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Open data
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Basic information
| Entry | Database: PDB / ID: 11be | ||||||
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| Title | HIV-1 Rev Filament | ||||||
Components | Protein Rev | ||||||
Keywords | VIRAL PROTEIN / HIV-1 / Rev / Filament / Rev Response Element / RNA / RNA binding protein | ||||||
| Function / homology | Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / host cell nucleolus / viral process / mRNA transport / host cell cytoplasm / DNA-binding transcription factor activity / RNA binding / Protein Rev Function and homology information | ||||||
| Biological species | ![]() Human immunodeficiency virus 1 | ||||||
| Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8.3 Å | ||||||
Authors | Eren, E. | ||||||
| Funding support | United States, 1items
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Citation | Journal: J Biol Chem / Year: 2026Title: Structural Basis for HIV-1 Rev Recognition by the Histone Chaperone Human Nap1. Authors: Elif Eren / Norman R Watts / Dennis C Winkler / Paul T Wingfield / ![]() Abstract: Human Nap1 (hNap1) is a histone chaperone involved in chromatin dynamics and has been shown to interact with the HIV-1 regulatory protein Rev, which is essential for nuclear export of viral RNA. ...Human Nap1 (hNap1) is a histone chaperone involved in chromatin dynamics and has been shown to interact with the HIV-1 regulatory protein Rev, which is essential for nuclear export of viral RNA. Despite the functional significance of this interaction, its structural basis has remained elusive. Here, we present the X-ray crystal structure of hNap1 and the cryo-electron microscopy structure of the core domain of hNap1-Rev complex. The structure reveals that hNap1 binds Rev dimers via its acidic concave surface, engaging the Rev arginine-rich motif and oligomerization domain, and stabilizes Rev as a dimer-of-dimers tetramer. This interaction prevents higher-order Rev aggregation and enhances Rev's cooperative binding to the Rev Response Element. Surface plasmon resonance measurements confirm the formation of a stable complex with an apparent low-micromolar affinity between hNap1 and Rev, supporting a chaperone-like, reversible association. Our findings provide molecular insight into how hNap1 modulates Rev assembly and function, suggesting a model in which hNap1 primes Rev for productive engagement with viral RNA, thereby facilitating HIV-1 replication. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 11be.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb11be.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 11be.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/1b/11be ftp://data.pdbj.org/pub/pdb/validation_reports/1b/11be | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 6439M ![]() 11bcC ![]() 11bdC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
| #1: Protein | Mass: 13142.856 Da / Num. of mol.: 155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Human immunodeficiency virus 1 / Gene: rev / Production host: ![]() Has protein modification | N | |
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-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
| Component | Name: Rev Filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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| Molecular weight | Experimental value: NO |
| Source (natural) | Organism: ![]() Human immunodeficiency virus 1 |
| Source (recombinant) | Organism: ![]() |
| Buffer solution | pH: 7 |
| Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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| Microscopy | Model: FEI POLARA 300 |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3090 nm / Nominal defocus min: 990 nm |
| Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
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| CTF correction | Type: PHASE FLIPPING ONLY | |||||||||
| Helical symmerty | Angular rotation/subunit: 22 ° / Axial rise/subunit: 21 Å / Axial symmetry: C6 | |||||||||
| 3D reconstruction | Resolution: 8.3 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 300 / Symmetry type: HELICAL |
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About Yorodumi





Human immunodeficiency virus 1
United States, 1items
Citation



PDBj



FIELD EMISSION GUN