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Open data
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Basic information
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Title | Structure of HIV-1 capsid declination | |||||||||
![]() | Declination of in vitro HIV-1 capsids | |||||||||
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![]() | HIV-1 / capsid / declination / pentamer / hexamer / VIRUS LIKE PARTICLE | |||||||||
Function / homology | ![]() viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.43 Å | |||||||||
![]() | Pornillos O / Ganser-Pornillos BK / Schirra RT | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A molecular switch modulates assembly and host factor binding of the HIV-1 capsid. Authors: Randall T Schirra / Nayara F B Dos Santos / Kaneil K Zadrozny / Iga Kucharska / Barbie K Ganser-Pornillos / Owen Pornillos / ![]() ![]() Abstract: The HIV-1 capsid is a fullerene cone made of quasi-equivalent hexamers and pentamers of the viral CA protein. Typically, quasi-equivalent assembly of viral capsid subunits is controlled by a ...The HIV-1 capsid is a fullerene cone made of quasi-equivalent hexamers and pentamers of the viral CA protein. Typically, quasi-equivalent assembly of viral capsid subunits is controlled by a molecular switch. Here, we identify a Thr-Val-Gly-Gly motif that modulates CA hexamer/pentamer switching by folding into a 3 helix in the pentamer and random coil in the hexamer. Manipulating the coil/helix configuration of the motif allowed us to control pentamer and hexamer formation in a predictable manner, thus proving its function as a molecular switch. Importantly, the switch also remodels the common binding site for host factors that are critical for viral replication and the new ultra-potent HIV-1 inhibitor lenacapavir. This study reveals that a critical assembly element also modulates the post-assembly and viral replication functions of the HIV-1 capsid and provides new insights on capsid function and inhibition. | |||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 104.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.4 KB 15.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 240.2 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 474.7 MB 474.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 863.9 KB | Display | ![]() |
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Full document | ![]() | 863.4 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7urnMC ![]() 7urtC ![]() 8eepC ![]() 8eetC ![]() 8ejlC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Declination of in vitro HIV-1 capsids | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B
File | emd_26715_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_26715_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Capsid-like particles of in vitro assembled HIV-1 CA protein
Entire | Name: Capsid-like particles of in vitro assembled HIV-1 CA protein |
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Components |
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-Supramolecule #1: Capsid-like particles of in vitro assembled HIV-1 CA protein
Supramolecule | Name: Capsid-like particles of in vitro assembled HIV-1 CA protein type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: HIV-1 capsid protein
Macromolecule | Name: HIV-1 capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.630426 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF ...String: PIVQNLQGQM VHQAISPRTL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPG ATLEEMMTAC QGVGGPGHKA RVL UniProtKB: Gag polyprotein |
-Macromolecule #2: INOSITOL HEXAKISPHOSPHATE
Macromolecule | Name: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: IHP |
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Molecular weight | Theoretical: 660.035 Da |
Chemical component information | ![]() ChemComp-IHP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Manual plunge-freezing. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | The following protein chains were refined separately in real space using Phenix: A (pentamer); L, M and N (half-hexamer). Chain M was then rigid-body fit to generate chains O, P and Q to complete the hexamer. Chains O, P and Q are deposited as polyALA models. |
Refinement | Space: REAL / Protocol: OTHER |
Output model | ![]() PDB-7urn: |