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- EMDB-3308: HIV-1 cleaved wild type JR-FL EnvdCT trimer in complex with PGT15... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3308 | |||||||||
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Title | HIV-1 cleaved wild type JR-FL EnvdCT trimer in complex with PGT151 at 4.19 A resolution | |||||||||
![]() | Wild type JR-FL EnvdCT in complex with PGT151, with Fab constant region and detergent micelle masked out. | |||||||||
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![]() | HIV-1 / Env / PGT151 / broadly neutralizing antibody | |||||||||
Function / homology | ![]() positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.19 Å | |||||||||
![]() | Lee JH / Ozorowski G / Ward AB | |||||||||
![]() | ![]() Title: Cryo-EM structure of a native, fully glycosylated, cleaved HIV-1 envelope trimer. Authors: Jeong Hyun Lee / Gabriel Ozorowski / Andrew B Ward / ![]() Abstract: The envelope glycoprotein trimer (Env) on the surface of HIV-1 recognizes CD4(+) T cells and mediates viral entry. During this process, Env undergoes substantial conformational rearrangements, making ...The envelope glycoprotein trimer (Env) on the surface of HIV-1 recognizes CD4(+) T cells and mediates viral entry. During this process, Env undergoes substantial conformational rearrangements, making it difficult to study in its native state. Soluble stabilized trimers have provided valuable insights into the Env structure, but they lack the hydrophobic membrane proximal external region (MPER, an important target of broadly neutralizing antibodies), the transmembrane domain, and the cytoplasmic tail. Here we present (i) a cryogenic electron microscopy (cryo-EM) structure of a clade B virus Env, which lacks only the cytoplasmic tail and is stabilized by the broadly neutralizing antibody PGT151, at a resolution of 4.2 angstroms and (ii) a reconstruction of this form of Env in complex with PGT151 and MPER-targeting antibody 10E8 at a resolution of 8.8 angstroms. These structures provide new insights into the wild-type Env structure. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.9 KB 17.9 KB | Display Display | ![]() |
Images | ![]() | 904.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 273.2 KB | Display | ![]() |
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Full document | ![]() | 272.3 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fuuMC ![]() 3309C ![]() 3312C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Wild type JR-FL EnvdCT in complex with PGT151, with Fab constant region and detergent micelle masked out. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Cleaved JR-FL EnvdCT in complex with PGT151 Fab
Entire | Name: Cleaved JR-FL EnvdCT in complex with PGT151 Fab |
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Components |
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-Supramolecule #1000: Cleaved JR-FL EnvdCT in complex with PGT151 Fab
Supramolecule | Name: Cleaved JR-FL EnvdCT in complex with PGT151 Fab / type: sample / ID: 1000 / Oligomeric state: Two PGT151 Fabs bind one Env trimer / Number unique components: 2 |
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Molecular weight | Theoretical: 535 KDa |
-Macromolecule #1: HIV-1 Envelope glycoprotein
Macromolecule | Name: HIV-1 Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: HIV-1 Env Details: wild-type JR-FL Env trimer with the cytoplasmic tail truncated Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 435 KDa |
Recombinant expression | Organism: Mammalian (mammals) / Recombinant strain: Human / Recombinant cell: HEK293F / Recombinant plasmid: phCMV3 |
-Macromolecule #2: Immunoglobulin G PGT151
Macromolecule | Name: Immunoglobulin G PGT151 / type: protein_or_peptide / ID: 2 / Name.synonym: IgG PGT151 / Details: PGT151 cleaved into Fab / Number of copies: 2 / Oligomeric state: Heterodimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 50 KDa |
Recombinant expression | Organism: Mammalian (mammals) / Recombinant strain: Human / Recombinant cell: HEK293F |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.5 mg/mL |
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Buffer | pH: 7.4 Details: 50 mM Tris pH 7.4, 150 mM NaCl, 0.1% DDM, 0.03 mg/mL sodium deoxycholate |
Grid | Details: 400 mesh C-Flat, CF-2/2-4C, plasma cleaned for 5 seconds |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER Details: Samples were treated with biobeads prior to freezing Method: Grids were manually plunged at RT. |
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Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Alignment procedure | Legacy - Astigmatism: Objective astigmatism corrected at 22,500x magnification. |
Date | Nov 8, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Sampling interval: 5.0 µm / Number real images: 8759 / Average electron dose: 35.1 e/Å2 Details: Each full dose image is an aligned stack of frames recorded each using a dose of ~10 e-/Angstrom^2/sec. |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 22500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Electron microscopy #2
Microscopy ID | 2 |
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Microscope | FEI TITAN KRIOS |
Alignment procedure | Legacy - Astigmatism: Objective astigmatism corrected at 22,500x magnification. |
Date | Oct 24, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Sampling interval: 5.0 µm / Number real images: 8759 / Average electron dose: 33.7 e/Å2 Details: Each full dose image is an aligned stack of frames recorded each using a dose of ~10 e-/Angstrom^2/sec. |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 22500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Electron microscopy #3
Microscopy ID | 3 |
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Microscope | FEI TITAN KRIOS |
Alignment procedure | Legacy - Astigmatism: Objective astigmatism corrected at 22,500x magnification. |
Date | Sep 11, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Sampling interval: 5.0 µm / Number real images: 8759 / Average electron dose: 32.2 e/Å2 Details: Each full dose image is an aligned stack of frames recorded each using a dose of ~10 e-/Angstrom^2/sec. |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 22500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Electron microscopy #4
Microscopy ID | 4 |
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Microscope | FEI TITAN KRIOS |
Alignment procedure | Legacy - Astigmatism: Objective astigmatism corrected at 22,500x magnification. |
Date | Feb 27, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Sampling interval: 5.0 µm / Number real images: 8759 / Average electron dose: 32.4 e/Å2 Details: Each full dose image is an aligned stack of frames recorded each using a dose of ~10 e-/Angstrom^2/sec. |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 22500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | At the end of refinement which gave the 4.3 Angstrom resolution structure, a mask was applied to exclude the flexible micelle and Fab constant regions, following which the model refined for an additional 3 iterations (until convergence). |
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CTF correction | Details: Each micrograph |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.19 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 201386 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: B / Chain - #1 - Chain ID: G |
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Software | Name: ![]() |
Details | The trimer was used as an initial model for model building and refinement. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-5fuu: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: H / Chain - #1 - Chain ID: L |
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Software | Name: ![]() |
Details | The Fab was used as an initial model for model building and refinement. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-5fuu: |