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- PDB-11bc: Human Nap1 in complex with HIV-1 Rev -

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Basic information

Entry
Database: PDB / ID: 11bc
TitleHuman Nap1 in complex with HIV-1 Rev
Components
  • Nucleosome assembly protein 1-like 1
  • Protein Rev
KeywordsCHAPERONE / histone chaperone / H2A-H2B / Nap1 / HIV-1 Rev / Nucleosome assembly protein 1 / Nucleosome assembly protein like 1
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsEren, E.
Funding support United States, 1items
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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 20, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1May 20, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleosome assembly protein 1-like 1
B: Nucleosome assembly protein 1-like 1
C: Protein Rev
D: Protein Rev
F: Protein Rev
E: Protein Rev


Theoretical massNumber of molelcules
Total (without water)143,4316
Polymers143,4316
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Nucleosome assembly protein 1-like 1 / Histone H2A-H2B chaperone NAP1L1 / NAP-1-related protein / hNRP


Mass: 45429.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAP1L1, NRP / Production host: Escherichia coli (E. coli) / References: UniProt: P55209
#2: Protein
Protein Rev / ART/TRS / Anti-repression transactivator / Regulator of expression of viral proteins


Mass: 13142.856 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: rev / Production host: Escherichia coli (E. coli) / References: UniProt: Q76PP8
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human Nap1 in complex with HIV-1 Rev / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.154 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.18.2_3874model refinement
3SerialEMimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 275000 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056937
ELECTRON MICROSCOPYf_angle_d0.799361
ELECTRON MICROSCOPYf_dihedral_angle_d4.877924
ELECTRON MICROSCOPYf_chiral_restr0.046995
ELECTRON MICROSCOPYf_plane_restr0.0071243

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