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- PDB-11be: HIV-1 Rev Filament -

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Basic information

Entry
Database: PDB / ID: 11be
TitleHIV-1 Rev Filament
ComponentsProtein Rev
KeywordsVIRAL PROTEIN / HIV-1 / Rev / Filament / Rev Response Element / RNA / RNA binding protein
Function / homologyAnti-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 speciesHuman immunodeficiency virus 1
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8.3 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 1.1May 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

Downloads & links

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Assembly

Deposited unit
A1: Protein Rev
B1: Protein Rev
C1: Protein Rev
D1: Protein Rev
E1: Protein Rev
F1: Protein Rev
G1: Protein Rev
H1: Protein Rev
I1: Protein Rev
J1: Protein Rev
K1: Protein Rev
L1: Protein Rev
M1: Protein Rev
N1: Protein Rev
O1: Protein Rev
P1: Protein Rev
R1: Protein Rev
S1: Protein Rev
T1: Protein Rev
U1: Protein Rev
V1: Protein Rev
W1: Protein Rev
X1: Protein Rev
Y1: Protein Rev
c2: Protein Rev
d2: Protein Rev
e2: Protein Rev
f2: Protein Rev
g2: Protein Rev
h2: Protein Rev
v2: Protein Rev
w2: Protein Rev
x2: Protein Rev
y2: Protein Rev
a3: Protein Rev
b3: Protein Rev
i3: Protein Rev
j3: Protein Rev
k3: Protein Rev
l3: Protein Rev
m3: Protein Rev
n3: Protein Rev
o3: Protein Rev
p3: Protein Rev
r3: Protein Rev
s3: Protein Rev
t3: Protein Rev
u3: Protein Rev
A4: Protein Rev
B4: Protein Rev
I4: Protein Rev
J4: Protein Rev
K4: Protein Rev
L4: Protein Rev
M4: Protein Rev
N4: Protein Rev
O4: Protein Rev
R4: Protein Rev
S4: Protein Rev
T4: Protein Rev
U4: Protein Rev
A5: Protein Rev
B5: Protein Rev
C5: Protein Rev
D5: Protein Rev
E5: Protein Rev
F5: Protein Rev
G5: Protein Rev
H5: Protein Rev
M5: Protein Rev
N5: Protein Rev
O5: Protein Rev
P5: Protein Rev
T5: Protein Rev
U5: Protein Rev
V5: Protein Rev
W5: Protein Rev
X5: Protein Rev
Y5: Protein Rev
C6: Protein Rev
D6: Protein Rev
E6: Protein Rev
F6: Protein Rev
G6: Protein Rev
H6: Protein Rev
V6: Protein Rev
W6: Protein Rev
X6: Protein Rev
Y6: Protein Rev
a7: Protein Rev
b7: Protein Rev
c7: Protein Rev
d7: Protein Rev
e7: Protein Rev
f7: Protein Rev
g7: Protein Rev
h7: Protein Rev
i7: Protein Rev
j7: Protein Rev
k7: Protein Rev
l7: Protein Rev
m7: Protein Rev
n7: Protein Rev
o7: Protein Rev
p7: Protein Rev
r7: Protein Rev
s7: Protein Rev
t7: Protein Rev
u7: Protein Rev
v7: Protein Rev
w7: Protein Rev
x7: Protein Rev
y7: Protein Rev
a8: Protein Rev
b8: Protein Rev
c8: Protein Rev
d8: Protein Rev
e8: Protein Rev
f8: Protein Rev
g8: Protein Rev
h8: Protein Rev
m8: Protein Rev
n8: Protein Rev
o8: Protein Rev
p8: Protein Rev
t8: Protein Rev
u8: Protein Rev
v8: Protein Rev
w8: Protein Rev
x8: Protein Rev
y8: Protein Rev
A9: Protein Rev
B9: Protein Rev
C9: Protein Rev
D9: Protein Rev
E9: Protein Rev
F9: Protein Rev
G9: Protein Rev
H9: Protein Rev
I9: Protein Rev
J9: Protein Rev
K9: Protein Rev
L9: Protein Rev
M9: Protein Rev
N9: Protein Rev
O9: Protein Rev
P9: Protein Rev
R9: Protein Rev
S9: Protein Rev
T9: Protein Rev
U9: Protein Rev
V9: Protein Rev
W9: Protein Rev
X9: Protein Rev
Y9: Protein Rev


Theoretical massNumber of molelcules
Total (without water)2,037,143155
Polymers2,037,143155
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 ...
Protein Rev / ART/TRS / Anti-repression transactivator / Regulator of expression of viral proteins


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: 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: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Rev Filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3090 nm / Nominal defocus min: 990 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1Bsoftparticle selection
13Bsoft3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 22 ° / Axial rise/subunit: 21 Å / Axial symmetry: C6
3D reconstructionResolution: 8.3 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 300 / Symmetry type: HELICAL

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