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Yorodumi- EMDB-5020: Molecular Structure of the Native HIV-1 gp120 trimer bound to CD4... -
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-Basic information
Entry | Database: EMDB / ID: EMD-5020 | |||||||||
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Title | Molecular Structure of the Native HIV-1 gp120 trimer bound to CD4 and 17b: Spike region | |||||||||
Map data | CD4 and 17b-bound HIV-1 BaL spike | |||||||||
Sample |
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Keywords | HIV-1 / envelope glycoprotein. immunodeficiency virus / gp120 | |||||||||
Function / homology | Function and homology information helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / Synthesis and processing of ENV and VPU / MHC class II protein binding / evasion of host immune response / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / Synthesis and processing of ENV and VPU / MHC class II protein binding / evasion of host immune response / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Dectin-2 family / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of establishment of T cell polarity / T cell activation / positive regulation of interleukin-2 production / protein tyrosine kinase binding / host cell endosome membrane / Vpu mediated degradation of CD4 / calcium-mediated signaling / actin filament organization / Assembly Of The HIV Virion / clathrin-coated endocytic vesicle membrane / Budding and maturation of HIV virion / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / MHC class II protein complex binding / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / early endosome / viral protein processing / cell adhesion / symbiont entry into host cell / positive regulation of protein phosphorylation / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / virion attachment to host cell / endoplasmic reticulum membrane / protein kinase binding / host cell plasma membrane / structural molecule activity / positive regulation of DNA-templated transcription / virion membrane / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | envelope glycoprotein (unknown) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 20.0 Å | |||||||||
Authors | Bartesaghi A / Borgnia M / Liu J / Sapiro G / Subramaniam S | |||||||||
Citation | Journal: Nature / Year: 2008 Title: Molecular architecture of native HIV-1 gp120 trimers. Authors: Jun Liu / Alberto Bartesaghi / Mario J Borgnia / Guillermo Sapiro / Sriram Subramaniam / Abstract: The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. ...The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. Env is a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120), and forms trimers on the surface of the viral membrane. Using cryo-electron tomography combined with three-dimensional image classification and averaging, we report the three-dimensional structures of trimeric Env displayed on native HIV-1 in the unliganded state, in complex with the broadly neutralizing antibody b12 and in a ternary complex with CD4 and the 17b antibody. By fitting the known crystal structures of the monomeric gp120 core in the b12- and CD4/17b-bound conformations into the density maps derived by electron tomography, we derive molecular models for the native HIV-1 gp120 trimer in unliganded and CD4-bound states. We demonstrate that CD4 binding results in a major reorganization of the Env trimer, causing an outward rotation and displacement of each gp120 monomer. This appears to be coupled with a rearrangement of the gp41 region along the central axis of the trimer, leading to closer contact between the viral and target cell membranes. Our findings elucidate the structure and conformational changes of trimeric HIV-1 gp120 relevant to antibody neutralization and attachment to target cells. | |||||||||
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_5020.map.gz | 188.7 KB | EMDB map data format | |
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Header (meta data) | emd-5020-v30.xml emd-5020.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_5020_1.jpg | 576 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5020 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5020 | HTTPS FTP |
-Validation report
Summary document | emd_5020_validation.pdf.gz | 285.6 KB | Display | EMDB validaton report |
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Full document | emd_5020_full_validation.pdf.gz | 285.2 KB | Display | |
Data in XML | emd_5020_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5020 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5020 | HTTPS FTP |
-Related structure data
Related structure data | 3dnoMC 3j70M 5018C 5019C 5021C 5022C 5023C 3dnlC 3dnnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5020.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CD4 and 17b-bound HIV-1 BaL spike | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 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 : HIV-1 BaL virus
Entire | Name: HIV-1 BaL virus |
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Components |
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-Supramolecule #1000: HIV-1 BaL virus
Supramolecule | Name: HIV-1 BaL virus / type: sample / ID: 1000 Details: Structures determined by cryo-electron tomography combined with 3D averaging Number unique components: 1 |
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-Supramolecule #1: envelope glycoprotein
Supramolecule | Name: envelope glycoprotein / type: virus / ID: 1 / Name.synonym: envelope glycoprotein / Sci species name: envelope glycoprotein / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: envelope glycoprotein |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
-Sample preparation
Buffer | pH: 7.2 / Details: 0.01 M Tris, 0.1 M NaCl, 1 mM EDTA |
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Grid | Details: home-made holey carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot and plunge |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 77 K |
Specialist optics | Energy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Average electron dose: 80 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 34000 |
Sample stage | Specimen holder: Cartridge / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 ° |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Average number of tilts used in the 3D reconstructions: 400. Average tomographic tilt angle increment: 1. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD and in-house procedures |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | Automated fitting procedures |
Refinement | Space: REAL / Target criteria: correlation coefficient |
Output model | PDB-3dno: PDB-3j70: |