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- EMDB-16711: HIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to Sec24C peptide. -

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Basic information

Entry
Database: EMDB / ID: EMD-16711
TitleHIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to Sec24C peptide.
Map data
Sample
  • Complex: HIV-1 Mature Capsid
    • Protein or peptide: Gag polyproteinGroup-specific antigen
    • Protein or peptide: Protein transport protein Sec24CProtein targeting
Function / homology
Function and homology information


COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / MHC class II antigen presentation / viral process / SNARE binding ...COPII-coated vesicle cargo loading / COPII vesicle coat / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / MHC class II antigen presentation / viral process / SNARE binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / viral nucleocapsid / in utero embryonic development / host cell cytoplasm / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain ...Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Sec23/Sec24 beta-sandwich domain / Gelsolin-like domain superfamily / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / gag protein p24 N-terminal domain / von Willebrand factor A-like domain superfamily / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Gag polyprotein / Protein transport protein Sec24C
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsStacey JCV / Briggs JAG
Funding support Germany, United States, United Kingdom, 5 items
OrganizationGrant numberCountry
Max Planck Society Germany
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI147890 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5U54AI150472-09 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI170855-01 United States
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
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
DepositionFeb 16, 2023-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateApr 26, 2023-
Current statusApr 26, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16711.png

Downloads & links

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Map

FileDownload / File: emd_16711.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 357.12 Å		0.93 Å/pix.
x 384 pix.
= 357.12 Å		0.93 Å/pix.
x 384 pix.
= 357.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.357
Minimum - Maximum-2.7109857 - 3.2564723
Average (Standard dev.)0.00066471775 (±0.04110066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 357.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16711_msk_1.map
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Half map: #2

Fileemd_16711_half_map_1.map
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Half map: #1

Fileemd_16711_half_map_2.map
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Sample components

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Entire : HIV-1 Mature Capsid

EntireName: HIV-1 Mature Capsid
Components
  • Complex: HIV-1 Mature Capsid
    • Protein or peptide: Gag polyproteinGroup-specific antigen
    • Protein or peptide: Protein transport protein Sec24CProtein targeting

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Supramolecule #1: HIV-1 Mature Capsid

SupramoleculeName: HIV-1 Mature Capsid / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Details: Hexamer from CA-IP6 cores bound to FG repeat containing Sec24C peptide.
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 27 KDa

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Macromolecule #1: Gag polyprotein

MacromoleculeName: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 25.761623 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: 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

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Macromolecule #2: Protein transport protein Sec24C

MacromoleculeName: Protein transport protein Sec24C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.399549 KDa
SequenceString:
GPLLPGQSFG GPSVS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 6.1
Component:
ConcentrationFormulaName
300.0 mMNaClSodium chloridesodium chloride
2.0 mMC9H15O6PTCEP
50.0 mMC6H13NO4SMES
2.5 mMC6H18O24P6inositol hexakisphosphatePhytic acid
0.1 %C2H6OSDMSODimethyl sulfoxide
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
DetailsVLP assembly, bound to Sec24C peptide

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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: 8784 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2464856
Startup modelType of model: OTHER / Details: Subtomogram average reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 8 / Software - Name: cryoSPARC (ver. 3.3.2) / Details: Heterogenous refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 839656
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(Chain: PDB, experimental model, PDB, experimental model)
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation
Output model

PDB-8cl3:
HIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to Sec24C peptide.

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