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- PDB-5dhz: HIV-1 Rev NTD dimers with variable crossing angles -

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Basic information

Entry
Database: PDB / ID: 5dhz
TitleHIV-1 Rev NTD dimers with variable crossing angles
Components
  • Anti-Rev Antibody Fab single-chain variable fragment, heavy chain
  • Anti-Rev Antibody Fab single-chain variable fragment, light chain
  • Protein Rev
KeywordsIMMUNE SYSTEM / HIV / helical hairpin / nuclear export / RNA-binding
Function / homology
Function and homology information


host cell nucleolus / mRNA transport / viral process / protein export from nucleus / host cell cytoplasm / DNA-binding transcription factor activity / RNA binding
Similarity search - Function
Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein)
Similarity search - Domain/homology
Protein Rev / Protein Rev
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsDiMattia, M.A. / Watts, N.R. / Wingfield, P.T. / Grimes, J.M. / Stuart, D.I. / Steven, A.C.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
National Institutes of Health United States
SPINE2COMPLEXESLSHGST-2006-031220 United Kingdom
Medical Research Council (United Kingdom)G100099 United Kingdom
CitationJournal: Structure / Year: 2016
Title: The Structure of HIV-1 Rev Filaments Suggests a Bilateral Model for Rev-RRE Assembly.
Authors: Michael A DiMattia / Norman R Watts / Naiqian Cheng / Rick Huang / J Bernard Heymann / Jonathan M Grimes / Paul T Wingfield / David I Stuart / Alasdair C Steven /
Abstract: HIV-1 Rev protein mediates the nuclear export of viral RNA genomes. To do so, Rev oligomerizes cooperatively onto an RNA motif, the Rev response element (RRE), forming a complex that engages with the ...HIV-1 Rev protein mediates the nuclear export of viral RNA genomes. To do so, Rev oligomerizes cooperatively onto an RNA motif, the Rev response element (RRE), forming a complex that engages with the host nuclear export machinery. To better understand Rev oligomerization, we determined four crystal structures of Rev N-terminal domain dimers, which show that they can pivot about their dyad axis, giving crossing angles of 90° to 140°. In parallel, we performed cryoelectron microscopy of helical Rev filaments. Filaments vary from 11 to 15 nm in width, reflecting variations in dimer crossing angle. These structures contain additional density, indicating that C-terminal domains become partially ordered in the context of filaments. This conformational variability may be exploited in the assembly of RRE/Rev complexes. Our data also revealed a third interface between Revs, which offers an explanation for how the arrangement of Rev subunits adapts to the "A"-shaped architecture of the RRE in export-active complexes.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jun 14, 2017Group: Refinement description / Category: refine
Item: _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Anti-Rev Antibody Fab single-chain variable fragment, heavy chain
L: Anti-Rev Antibody Fab single-chain variable fragment, light chain
M: Protein Rev


Theoretical massNumber of molelcules
Total (without water)31,9883
Polymers31,9883
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-17 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.540, 48.540, 264.482
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Antibody Anti-Rev Antibody Fab single-chain variable fragment, heavy chain


Mass: 12579.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli)
#2: Antibody Anti-Rev Antibody Fab single-chain variable fragment, light chain


Mass: 11656.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli)
#3: Protein Protein Rev


Mass: 7750.793 Da / Num. of mol.: 1
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, UniProt: P04616*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5
PH range: 6.5 - 8.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. obs: 2588 / % possible obs: 98.3 % / Redundancy: 3.1 % / Net I/σ(I): 20.4
Reflection shellResolution: 4.3→4.4 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.3→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.324 --
Rwork0.328 --
obs-2588 100 %
Refinement stepCycle: LAST / Resolution: 4.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 0 0 2151

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