTDISVDRS TGQIALRGQF DNPEGVLLPG MYVRVRTPQG LNQNAILVPQ RAVQRSADGQ ASV MLLGEG DTVEVRQVTT GAMQGSRWQI SEGLQAGDKV ITSSLAAIRP GAKVIPREQG AAEKAPQSQA QWSHPQFEK

UniProtKB: RND efflux system, MexC-like protein

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Macromolecule #3: Efflux pump membrane transporter

MacromoleculeName: Efflux pump membrane transporter / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 112.289445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPLFFIRRPN FAWVVALFIS LGGLLVIPFL PVAQYPNVAP PQITVTATYP GASAQVLTDS VTSVIEEELN GAKNLLYFES TSNANGIAE ITVTFQPGTD PELAQVDVQN RLKKAEARMP QAVLTLGIQT EQATAGFLLI YSLRYKDGDK NANTTALADY A VRNVNNEI ...String:
MPLFFIRRPN FAWVVALFIS LGGLLVIPFL PVAQYPNVAP PQITVTATYP GASAQVLTDS VTSVIEEELN GAKNLLYFES TSNANGIAE ITVTFQPGTD PELAQVDVQN RLKKAEARMP QAVLTLGIQT EQATAGFLLI YSLRYKDGDK NANTTALADY A VRNVNNEI RRLPGVGKLQ FFDSEAAMRV WIDPQKLVGY GLSIDDVNNA IRTQNVQVPA GAFGSTPGSS EQELTATLTV KG TLDNPEE FAAIVLRANQ DGSRLTLGDV ARIEVGSQDY NFGSRQDGKP AVAAAVQLSP GANAIQTAEA VKQRLTELSA NFP DNVEFS VPYDTSRFVD VAIDKVIMTL IEAMVLVFLV MFLFLQNVRY TLIPSIVVPV CLLGTLTFMY LLGFSVNMMT MFGM VLAIG ILVDDAIVVV ENVERIMAEE GLAPVPATIK AMGQVSGAII GITLVLSAVF LPLAFMAGSV GVIYQQFSLS LAVSI LFSG FLALTFTPAL CATLLKPIPV GHHEKTGFFG WFNRKFTSLT SRYTKLNDKL VPRAGRVMFI YLGVVVLMGF LYMRLP ESF VPVEDQGYMI VDIQLPPGAT RERTSAAGGE LESFLMAREA VQTTFLVLGF SFSGMGENAA IAFPLLKDWS ERDSSQS PE AESAAVNQHF ANLDDGAIMA VPPPPVEGLG NSGGFALRLQ DRAGLGRDAL LAARDEVLGK VNGNPKFLYA MMEGLAEA P QLRLVIDREQ ARTLGVSFEA ISSALSTAFG SSVINDFANA GRQQRVVVQA EQAERMTPES VLRLHVPNDS GSLVPLSAF VTTSWEEGPV QVARYNGYPS IRIAGDAAPG VSTGEAMLEL ERIAAELPEG IGYEWTGLSY QERVASGQAT MLFALAITVV FLLLVALYE SWAIPLTVML IVPVGALGAV LAVTAIGLPN DVYFKVGLIT VIGLAAKNAI LIVEFAKDLW EDGYSLRDAA V EAARLRFR PIIMTSMAFM LGVVPLAIAT GAGAASQRAL GTGVLGGMLS ATMLGVIFVP IFFVWVLSLL RTKPQQTDNH PL HKAE

UniProtKB: Efflux pump membrane transporter

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Macromolecule #4: 1-(naphthalen-1-ylmethyl)piperazine

MacromoleculeName: 1-(naphthalen-1-ylmethyl)piperazine / type: ligand / ID: 4 / Number of copies: 3 / Formula: A1EAN
Molecular weightTheoretical: 226.317 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52844
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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