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- PDB-6cf2: Crystal structure of HIV-1 Rev (residues 1-93)-RNA aptamer complex -

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Basic information

Entry
Database: PDB / ID: 6cf2
TitleCrystal structure of HIV-1 Rev (residues 1-93)-RNA aptamer complex
Components
  • Anti-Rev Antibody, heavy chain
  • Anti-Rev Antibody, light chain
  • Protein Rev
  • RNA (35-MER)
KeywordsRNA BINDING PROTEIN/RNA / HIV-1 / Rev / RNA aptamer / RNA BINDING PROTEIN-RNA complex
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
Helix Hairpins - #630 / Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein Rev / Protein Rev
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsEren, E. / Dearborn, A.D. / Wingfield, P.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)Intramural Research Program United States
CitationJournal: Structure / Year: 2018
Title: Structure of an RNA Aptamer that Can Inhibit HIV-1 by Blocking Rev-Cognate RNA (RRE) Binding and Rev-Rev Association.
Authors: Dearborn, A.D. / Eren, E. / Watts, N.R. / Palmer, I.W. / Kaufman, J.D. / Steven, A.C. / Wingfield, P.T.
History
DepositionFeb 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-Rev Antibody, heavy chain
B: Anti-Rev Antibody, light chain
F: Protein Rev
G: RNA (35-MER)


Theoretical massNumber of molelcules
Total (without water)47,0884
Polymers47,0884
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-29 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.190, 97.680, 87.836
Angle α, β, γ (deg.)90.00, 109.70, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Antibody Anti-Rev Antibody, heavy chain


Mass: 13408.822 Da / Num. of mol.: 1 / Fragment: Fab single-chain variable fragment
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, light chain


Mass: 11656.958 Da / Num. of mol.: 1 / Fragment: Fab single-chain variable fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli)
#3: Protein Protein Rev / ART/TRS / Anti-repression transactivator / Regulator of expression of viral proteins


Mass: 10746.137 Da / Num. of mol.: 1 / Fragment: UNP residues 1-93
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
#4: RNA chain RNA (35-MER)


Mass: 11275.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2% v/v 1,4-dioxane, 0.1 M Tris, pH 8.0, 15% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→38 Å / Num. obs: 10201 / % possible obs: 99.2 % / Redundancy: 2 % / CC1/2: 0.975 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.088 / Rrim(I) all: 0.124 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.424 / Rpim(I) all: 0.634 / Rrim(I) all: 0.897 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5DHV & 1ULL

5dhv

1ull


Resolution: 3→38 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.241 1091 10 %
Rwork0.2081 --
obs-9172 99.2 %
Refinement stepCycle: LAST / Resolution: 3→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 749 0 0 2934
LS refinement shellResolution: 3→3.158 Å
RfactorNum. reflection
Rfree0.3212 -
Rwork0.2882 -
obs-1287

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