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- EMDB-75601: Human Nap1 in complex with HIV-1 Rev -

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Basic information

Entry
Database: EMDB / ID: EMD-75601
TitleHuman Nap1 in complex with HIV-1 Rev
Map data
Sample
  • Complex: human Nap1 in complex with HIV-1 Rev
    • Protein or peptide: Nucleosome assembly protein 1-like 1
    • Protein or peptide: Protein Rev
Keywordshistone chaperone / H2A-H2B / Nap1 / HIV-1 Rev / Nucleosome assembly protein 1 / Nucleosome assembly protein like 1 / CHAPERONE
Function / homology
Function and homology information


histone chaperone activity / host cell nucleolus / positive regulation of neural precursor cell proliferation / positive regulation of neurogenesis / viral process / mRNA transport / melanosome / nervous system development / nucleosome assembly / histone binding ...histone chaperone activity / host cell nucleolus / positive regulation of neural precursor cell proliferation / positive regulation of neurogenesis / viral process / mRNA transport / melanosome / nervous system development / nucleosome assembly / histone binding / host cell cytoplasm / DNA replication / DNA-binding transcription factor activity / positive regulation of cell population proliferation / chromatin binding / chromatin / RNA binding / membrane / nucleus / cytoplasm
Similarity search - Function
Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Nucleosome assembly protein 1-like 1 / Protein Rev
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsEren E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS) United States
CitationJournal: J Biol Chem / Year: 2026
Title: 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.
History
DepositionFeb 15, 2026-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75601.png

Downloads & links

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Map

FileDownload / File: emd_75601.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 200 pix.
= 172. Å		0.86 Å/pix.
x 200 pix.
= 172. Å		0.86 Å/pix.
x 200 pix.
= 172. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0489
Minimum - Maximum-0.16843526 - 1.11051
Average (Standard dev.)0.004401642 (±0.017068457)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 172.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_75601_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_75601_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : human Nap1 in complex with HIV-1 Rev

EntireName: human Nap1 in complex with HIV-1 Rev
Components
  • Complex: human Nap1 in complex with HIV-1 Rev
    • Protein or peptide: Nucleosome assembly protein 1-like 1
    • Protein or peptide: Protein Rev

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Supramolecule #1: human Nap1 in complex with HIV-1 Rev

SupramoleculeName: human Nap1 in complex with HIV-1 Rev / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 154 KDa

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Macromolecule #1: Nucleosome assembly protein 1-like 1

MacromoleculeName: Nucleosome assembly protein 1-like 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.429996 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADIDNKEQS ELDQDLDDVE EVEEEETGEE TKLKARQLTV QMMQNPQILA ALQERLDGLV ETPTGYIESL PRVVKRRVNA LKNLQVKCA QIEAKFYEEV HDLERKYAVL YQPLFDKRFE IINAIYEPTE EECEWKPDEE DEISEELKEK AKIEDEKKDE E KEDPKGIP ...String:
MADIDNKEQS ELDQDLDDVE EVEEEETGEE TKLKARQLTV QMMQNPQILA ALQERLDGLV ETPTGYIESL PRVVKRRVNA LKNLQVKCA QIEAKFYEEV HDLERKYAVL YQPLFDKRFE IINAIYEPTE EECEWKPDEE DEISEELKEK AKIEDEKKDE E KEDPKGIP EFWLTVFKNV DLLSDMVQEH DEPILKHLKD IKVKFSDAGQ PMSFVLEFHF EPNEYFTNEV LTKTYRMRSE PD DSDPFSF DGPEIMGCTG CQIDWKKGKN VTLKTIKKKQ KHKGRGTVRT VTKTVSNDSF FNFFAPPEVP ESGDLDDDAE AIL AADFEI GHFLRERIIP RSVLYFTGEA IEDDDDDYDE EGEEADEEGE EEGDEENDPD YDPKKDQNPA ECKQQ

UniProtKB: Nucleosome assembly protein 1-like 1

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Macromolecule #2: Protein Rev

MacromoleculeName: Protein Rev / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 13.142856 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGRSGDSDE DLLKTVRLIK FLYQSNPPPN PEGTRQARRN RRRRWRERRR QIHSISRRIL STYLGRSAEP VPLQLPPLER LTLDCNEDC GTSGTQGVGS PQILVESPTV LESGAKE

UniProtKB: Protein Rev

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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
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 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 / Details: Ab Initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 275000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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