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- EMDB-16709: HIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to CPSF6 peptide. -
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Open data
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Basic information
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Title | HIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to CPSF6 peptide. | ||||||||||||||||||
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Function / homology | ![]() exon-exon junction complex binding / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles ...exon-exon junction complex binding / : / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / paraspeckles / mRNA 3'-end processing / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / RNA Polymerase II Transcription Termination / protein heterotetramerization / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / localization / Signaling by FGFR1 in disease / viral process / protein tetramerization / mRNA processing / viral nucleocapsid / host cell cytoplasm / nuclear speck / ribonucleoprotein complex / mRNA binding / host cell nucleus / virion membrane / structural molecule activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | ||||||||||||||||||
![]() | Stacey JCV / Briggs JAG | ||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Two structural switches in HIV-1 capsid regulate capsid curvature and host factor binding. Authors: James C V Stacey / Aaron Tan / John M Lu / Leo C James / Robert A Dick / John A G Briggs / ![]() ![]() ![]() Abstract: The mature HIV-1 capsid protects the viral genome and interacts with host proteins to travel from the cell periphery into the nucleus. To achieve this, the capsid protein, CA, constructs conical ...The mature HIV-1 capsid protects the viral genome and interacts with host proteins to travel from the cell periphery into the nucleus. To achieve this, the capsid protein, CA, constructs conical capsids from a lattice of hexamers and pentamers, and engages in and then relinquishes multiple interactions with cellular proteins in an orchestrated fashion. Cellular host factors including Nup153, CPSF6, and Sec24C engage the same pocket within CA hexamers. How CA assembles pentamers and hexamers of different curvatures, how CA oligomerization states or curvature might modulate host-protein interactions, and how binding of multiple cofactors to a single site is coordinated, all remain to be elucidated. Here, using single-particle cryoEM, we have determined the structure of the mature HIV-1 CA pentamer and hexamer from conical CA-IP polyhedra to ~3 Å resolution. We also determined structures of hexamers in the context of multiple lattice curvatures and number of pentamer contacts. Comparison of these structures, bound or not to host protein peptides, revealed two structural switches within HIV-1 CA that modulate peptide binding according to CA lattice curvature and whether CA is hexameric or pentameric. These observations suggest that the conical HIV-1 capsid has different host-protein binding properties at different positions on its surface, which may facilitate cell entry and represent an evolutionary advantage of conical morphology. | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 202.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.5 KB 21.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.3 KB | Display | ![]() |
Images | ![]() | 124.6 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Others | ![]() ![]() | 196.3 MB 196.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 756.3 KB | Display | ![]() |
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Full document | ![]() | 755.9 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cl1MC ![]() 8ckvC ![]() 8ckwC ![]() 8ckxC ![]() 8ckyC ![]() 8ckzC ![]() 8cl0C ![]() 8cl2C ![]() 8cl3C ![]() 8cl4C 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
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Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16709_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16709_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : HIV-1 Mature Capsid
Entire | Name: HIV-1 Mature Capsid |
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Components |
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-Supramolecule #1: HIV-1 Mature Capsid
Supramolecule | Name: HIV-1 Mature Capsid / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all Details: Hexamer bound to FG repeat containing CPSF6 peptide. |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 27 KDa |
-Macromolecule #1: Gag polyprotein
Macromolecule | Name: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.761623 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPIVQNLQGQ MVHQAISPRT LNAWVKVVEE KAFSPEVIPM FSALSEGATP QDLNTMLNTV GGHQAAMQML KETINEEAAE WDRLHPVHA GPIAPGQMRE PRGSDIAGTT STLQEQIGWM THNPPIPVGE IYKRWIILGL NKIVRMYSPT SILDIRQGPK E PFRDYVDR ...String: MPIVQNLQGQ MVHQAISPRT LNAWVKVVEE KAFSPEVIPM FSALSEGATP QDLNTMLNTV GGHQAAMQML KETINEEAAE WDRLHPVHA GPIAPGQMRE PRGSDIAGTT STLQEQIGWM THNPPIPVGE IYKRWIILGL NKIVRMYSPT SILDIRQGPK E PFRDYVDR FYKTLRAEQA SQEVKNWMTE TLLVQNANPD CKTILKALGP GATLEEMMTA CQGVGGPGHK ARVL |
-Macromolecule #2: Cleavage and polyadenylation specificity factor subunit 6
Macromolecule | Name: Cleavage and polyadenylation specificity factor subunit 6 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.550796 KDa |
Sequence | String: PVLFPGQPFG QPPLG |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL | ||||||||||||||||||
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Buffer | pH: 6.1 Component:
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Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | VLP assembly, bound to CPSF6 peptide |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 21765 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | (Chain: PDB, experimental model, PDB, experimental model) |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation |
Output model | ![]() PDB-8cl1: |