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- EMDB-76854: HIV-1 Gag (CASP1NCSP2p6) assembled with core encapsidation signal... -

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Basic information

Entry
Database: EMDB / ID: EMD-76854
TitleHIV-1 Gag (CASP1NCSP2p6) assembled with core encapsidation signal - C6 symmetry
Map datamain map
Sample
  • Complex: Gag-RNA ribonucleoprotein complex
    • Protein or peptide: HIV-1 Gag CASP1NCSP2p6
    • RNA: HIV-1 CES
KeywordsHIV-1 / RNA packaging / Gag polyprotein / ribonucleoprotein complex (RNP) / viral assembly / viral genome selectivity / VIRUS LIKE PARTICLE
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 22, 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_76854.png

Downloads & links

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Map

FileDownload / File: emd_76854.map.gz / Format: CCP4 / Size: 325 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.)
0.94 Å/pix.
x 440 pix.
= 413.6 Å		0.94 Å/pix.
x 440 pix.
= 413.6 Å		0.94 Å/pix.
x 440 pix.
= 413.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.24252509 - 0.39531106
Average (Standard dev.)0.0016414372 (±0.015345663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 413.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_76854_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_76854_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: HIV-1 CES

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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: HIV-1 CES

MacromoleculeName: HIV-1 CES / type: rna / ID: 2
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
SequenceString:
GGUGCCCGUC UGUUGUGUGA CUCUGGUGAG AGCCAGAGGA GAUCUCUCGA CGCAGGACUC GGCUUGCUGA AGCGCGCACG GCAAGAGGCG AGGGGCGGCG ACUGGUGAGU ACGCCAAAAA UUUUGACUAG CGGAGGCUAG AAGGAGAGAG AUGGGUGCC

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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: 7.4
Component:
ConcentrationName
20.0 mMMOPS
10.0 mMNaCl
140.0 mMKCl
1.0 mMIP6
5.0 mMTCEP
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: FEI FALCON I (4k 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: 2.0 µm / Nominal defocus min: 1.2 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 164683
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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