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- PDB-3lph: Crystal structure of the HIV-1 Rev dimer -

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Basic information

Entry
Database: PDB / ID: 3lph
TitleCrystal structure of the HIV-1 Rev dimer
ComponentsProtein Rev
KeywordsVIRAL PROTEIN / Helix-loop-helix / RNA-binding Arginine Rich Motif / protein oligomerization / AIDS / Host cytoplasm / Host nucleus / Host-virus interaction / mRNA transport / Phosphoprotein / RNA-binding / Transport
Function / homology
Function and homology information


protein localization to nucleoplasm / host cell nucleolus / mRNA transport / viral process / 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
BROMIDE ION / MALONATE ION / Protein Rev
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD; MOLECULAR REPLACEMENT / MAD / Resolution: 2.5 Å
AuthorsDaugherty, M.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis for cooperative RNA binding and export complex assembly by HIV Rev.
Authors: Daugherty, M.D. / Liu, B. / Frankel, A.D.
History
DepositionFeb 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Rev
B: Protein Rev
C: Protein Rev
D: Protein Rev
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,18921
Polymers33,7544
Non-polymers1,43517
Water1,06359
1
A: Protein Rev
B: Protein Rev
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,83213
Polymers16,8772
Non-polymers95611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-22 kcal/mol
Surface area8480 Å2
MethodPISA
2
C: Protein Rev
D: Protein Rev
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3568
Polymers16,8772
Non-polymers4796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-22 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.801, 115.801, 81.163
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11C-74-

BR

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Components

#1: Protein
Protein Rev / Regulator of expression of viral proteins / Anti-repression transactivator / ART/TRS


Mass: 8438.456 Da / Num. of mol.: 4
Fragment: Oligomerization and RNA-binding domains, residues 1-70
Mutation: L12S,L60R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: HXB3 / Gene: rev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 / References: UniProt: P69718
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris pH 8.0, 50 mM NaCl, 1.45-1.55 M (NH4)2SO4, 3% PEG1000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2009 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KOHZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 11594 / Num. obs: 11561 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 35.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.4 / % possible all: 99

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXversion 1.5-2phasing
RefinementMethod to determine structure: MAD; MOLECULAR REPLACEMENT
Starting model: An initial model was generated using MAD data sets. This lower resolution model was used for molecular replacement with the final native data set.

Resolution: 2.5→47.136 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.37 / Isotropic thermal model: Isotropic / σ(F): 0.11 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 540 4.9 %
Rwork0.2262 --
obs0.2279 11031 95.17 %
all-11594 -
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.076 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 62.965 Å2
Baniso -1Baniso -2Baniso -3
1--2.315 Å20 Å20 Å2
2---2.315 Å2-0 Å2
3---4.629 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 37 59 1964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041924
X-RAY DIFFRACTIONf_angle_d0.6772591
X-RAY DIFFRACTIONf_dihedral_angle_d16.175757
X-RAY DIFFRACTIONf_chiral_restr0.044267
X-RAY DIFFRACTIONf_plane_restr0.004343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.75160.30281290.272376X-RAY DIFFRACTION89
2.7516-3.14970.27841250.25232577X-RAY DIFFRACTION95
3.1497-3.9680.24341440.1882668X-RAY DIFFRACTION98
3.968-47.1440.24641420.22112870X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0461-0.19870.19240.6544-0.79561.1456-0.0637-0.11040.0975-0.02890.2456-0.2053-0.2164-0.1096-0.12510.184-0.04110.03660.358-0.09230.2261-16.960440.11461.9113
21.2552-0.28750.75921.8690.42271.1294-0.1172-0.12380.36470.22240.5105-0.3129-0.0192-0.0378-0.23440.3513-0.01160.0860.48010.12080.312-28.243535.22238.6079
31.6981-0.5740.511.5242-0.17641.00020.20250.3801-0.0409-0.1855-0.0370.2025-0.3766-0.0673-0.02810.4243-0.18420.07590.3076-0.08860.2885-36.435828.7934-10.0082
42.4293-1.6895-1.24113.31410.43232.2646-0.3188-0.3367-0.01890.45030.7117-0.19140.0082-0.1341-0.14520.4278-0.12370.01080.25510.01570.3331-43.563917.8464-2.2036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 9:70)
2X-RAY DIFFRACTION2(chain B and resid 9:63)
3X-RAY DIFFRACTION3(chain C and resid 8:65)
4X-RAY DIFFRACTION4(chain D and resid 8:64)

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