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- EMDB-43396: Cryo-EM structure of the ABC transporter PCAT1 cysteine-free core... -

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Basic information

Entry
Database: EMDB / ID: EMD-43396
TitleCryo-EM structure of the ABC transporter PCAT1 cysteine-free core bound with MgADP and substrate
Map data
Sample
  • Complex: PCAT1
    • Protein or peptide: ABC-type bacteriocin transporter
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: 3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxypropyl hexadecanoate
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
KeywordsABC transporter / Nucleotide / Membrane Protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type bacteriocin transporter activity / ABC-type oligopeptide transporter activity / cysteine-type peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
Peptidase C39, ABC-type bacteriocin transporter / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter ...Peptidase C39, ABC-type bacteriocin transporter / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC-type bacteriocin transporter
Similarity search - Component
Biological speciesAcetivibrio thermocellus ATCC 27405 (bacteria)
Methodsingle particle reconstruction / Resolution: 3.03 Å
AuthorsZhang R / Jagessar KL / Polasa A / Brownd M / Stein R / Moradi M / Karakas E / Mchaourab HS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 128087 United States
CitationJournal: J Gen Virol / Year: 1984
Title: Investigation of varicella-zoster virus-infected cell proteins that elicit antibody production during primary varicella using the immune transfer method.
Abstract: The varicella-zoster virus-infected cell proteins (VZV-ICPs) against which IgG, IgM and IgA antibodies were made in the course of primary varicella-zoster virus (VZV) infection were analysed by the ...The varicella-zoster virus-infected cell proteins (VZV-ICPs) against which IgG, IgM and IgA antibodies were made in the course of primary varicella-zoster virus (VZV) infection were analysed by the immune transfer method. IgG antibodies were made against one or more of 18 VZV-ICPs by patients with varicella. IgM antibodies were produced which reacted with 21 VZV-ICPs. The spectrum of IgG antibody production during the first week after the onset of infection was limited to an average of three VZV-ICPs while IgM antibodies which reacted with an average of seven VZV-ICPs were detectable in the acute phase of varicella. Equivalent VZV IgG or IgM antibody titres by radioimmunoassay did not correlate with a similar pattern of antibody specificity for VZV-ICPs by immune transfer. A detectable immune response to all VZV-ICPs was not required for the recovery of individual patients from primary VZV infection.
History
DepositionJan 16, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43396.png

Downloads & links

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Map

FileDownload / File: emd_43396.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.)
0.65 Å/pix.
x 360 pix.
= 232.92 Å		0.65 Å/pix.
x 360 pix.
= 232.92 Å		0.65 Å/pix.
x 360 pix.
= 232.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.61163956 - 1.1267639
Average (Standard dev.)0.0006254176 (±0.027396677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 232.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43396_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43396_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PCAT1

EntireName: PCAT1
Components
  • Complex: PCAT1
    • Protein or peptide: ABC-type bacteriocin transporter
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: 3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxypropyl hexadecanoate
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

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Supramolecule #1: PCAT1

SupramoleculeName: PCAT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acetivibrio thermocellus ATCC 27405 (bacteria)
Molecular weightTheoretical: 1.29 MDa

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Macromolecule #1: ABC-type bacteriocin transporter

MacromoleculeName: ABC-type bacteriocin transporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetivibrio thermocellus ATCC 27405 (bacteria)
Molecular weightTheoretical: 67.077984 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGHHHHHHHH HHSSGHIDDD DKHMTQNMMV KFAGFLKPLK KTVLAIFLAS LLYTALGIAG SFYIKFLFDD LIKFEKLNDL HIISAGFAV IFLLQIFLNY YRSILVTKLG MSIDKSIMME YYSHVLKLPM NFFNSRKVGE IISRFMDASK IRQAISGATL T IMIDTIMA ...String:
MGHHHHHHHH HHSSGHIDDD DKHMTQNMMV KFAGFLKPLK KTVLAIFLAS LLYTALGIAG SFYIKFLFDD LIKFEKLNDL HIISAGFAV IFLLQIFLNY YRSILVTKLG MSIDKSIMME YYSHVLKLPM NFFNSRKVGE IISRFMDASK IRQAISGATL T IMIDTIMA VIGGILLYIQ NSSLFFISFI IILLYGIIVT VFNKPIQNAN RQIMEDNAKL TSALVESVKG IETIKSFGAE EQ TEKSTRD KIETVMKSSF KEGMLYINLS SLTGIVAGLG GIVILWAGAY NVIKGNMSGG QLLAFNALLA YFLTPVKNLI DLQ PLIQTA VVASNRLGEI LELATEKELR EDSDDFVISL KGDIEFRNVD FRYGLRKPVL KNINLTIPKG KTVAIVGESG SGKT TLAKL LMNFYSPEKG DILINGHSIK NISLELIRKK IAFVSQDVFI FSGTVKENLA LGNENVDMDE IIKAAKMANA HDFIE KLPL KYDTFLNESG ANLSEGQKQR LAIARALLKK PDILILDEAT SNLDSITENH IKDAIYGLED DVTVIIIAHR LSTIVN LDK IYLLKDGEIV ESGSHTELIA LKGAYFKMWK QTENTLAS

UniProtKB: ABC-type bacteriocin transporter

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: 3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxyprop...

MacromoleculeName: 3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxypropyl hexadecanoate
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1ACX
Molecular weightTheoretical: 480.639 Da

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Macromolecule #5: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 5 / Number of copies: 1 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMMOPS3-(N-morpholino)propanesulfonic acid
50.0 mMNaClSodium chloride

Details: 50mM MOPS, 50mM NaCl, PH 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12430 / Average electron dose: 1.04302 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 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: 1676061
Startup modelType of model: OTHER / Details: Model Angelo
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 453585
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.2.1)

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