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- PDB-7u0f: HIV-1 Rev in complex with tubulin -

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Basic information

Entry
Database: PDB / ID: 7u0f
TitleHIV-1 Rev in complex with tubulin
Components
  • Protein Rev
  • Tubulin alpha-1A chain
  • Tubulin beta chain
KeywordsVIRAL PROTEIN / Rev / tubulin / HIV-1
Function / homology
Function and homology information


host cell nucleolus / motile cilium / viral process / mRNA transport / protein export from nucleus / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...host cell nucleolus / motile cilium / viral process / mRNA transport / protein export from nucleus / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / host cell cytoplasm / hydrolase activity / DNA-binding transcription factor activity / GTPase activity / GTP binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin ...Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tubulin alpha-1A chain / Tubulin beta chain / Protein Rev
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 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)Intramural United States
CitationJournal: Structure / Year: 2023
Title: Structural basis of microtubule depolymerization by the kinesin-like activity of HIV-1 Rev.
Authors: Elif Eren / Norman R Watts / Davide Randazzo / Ira Palmer / Dan L Sackett / Paul T Wingfield /
Abstract: HIV-1 Rev is an essential regulatory protein that transports unspliced and partially spliced viral mRNAs from the nucleus to the cytoplasm for the expression of viral structural proteins. During its ...HIV-1 Rev is an essential regulatory protein that transports unspliced and partially spliced viral mRNAs from the nucleus to the cytoplasm for the expression of viral structural proteins. During its nucleocytoplasmic shuttling, Rev interacts with several host proteins to use the cellular machinery for the advantage of the virus. Here, we report the 3.5 Å cryo-EM structure of a 4.8 MDa Rev-tubulin ring complex. Our structure shows that Rev's arginine-rich motif (ARM) binds to both the acidic surfaces and the C-terminal tails of α/β-tubulin. The Rev-tubulin interaction is functionally homologous to that of kinesin-13, potently destabilizing microtubules at sub-stoichiometric levels. Expression of Rev in astrocytes and HeLa cells shows that it can modulate the microtubule cytoskeleton within the cellular environment. These results show a previously undefined regulatory role of Rev.
History
DepositionFeb 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tubulin alpha-1A chain
B: Tubulin beta chain
C: Tubulin alpha-1A chain
D: Tubulin beta chain
E: Protein Rev
F: Protein Rev
G: Protein Rev
H: Protein Rev
I: Protein Rev
J: Protein Rev


Theoretical massNumber of molelcules
Total (without water)278,39210
Polymers278,39210
Non-polymers00
Water00
1
A: Tubulin alpha-1A chain
B: Tubulin beta chain
C: Tubulin alpha-1A chain
D: Tubulin beta chain
E: Protein Rev
F: Protein Rev
G: Protein Rev
H: Protein Rev
I: Protein Rev
J: Protein Rev
x 15


Theoretical massNumber of molelcules
Total (without water)4,175,883150
Polymers4,175,883150
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation14
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C15 (15 fold cyclic))

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Components

#1: Protein Tubulin alpha-1A chain / Alpha-tubulin 1 / Tubulin alpha-1 chain


Mass: 50121.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02550
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#3: Protein
Protein Rev / ART/TRS / Anti-repression transactivator / Regulator of expression of viral proteins


Mass: 13055.686 Da / Num. of mol.: 6
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: P04616

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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: HIV-1 Rev in complex with tubulin / Type: COMPLEX / Details: Rev-tubulin ring-like complex with C15 symmetry / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 4.6 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Human immunodeficiency virus 1Human immunodeficiency virus 111676
21Sus scrofa (pig)9823
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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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 / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 73 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
7PHENIXmodel fitting
12cisTEM3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 91719
SymmetryPoint symmetry: C15 (15 fold cyclic)
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34534 / Symmetry type: POINT
Atomic model buildingB value: 123 / Protocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416929
ELECTRON MICROSCOPYf_angle_d0.88422919
ELECTRON MICROSCOPYf_dihedral_angle_d6.7092315
ELECTRON MICROSCOPYf_chiral_restr0.0542471
ELECTRON MICROSCOPYf_plane_restr0.0073036

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