[English] 日本語
Yorodumi- EMDB-28954: Asymmetric structure of cleaved HIV-1 AE2 envelope glycoprotein t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28954 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Asymmetric structure of cleaved HIV-1 AE2 envelope glycoprotein trimer in styrene-maleic acid lipid nanoparticles (AE2.1) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | HIV-1 / envelope glycoprotein / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information : / 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 ...: / 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 / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Wang K / Zhang S / Sodroski J / Mao Y | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: Commun Biol / Year: 2023 Title: Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles. Authors: Kunyu Wang / Shijian Zhang / Eden P Go / Haitao Ding / Wei Li Wang / Hanh T Nguyen / John C Kappes / Heather Desaire / Joseph Sodroski / Youdong Mao / Abstract: During virus entry, the pretriggered human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer initially transits into a default intermediate state (DIS) that remains structurally ...During virus entry, the pretriggered human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer initially transits into a default intermediate state (DIS) that remains structurally uncharacterized. Here, we present cryo-EM structures at near-atomic resolution of two cleaved full-length HIV-1 Env trimers purified from cell membranes in styrene-maleic acid lipid nanoparticles without antibodies or receptors. The cleaved Env trimers exhibited tighter subunit packing than uncleaved trimers. Cleaved and uncleaved Env trimers assumed remarkably consistent yet distinct asymmetric conformations, with one smaller and two larger opening angles. Breaking conformational symmetry is allosterically coupled with dynamic helical transformations of the gp41 N-terminal heptad repeat (HR1) regions in two protomers and with trimer tilting in the membrane. The broken symmetry of the DIS potentially assists Env binding to two CD4 receptors-while resisting antibody binding-and promotes extension of the gp41 HR1 helical coiled-coil, which relocates the fusion peptide closer to the target cell membrane. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_28954.map.gz | 14.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-28954-v30.xml emd-28954.xml | 16 KB 16 KB | Display Display | EMDB header |
Images | emd_28954.png | 121 KB | ||
Others | emd_28954_half_map_1.map.gz emd_28954_half_map_2.map.gz | 11.9 MB 11.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28954 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28954 | HTTPS FTP |
-Validation report
Summary document | emd_28954_validation.pdf.gz | 801.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_28954_full_validation.pdf.gz | 801.5 KB | Display | |
Data in XML | emd_28954_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | emd_28954_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28954 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28954 | HTTPS FTP |
-Related structure data
Related structure data | 8faeMC 8fadC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_28954.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.65 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #1
File | emd_28954_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_28954_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : HIV-1 Env AE2.1
Entire | Name: HIV-1 Env AE2.1 |
---|---|
Components |
|
-Supramolecule #1: HIV-1 Env AE2.1
Supramolecule | Name: HIV-1 Env AE2.1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: Human immunodeficiency virus 1 |
-Macromolecule #1: Envelope glycoprotein gp41
Macromolecule | Name: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 16.639076 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: FLGFLGAAGS TMGAASITLT VQARLLLSGI VQQQNNLLKA IEAQQHLLKL TVWGIKQLQA RVLTVERYLR DQQLLGIWGC SGKLICTTA VPWNASWSNK TLDMIWNNMT WMEWEKEIDN YTGLIYTLIE ESQNQQEKNE KELLELD |
-Macromolecule #2: Envelope glycoprotein gp120
Macromolecule | Name: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 53.025961 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EKLWVTVYYG VPVWKEATTT LFCASDAKAY DTEVHNVWAT HACVPTDPNP QEVVLENVTE NFNMWKNNMV EQMHEDIISL WDESLKPCV KLTPLCVTLN CTDLRNVTNI NNSSEGMRGE IKNCSFNITT SIKDKVKKDY ALFYKLDVVP IDNDNTSYRL I NCNTSTIT ...String: EKLWVTVYYG VPVWKEATTT LFCASDAKAY DTEVHNVWAT HACVPTDPNP QEVVLENVTE NFNMWKNNMV EQMHEDIISL WDESLKPCV KLTPLCVTLN CTDLRNVTNI NNSSEGMRGE IKNCSFNITT SIKDKVKKDY ALFYKLDVVP IDNDNTSYRL I NCNTSTIT QACPKVSFEP IPIHYCTPAG FAILKCKDKK FNGTGPCKNV STVQCTHGIK PVVSTQLLLN GSLAEEEVVI RS SNFTDNA KNIIVQLKES VEINCTRPNN NTRKSIHIGP GKAFYTTGDI IGDIRQAHCN ISRTKWNNTL NQIATKLKEQ FGN NKTIVF NQSSGGDPEI VMHSFNCGGE FFYCNSTQLF NSTWNFNGTW NLTQSNGTEG NDTITLPCKI KQIINMWQEV GKAM YAPPI RGQIRCSSNI TGLILTRDGG NNHNNDTETF RPGGGDMRDN WRSELYKYKV VKIEPLGVAP TKAKRRV |
-Macromolecule #18: 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-...
Macromolecule | Name: 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione type: ligand / ID: 18 / Number of copies: 3 / Formula: 83G |
---|---|
Molecular weight | Theoretical: 406.434 Da |
Chemical component information | ChemComp-83G: |
-Macromolecule #19: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 19 / Number of copies: 3 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140035 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |