11BC | pdb_000011bc

Human Nap1 in complex with HIV-1 Rev


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 11BC

This is version 1.1 of the entry. See complete history

Literature

Structural Basis for HIV-1 Rev Recognition by the Histone Chaperone Human Nap1.

Eren, E.Watts, N.R.Winkler, D.C.Wingfield, P.T.

(2026) J Biological Chem : 113120-113120

  • DOI: https://doi.org/10.1016/j.jbc.2026.113120
  • Primary Citation Related Structures: 
    11BC, 11BD, 11BE

  • PubMed 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. 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.


  • Organizational Affiliation
    • Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 143.43 kDa 
  • Atom Count: 6,793 
  • Modeled Residue Count: 826 
  • Deposited Residue Count: 1,246 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleosome assembly protein 1-like 1
A, B
391Homo sapiensMutation(s): 0 
Gene Names: NAP1L1NRP
UniProt & NIH Common Fund Data Resources
Find proteins for P55209 (Homo sapiens)
Explore P55209 
Go to UniProtKB:  P55209
PHAROS:  P55209
GTEx:  ENSG00000187109 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55209
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein RevC,
D,
E [auth F],
F [auth E]
116Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: rev
UniProt
Find proteins for Q76PP8 (Human immunodeficiency virus type 1)
Explore Q76PP8 
Go to UniProtKB:  Q76PP8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76PP8
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-05-13 
  • Deposition Author(s): Eren, E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-13
    Type: Initial release
  • Version 1.1: 2026-05-20
    Changes: Data collection, Database references