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Yorodumi- EMDB-5951: Tomographic reconstruction of negatively-stained GALT tissue from... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5951 | |||||||||
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Title | Tomographic reconstruction of negatively-stained GALT tissue from an HIV-infected BLT (humanized) mouse. Shown is an HIV-1 budding profile that displays structures in the neck region that may represent portions of the host-encoded scission machinery (ESCRT). | |||||||||
Map data | negative-stain tomographic reconstruction of HIV-infected humanized mouse colon | |||||||||
Sample |
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Keywords | Cellular electron tomography / HIV / GALT / negative-stain / ESCRT / colon / tissue / humanized mouse / BLT / gag | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | electron tomography / cryo EM / negative staining | |||||||||
Authors | Ladinsky MS / Kieffer C / Olson G / Deruaz M / Vrbanac V / Tager AM / Kwon DS / Bjorkman PJ | |||||||||
Citation | Journal: PLoS Pathog / Year: 2014 Title: Electron tomography of HIV-1 infection in gut-associated lymphoid tissue. Authors: Mark S Ladinsky / Collin Kieffer / Gregory Olson / Maud Deruaz / Vladimir Vrbanac / Andrew M Tager / Douglas S Kwon / Pamela J Bjorkman / Abstract: Critical aspects of HIV-1 infection occur in mucosal tissues, particularly in the gut, which contains large numbers of HIV-1 target cells that are depleted early in infection. We used electron ...Critical aspects of HIV-1 infection occur in mucosal tissues, particularly in the gut, which contains large numbers of HIV-1 target cells that are depleted early in infection. We used electron tomography (ET) to image HIV-1 in gut-associated lymphoid tissue (GALT) of HIV-1-infected humanized mice, the first three-dimensional ultrastructural examination of HIV-1 infection in vivo. Human immune cells were successfully engrafted in the mice, and following infection with HIV-1, human T cells were reduced in GALT. Virions were found by ET at all stages of egress, including budding immature virions and free mature and immature viruses. Immuno-electron microscopy verified the virions were HIV-1 and showed CD4 sequestration in the endoplasmic reticulum of infected cells. Observation of HIV-1 in infected GALT tissue revealed that most HIV-1-infected cells, identified by immunolabeling and/or the presence of budding virions, were localized to intestinal crypts with pools of free virions concentrated in spaces between cells. Fewer infected cells were found in mucosal regions and the lamina propria. The preservation quality of reconstructed tissue volumes allowed details of budding virions, including structures interpreted as host-encoded scission machinery, to be resolved. Although HIV-1 virions released from infected cultured cells have been described as exclusively mature, we found pools of both immature and mature free virions within infected tissue. The pools could be classified as containing either mostly mature or mostly immature particles, and analyses of their proximities to the cell of origin supported a model of semi-synchronous waves of virion release. In addition to HIV-1 transmission by pools of free virus, we found evidence of transmission via virological synapses. Three-dimensional EM imaging of an active infection within tissue revealed important differences between cultured cell and tissue infection models and furthered the ultrastructural understanding of HIV-1 transmission within lymphoid tissue. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5951.map.gz | 119 MB | EMDB map data format | |
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Header (meta data) | emd-5951-v30.xml emd-5951.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | 400_5951.gif 80_5951.gif | 49.2 KB 2.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5951 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5951 | HTTPS FTP |
-Validation report
Summary document | emd_5951_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
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Full document | emd_5951_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_5951_validation.xml.gz | 498 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5951 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5951 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5951.map.gz / Format: CCP4 / Size: 141.5 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | negative-stain tomographic reconstruction of HIV-infected humanized mouse colon | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 9.557 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : negative-stain tomographic reconstruction of HIV-infected humaniz...
Entire | Name: negative-stain tomographic reconstruction of HIV-infected humanized mouse colon |
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Components |
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-Supramolecule #1000: negative-stain tomographic reconstruction of HIV-infected humaniz...
Supramolecule | Name: negative-stain tomographic reconstruction of HIV-infected humanized mouse colon type: sample / ID: 1000 / Details: Cellular Tomographic Reconstruction / Number unique components: 1 |
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-Supramolecule #1: HIV in Humanized Mouse GALT
Supramolecule | Name: HIV in Humanized Mouse GALT / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: Mouse / Location in cell: Gut associated lymphoid tissue |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | electron tomography |
Aggregation state | tissue |
-Sample preparation
Staining | Type: NEGATIVE Details: Negatively-stained (1% uranyl acetate), sucrose-impregnated cryosection of mouse tissue, imaged by electron tomography |
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Vitrification | Cryogen name: NITROGEN / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Date | Jul 13, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.5 µm / Nominal magnification: 6500 |
Sample stage | Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 1 ° |
-Image processing
Details | Tomogram acquired using SerialEM software package on a Tecai T-12 EM. Tomograms were analyzed using IMOD. |
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Final reconstruction | Software - Name: SerialEM, IMOD / Number images used: 242 |