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- EMDB-28186: Structure of HIV-1 capsid declination in complex with CPSF6-FG peptide -

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Basic information

Entry
Database: EMDB / ID: EMD-28186
TitleStructure of HIV-1 capsid declination in complex with CPSF6-FG peptide
Map dataHIV-1 capsid declination in complex with CPSF6-FG peptide
Sample
  • Complex: Capsid-like particles of in vitro assembled HIV-1 CA protein in complex with CPSF6-FG peptide
    • Protein or peptide: HIV-1 capsid protein
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 6
KeywordsHIV-1 / capsid / declination / pentamer / hexamer / VIRAL PROTEIN
Function / homology
Function and homology information


exon-exon junction complex binding / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-end processing ...exon-exon junction complex binding / positive regulation of RNA export from nucleus / mRNA cleavage factor complex / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / interchromatin granule / Processing of Intronless Pre-mRNAs / perichromatin fibrils / mRNA cleavage and polyadenylation specificity factor complex / mRNA alternative polyadenylation / mRNA 3'-end processing / Signaling by cytosolic FGFR1 fusion mutants / mRNA 3'-end processing / paraspeckles / RNA Polymerase II Transcription Termination / protein heterotetramerization / viral budding via host ESCRT complex / ribosomal large subunit binding / Processing of Capped Intron-Containing Pre-mRNA / Signaling by FGFR1 in disease / protein tetramerization / ISG15 antiviral mechanism / host multivesicular body / mRNA processing / viral nucleocapsid / nuclear speck / ribonucleoprotein complex / viral translational frameshifting / mRNA binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...Cleavage and polyadenylation specificity factor subunit 6 / CPSF6/7 family / Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Gag polyprotein / Cleavage and polyadenylation specificity factor subunit 6
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsPornillos O / Ganser-Pornillos BK / Schirra RT / dos Santos NFB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI167756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150464 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
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
DepositionSep 17, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28186.png

Downloads & links

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Map

FileDownload / File: emd_28186.map.gz / Format: CCP4 / Size: 61 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 capsid declination in complex with CPSF6-FG peptide
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 252 pix.
= 272.16 Å		1.08 Å/pix.
x 252 pix.
= 272.16 Å		1.08 Å/pix.
x 252 pix.
= 272.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.49480814 - 0.81491685
Average (Standard dev.)0.008540952 (±0.042877864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions252252252
Spacing252252252
CellA=B=C: 272.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28186_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28186_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Capsid-like particles of in vitro assembled HIV-1 CA protein in c...

EntireName: Capsid-like particles of in vitro assembled HIV-1 CA protein in complex with CPSF6-FG peptide
Components
  • Complex: Capsid-like particles of in vitro assembled HIV-1 CA protein in complex with CPSF6-FG peptide
    • Protein or peptide: HIV-1 capsid protein
    • Protein or peptide: Cleavage and polyadenylation specificity factor subunit 6

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Supramolecule #1: Capsid-like particles of in vitro assembled HIV-1 CA protein in c...

SupramoleculeName: Capsid-like particles of in vitro assembled HIV-1 CA protein in complex with CPSF6-FG peptide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Capsids (0.27 mM CA) were incubated with peptide (3 mM) for 1 hour in ice
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 capsid protein

MacromoleculeName: HIV-1 capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
Molecular weightTheoretical: 25.630426 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: Cleavage and polyadenylation specificity factor subunit 6

MacromoleculeName: Cleavage and polyadenylation specificity factor subunit 6
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.708952 KDa
SequenceString:
GTPVLFPGQP FGQPPLG

UniProtKB: Cleavage and polyadenylation specificity factor subunit 6

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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

BufferpH: 6
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Manual plunge-freezing.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.1) / Number images used: 166463
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7urn

chain_id: A, source_name: PDB, initial_model_type: experimental model

7urn

chain_id: L, source_name: PDB, initial_model_type: experimental model

7urn

chain_id: M, residue_range: 1-146, source_name: PDB, initial_model_type: experimental model

7urn

chain_id: N, residue_range: 146-221, source_name: PDB, initial_model_type: experimental model

4wym

chain_id: M, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8ejl:
Structure of HIV-1 capsid declination in complex with CPSF6-FG peptide

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