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- EMDB-70347: Low resolution single particle cryo-EM reconstruction of the HIV-... -

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Basic information

Entry
Database: EMDB / ID: EMD-70347
TitleLow resolution single particle cryo-EM reconstruction of the HIV-1 Rev/RRE (355 nt)
Map dataHIV-1 Rev with HIV-1 RRE (355 nucleotides) crosslinked with GTA using the GraFix protocol.
Sample
  • Complex: HIV-1 Rev/RRE RNP (ribonucleoprotein) complex
    • RNA: HIV-1 RRE
    • Protein or peptide: HIV-1 Rev
KeywordsHIV / Rev / RNA BINDING PROTEIN-RNA complex / RNA
Biological speciesHuman immunodeficiency virus 1 / Human immunodeficiency virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 10.03 Å
AuthorsSmith AM / Cheng Y / Frankel AD
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI170792 United States
National Institutes of Health/Office of the DirectorOD020054 United States
National Institutes of Health/Office of the DirectorOD021741 United States
National Institutes of Health/Office of the DirectorOD026881 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol Cell / Year: 2025
Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Authors: Amber M Smith / Yang Li / Arianna Velarde / Yifan Cheng / Alan D Frankel /
Abstract: HIV utilizes host proteins to manipulate cellular processes during replication. One key interaction involves the HIV regulatory protein Rev with the highly conserved nuclear exportin chromosome ...HIV utilizes host proteins to manipulate cellular processes during replication. One key interaction involves the HIV regulatory protein Rev with the highly conserved nuclear exportin chromosome region maintenance 1(CRM1), which exports >1,000 proteins and ribonucleoprotein (RNP) complexes from the nucleus to the cytoplasm. Rev, with its associated viral RNA, is the first identified RNP cargo of CRM1. Here, we present the cryogenic-electron microscopy (cryo-EM) structure of the HIV-1 Rev/Rev response element (RRE)/CRM1/Ran nuclear export complex. A Rev dimer engages a unique CRM1 dimer at an uncharacterized cargo-binding site at the core of the complex, positioning the RRE within a charged pocket inside one CRM1 subunit. Direct contacts between the RNA and CRM1/Ran-guanosine triphosphate (GTP) highlight the critical role of the RRE. The structure, together with guided mutations and cellular assays, provides not only an unprecedented view of HIV RNA transport but also illuminates how CRM1 can recognize a diverse range of protein and RNP cargos.
History
DepositionApr 25, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70347.png

Downloads & links

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Map

FileDownload / File: emd_70347.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 Rev with HIV-1 RRE (355 nucleotides) crosslinked with GTA using the GraFix protocol.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 200 pix.
= 230.1 Å		1.15 Å/pix.
x 200 pix.
= 230.1 Å		1.15 Å/pix.
x 200 pix.
= 230.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1505 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.028764794 - 0.07307899
Average (Standard dev.)-0.00002960314 (±0.0013152803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 230.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70347_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Particles from this 3D class were used for refinement.

Fileemd_70347_additional_1.map
AnnotationParticles from this 3D class were used for refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 Rev with HIV-1 RRE (355 nucleotides) crosslinked...

Fileemd_70347_half_map_1.map
AnnotationHIV-1 Rev with HIV-1 RRE (355 nucleotides) crosslinked with GTA using the GraFix protocol.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 Rev with HIV-1 RRE (355 nucleotides) crosslinked...

Fileemd_70347_half_map_2.map
AnnotationHIV-1 Rev with HIV-1 RRE (355 nucleotides) crosslinked with GTA using the GraFix protocol.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 Rev/RRE RNP (ribonucleoprotein) complex

EntireName: HIV-1 Rev/RRE RNP (ribonucleoprotein) complex
Components
  • Complex: HIV-1 Rev/RRE RNP (ribonucleoprotein) complex
    • RNA: HIV-1 RRE
    • Protein or peptide: HIV-1 Rev

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Supramolecule #1: HIV-1 Rev/RRE RNP (ribonucleoprotein) complex

SupramoleculeName: HIV-1 Rev/RRE RNP (ribonucleoprotein) complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 194376 MDa

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Macromolecule #1: HIV-1 RRE

MacromoleculeName: HIV-1 RRE / type: rna / ID: 1
Details: 355 nucleotide viral RNA from the HIV-1 strain SF-2.
Source (natural)Organism: Human immunodeficiency virus 2 / Strain: SF-2
SequenceString: ugaaccauua ggaauagcac ccaccaaggc aaagagaaga guggugcaga gagaaaaaag agcaguggga auaguaggag cuauguuccu uggguucuug ggagcagaag gaagcacuau gggcgcagug ucauugacgc ugacgguaca ggccagacaa uuauugucug ...String:
ugaaccauua ggaauagcac ccaccaaggc aaagagaaga guggugcaga gagaaaaaag agcaguggga auaguaggag cuauguuccu uggguucuug ggagcagaag gaagcacuau gggcgcagug ucauugacgc ugacgguaca ggccagacaa uuauugucug guauagugca acagcagaac aauuugcuga gggcuauuga ggcgcaacaa caucuguugc aacucacagu cuggggcauc aagcagcucc aggcaagagu ccuggcugug gaaagauacc uaagggauca acagcuccua gggatttggg guugcucugg aaaacucauu ugcaccacug cugug

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Macromolecule #2: HIV-1 Rev

MacromoleculeName: HIV-1 Rev / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
GAMAGRSGDS DEDLLKAVRL IKFLYQSNPP PNPEGTRQAR RNRRRRWRER QRQIHSISER ILSTYLGRSA EPVPLQTVDE MTKKFGTLT IDC

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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

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
50.0 mMKClPotassium Chloride
2.0 mMHOCH2CH2SHBeta-mercaptoethanol
2.5 % (v/v)C3H8O3glycerol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV / Details: Botting time 6 seconds.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 95.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: subtomo averaged reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126797
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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