+Open data
-Basic information
Entry | Database: PDB / ID: 5dhv | ||||||||||||
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Title | HIV-1 Rev NTD dimers with variable crossing angles | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV / helical hairpin / RNA-binding / nuclear export | ||||||||||||
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 | ||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) Human immunodeficiency virus 1 | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | DiMattia, M.A. / Watts, N.R. / Wingfield, P.T. / Grimes, J.M. / Stuart, D.I. / Steven, A.C. | ||||||||||||
Funding support | United States, United Kingdom, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dhv.cif.gz | 238.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dhv.ent.gz | 200.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dhv_validation.pdf.gz | 464.4 KB | Display | wwPDB validaton report |
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Full document | 5dhv_full_validation.pdf.gz | 467.9 KB | Display | |
Data in XML | 5dhv_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 5dhv_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/5dhv ftp://data.pdbj.org/pub/pdb/validation_reports/dh/5dhv | HTTPS FTP |
-Related structure data
Related structure data | 6439C 5dhxC 5dhyC 5dhzC 3x7lS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules MN
#4: Protein | Mass: 7750.793 Da / Num. of mol.: 2 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 |
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-Antibody , 3 types, 4 molecules ABLH
#1: Antibody | Mass: 13408.822 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) | ||
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#2: Antibody | Mass: 11656.958 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli) #3: Antibody | | 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) |
-Non-polymers , 2 types, 177 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.25 % |
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Crystal grow | Temperature: 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. |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9779 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.5 Å / Num. obs: 30611 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 49.88 Å2 / Rsym value: 0.103 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 5 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3X7L Resolution: 2.3→20.28 Å / Cor.coef. Fo:Fc: 0.9453 / Cor.coef. Fo:Fc free: 0.9195 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 60.47 Å2
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Refine analyze | Luzzati coordinate error obs: 0.353 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→20.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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