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- EMDB-47475: Gag CA-SP1 (T8I) immature lattice bound with Bevirimat from envel... -

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Basic information

Entry
Database: EMDB / ID: EMD-47475
TitleGag CA-SP1 (T8I) immature lattice bound with Bevirimat from enveloped virus like particles
Map dataanisotrpic sharpened map by half maps
Sample
  • Virus: Human immunodeficiency virus type 1 (HBX2 ISOLATE)
    • Protein or peptide: Gag
  • Ligand: 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: water
KeywordsHIV-1 / Gag / CA-SP1 / Inhibitor / virion assembly / VIRAL PROTEIN
Function / homology
Function and homology information


Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs ...Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / 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 ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / 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.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1 (HBX2 ISOLATE)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsWu C / Meuser ME / Xiong Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI170791 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI178846 United States
CitationJournal: To Be Published
Title: Structural insights into inhibitor mechanisms on immature HIV-1 Gag lattice revealed by high-resolution in situ single-particle cryo-EM
Authors: Wu C / Meuser ME / Rey JS / Meshkin H / Yang R / Devarkar SC / Freniere C / Shi J / Aiken C / Perilla JR / Xiong Y
History
DepositionOct 23, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47475.png

Downloads & links

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Map

FileDownload / File: emd_47475.map.gz / Format: CCP4 / Size: 286.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationanisotrpic sharpened map by half maps
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.71 Å/pix.
x 422 pix.
= 301.181 Å		0.71 Å/pix.
x 422 pix.
= 301.181 Å		0.71 Å/pix.
x 422 pix.
= 301.181 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7137 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.19390394 - 0.3116609
Average (Standard dev.)0.00039963948 (±0.010838065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions422422422
Spacing422422422
CellA=B=C: 301.1814 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47475_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: raw map without sharpening

Fileemd_47475_additional_1.map
Annotationraw map without sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47475_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47475_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 : Human immunodeficiency virus type 1 (HBX2 ISOLATE)

EntireName: Human immunodeficiency virus type 1 (HBX2 ISOLATE)
Components
  • Virus: Human immunodeficiency virus type 1 (HBX2 ISOLATE)
    • Protein or peptide: Gag
  • Ligand: 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: water

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Supramolecule #1: Human immunodeficiency virus type 1 (HBX2 ISOLATE)

SupramoleculeName: Human immunodeficiency virus type 1 (HBX2 ISOLATE) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: A codon-optimized Gag plasmid with T8I mutation in the SP1 domain (pCMV-Gag-opt) was expressed in HEK293T cells. The enveloped virion-like particles were purified by filtration and ...Details: A codon-optimized Gag plasmid with T8I mutation in the SP1 domain (pCMV-Gag-opt) was expressed in HEK293T cells. The enveloped virion-like particles were purified by filtration and ultracentrifugation, and directly used as cryo-EM sample.
NCBI-ID: 11706
Sci species name: Human immunodeficiency virus type 1 (HBX2 ISOLATE)
Sci species strain: Clone pNL4-3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Gag

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Macromolecule #1: Gag

MacromoleculeName: Gag / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus type 1 (HBX2 ISOLATE)
Strain: isolate HXB2
Molecular weightTheoretical: 25.500176 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HQAISPRTLN AWVKVVEEKA FSPEVIPMFS ALSEGATPQD LNTMLNTVGG HQAAMQMLKE TINEEAAEWD RVHPVHAGPI APGQMREPR GSDIAGTTST LQEQIGWMTN NPPIPVGEIY KRWIILGLNK IVRMYSPTSI LDIRQGPKEP FRDYVDRFYK T LRAEQASQ ...String:
HQAISPRTLN AWVKVVEEKA FSPEVIPMFS ALSEGATPQD LNTMLNTVGG HQAAMQMLKE TINEEAAEWD RVHPVHAGPI APGQMREPR GSDIAGTTST LQEQIGWMTN NPPIPVGEIY KRWIILGLNK IVRMYSPTSI LDIRQGPKEP FRDYVDRFYK T LRAEQASQ EVKNWMTETL LVQNANPDCK TILKALGPAA TLEEMMTACQ GVGGPGHKAR VLAEAMSQVI NSA

UniProtKB: Gag polyprotein

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Macromolecule #2: 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13a...

MacromoleculeName: 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: 2I4
Molecular weightTheoretical: 584.826 Da
Chemical component information

ChemComp-2I4:
3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid

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Macromolecule #3: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
10.0 mMTris-hydrocloride
100.0 mMsodium chlorideNaCl
1.0 mMEthylenediaminetetraacetic acid

Details: This is the final buffer in which the enveloped viral like particle was resuspended. The Gag-CA-SP1 lattice is inside the viral like particle and thus not in the direct environment of this buffer.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III
DetailsA codon-optimized Gag plasmid with T8I mutation in the SP1 domain (pCMV-Gag-opt) was expressed in HEK293T cells. The enveloped virion like particles were purified by filtration and ultracentrifugation, and directly used as cryo-EM sample.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Sample stageSpecimen 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

45975

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 477522
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9cwv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9e39:
Gag CA-SP1 (T8I) immature lattice bound with Bevirimat from enveloped virus like particles

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