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- EMDB-76864: HIV-1 Gag (CASP1NCSP2p6) assembled with dimerization signal - tom... -

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Basic information

Entry
Database: EMDB / ID: EMD-76864
TitleHIV-1 Gag (CASP1NCSP2p6) assembled with dimerization signal - tomography map
Map datamain map
Sample
  • Complex: Gag-RNA ribonucleoprotein complex
    • Protein or peptide: HIV-1 Gag CASP1NCSP2p6
    • RNA: dimerization signal of the core encapsidation signal
KeywordsHIV-1 / RNA packaging / Gag polyprotein / ribonucleoprotein complex (RNP) / viral assembly / viral genome selectivity / VIRUS LIKE PARTICLE
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsHollmann NM / Ganser-Pornillos BK / Pornillos O / Summers MF
Funding support United States, 5 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI70660 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI150498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI179691 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99AI186598 United States
CitationJournal: To Be Published
Title: Structural Basis for Dimeric Genome Selection by HIV-1
Authors: Hollmann NM / Kharytonchyk S / Buchannan A / Phillips C / Ledbetter A / Ahmed F / Adelstein A / Barry K / Geleta SA / Telesnitsky A / Ganser-Pornillos BK / Pornillos O / Summers MF
History
DepositionApr 23, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76864.png

Downloads & links

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Map

FileDownload / File: emd_76864.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.23 Å/pix.
x 112 pix.
= 361.984 Å		3.23 Å/pix.
x 112 pix.
= 361.984 Å		3.23 Å/pix.
x 112 pix.
= 361.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.232 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-20.564640000000001 - 13.45002
Average (Standard dev.)-0.4246589 (±1.3475761)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions112112112
Spacing112112112
CellA=B=C: 361.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_76864_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_76864_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gag-RNA ribonucleoprotein complex

EntireName: Gag-RNA ribonucleoprotein complex
Components
  • Complex: Gag-RNA ribonucleoprotein complex
    • Protein or peptide: HIV-1 Gag CASP1NCSP2p6
    • RNA: dimerization signal of the core encapsidation signal

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Supramolecule #1: Gag-RNA ribonucleoprotein complex

SupramoleculeName: Gag-RNA ribonucleoprotein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3

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Macromolecule #1: HIV-1 Gag CASP1NCSP2p6

MacromoleculeName: HIV-1 Gag CASP1NCSP2p6 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: VSQNYPIVQN LQGQMVHQAI SPRTLNAWVK VVEEKAFSPE VIPMFSALSE GATPQDLNTM LNTVGGHQAA MQMLKETINE EAAEWDRLHP VHAGPIAPGQ MREPRGSDIA GTTSTLQEQI GWMTHNPPIP VGEIYKRWII LGLNKIVRMY SPTSILDIRQ GPKEPFRDYV ...String:
VSQNYPIVQN LQGQMVHQAI SPRTLNAWVK VVEEKAFSPE VIPMFSALSE GATPQDLNTM LNTVGGHQAA MQMLKETINE EAAEWDRLHP VHAGPIAPGQ MREPRGSDIA GTTSTLQEQI GWMTHNPPIP VGEIYKRWII LGLNKIVRMY SPTSILDIRQ GPKEPFRDYV DRFYKTLRAE QASQEVKNWM TETLLVQNAN PDCKTILKAL GPGATLEEMM TACQGVGGPG HKARVLAEAM SQVTNPATIM IQKGNFRNQR KTVKCFNCGK EGHIAKNCRA PRKKGCWKCG KEGHQMKDCT ERQANFLGKI WPSHKGRPGN FLQSRPEPTA PPEESFRFGE ETTTPSQKQE PIDKELYPLA SLRSLFGSDP SSQ

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Macromolecule #2: dimerization signal of the core encapsidation signal

MacromoleculeName: dimerization signal of the core encapsidation signal / type: rna / ID: 2
Source (natural)Organism: Human immunodeficiency virus 1
SequenceString:
GGCAGGACUC GGCUUGCUGA AGCGCGCACG GCAAGAGGCG AGGGGCC

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationName
20.0 mMMOPS
10.0 mMNaCl
140.0 mMKCl
1.0 mMIP6
5.0 mMTCEP
GridModel: Quantifoil R1/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.46 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 657 / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: Dynamo / Number subtomograms used: 46
ExtractionNumber tomograms: 58 / Number images used: 63545 / Software - Name: Dynamo
CTF correctionSoftware - Name: RELION (ver. 5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: Dynamo

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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