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- PDB-11bd: human nucleosome assembly protein 1 (human Nap1) -

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Basic information

Entry
Database: PDB / ID: 11bd
Titlehuman nucleosome assembly protein 1 (human Nap1)
ComponentsNucleosome assembly protein 1-like 1
KeywordsCHAPERONE / Histone / H2A-H2B / nucleosome assembly protein 1 / nucleosome assembly protein like 1
Function / homology
Function and homology information


histone chaperone activity / positive regulation of neural precursor cell proliferation / positive regulation of neurogenesis / melanosome / nervous system development / nucleosome assembly / histone binding / DNA replication / positive regulation of cell population proliferation / chromatin binding ...histone chaperone activity / positive regulation of neural precursor cell proliferation / positive regulation of neurogenesis / melanosome / nervous system development / nucleosome assembly / histone binding / DNA replication / positive regulation of cell population proliferation / chromatin binding / chromatin / RNA binding / membrane / nucleus / cytoplasm
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Nucleosome assembly protein 1-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.1May 20, 2026Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleosome assembly protein 1-like 1
B: Nucleosome assembly protein 1-like 1


Theoretical massNumber of molelcules
Total (without water)68,7192
Polymers68,7192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-48 kcal/mol
Surface area33440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.610, 170.610, 60.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 34359.676 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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 26% PEG 400, 0.1 M sodium citrate, pH 4.5, 0.1 M magnesium chloride hexahydrate, 0.1 M sodium chloride, 2% 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→38.15 Å / Num. obs: 13151 / % possible obs: 96.8 % / Redundancy: 1.8 % / CC1/2: 0.94 / Rmerge(I) obs: 0.069 / Net I/σ(I): 6.5
Reflection shellResolution: 3.2→3.42 Å / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 1 / Num. unique obs: 1836 / CC1/2: 0.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→38.15 Å / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 28.051
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2665 1411 10.73 %
Rwork0.2267 11740 -
obs0.2306 13151 89.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 174.44 Å2
Refinement stepCycle: LAST / Resolution: 3.2→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 0 0 4639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524749
X-RAY DIFFRACTIONf_angle_d0.90436436
X-RAY DIFFRACTIONf_chiral_restr0.052695
X-RAY DIFFRACTIONf_plane_restr0.0075854
X-RAY DIFFRACTIONf_dihedral_angle_d6.3611612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.330.4307990.4136926X-RAY DIFFRACTION57.84
3.33-3.480.39961320.36961169X-RAY DIFFRACTION72.56
3.48-3.660.38691400.31131237X-RAY DIFFRACTION77.07
3.66-3.890.32181480.30751330X-RAY DIFFRACTION81.95
3.89-4.190.31321570.28731406X-RAY DIFFRACTION87.17
4.2-4.610.27921600.2421432X-RAY DIFFRACTION88.18
4.61-5.280.26161530.21281409X-RAY DIFFRACTION88.34
5.28-6.650.2821620.22711460X-RAY DIFFRACTION88.7
6.65-38.150.211610.17071470X-RAY DIFFRACTION86.62

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