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Yorodumi- EMDB-44402: Cryo-EM structure of the ABC transporter PCAT1 bound with Mg_class_1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44402 | |||||||||
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Title | Cryo-EM structure of the ABC transporter PCAT1 bound with Mg_class_1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ABC transporter / Nucleotide / Membrane Protein / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information ABC-type bacteriocin transporter activity / ATPase-coupled lipid transmembrane transporter activity / cysteine-type peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Acetivibrio thermocellus ATCC 27405 (bacteria) | |||||||||
Method | single particle reconstruction / Resolution: 3.39 Å | |||||||||
Authors | Zhang R / Jagessar KL / Polasa A / Brownd M / Stein R / Moradi M / Karakas E / Mchaourab HS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44402.map.gz | 168 MB | EMDB map data format | |
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Header (meta data) | emd-44402-v30.xml emd-44402.xml | 17 KB 17 KB | Display Display | EMDB header |
Images | emd_44402.png | 24.9 KB | ||
Filedesc metadata | emd-44402.cif.gz | 6 KB | ||
Others | emd_44402_half_map_1.map.gz emd_44402_half_map_2.map.gz | 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44402 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44402 | HTTPS FTP |
-Validation report
Summary document | emd_44402_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_44402_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_44402_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_44402_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44402 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44402 | HTTPS FTP |
-Related structure data
Related structure data | 9baaMC 8vowC 8voxC 8vozC 8vp1C 8vp3C 8vp5C 8vp6C 8vp8C 8vp9C 8vpaC 8vpbC 9azlC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_44402.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.647 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_44402_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_44402_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PCAT1
Entire | Name: PCAT1 |
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Components |
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-Supramolecule #1: PCAT1
Supramolecule | Name: PCAT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Acetivibrio thermocellus ATCC 27405 (bacteria) |
Molecular weight | Theoretical: 1.62 MDa |
-Macromolecule #1: ABC-type bacteriocin transporter
Macromolecule | Name: ABC-type bacteriocin transporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acetivibrio thermocellus ATCC 27405 (bacteria) |
Molecular weight | Theoretical: 83.688461 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGHHHHHHHH HHSSGHIDDD DKHMLRRLFK KKYVCVRQYD LTDCGAACLS SIAQYYGLKM SLAKIREMTG TDTQGTNAYG LIHAAKQLG FSAKGVKASK EDLLKDFRLP AIANVIVDNR LAHFVVIYSI KNRIITVADP GKGIVRYSMD DFCSIWTGGL V LLEPGEAF ...String: MGHHHHHHHH HHSSGHIDDD DKHMLRRLFK KKYVCVRQYD LTDCGAACLS SIAQYYGLKM SLAKIREMTG TDTQGTNAYG LIHAAKQLG FSAKGVKASK EDLLKDFRLP AIANVIVDNR LAHFVVIYSI KNRIITVADP GKGIVRYSMD DFCSIWTGGL V LLEPGEAF QKGDYTQNMM VKFAGFLKPL KKTVLCIFLA SLLYTALGIA GSFYIKFLFD DLIKFEKLND LHIISAGFAV IF LLQIFLN YYRSILVTKL GMSIDKSIMM EYYSHVLKLP MNFFNSRKVG EIISRFMDAS KIRQAISGAT LTIMIDTIMA VIG GILLYI QNSSLFFISF IIILLYGIIV TVFNKPIQNA NRQIMEDNAK LTSALVESVK GIETIKSFGA EEQTEKSTRD KIET VMKSS FKEGMLYINL SSLTGIVAGL GGIVILWAGA YNVIKGNMSG GQLLAFNALL AYFLTPVKNL IDLQPLIQTA VVASN RLGE ILELATEKEL REDSDDFVIS LKGDIEFRNV DFRYGLRKPV LKNINLTIPK GKTVAIVGES GSGKTTLAKL LMNFYS PEK GDILINGHSI KNISLELIRK KIAFVSQDVF IFSGTVKENL CLGNENVDMD EIIKAAKMAN AHDFIEKLPL KYDTFLN ES GANLSEGQKQ RLAIARALLK KPDILILDEA TSNLDSITEN HIKDAIYGLE DDVTVIIIAH RLSTIVNCDK IYLLKDGE I VESGSHTELI ALKGCYFKMW KQTENTLAS UniProtKB: ABC-type bacteriocin transporter |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: 50mM MOPS, 50mM NaCl, PH 7.4 |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16319 / Average electron dose: 1.14708 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |