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

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Basic information

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


protein localization to nucleoplasm / host cell nucleolus / mRNA transport / protein export from nucleus / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein Rev / Protein Rev
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 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
Medical Research Council (United Kingdom)G100099 United Kingdom
SPINE2COMPLEXESLSHGST-2006-031220 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 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Other
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,4144
Polymers68,4144
Non-polymers00
Water0
1
B: Anti-Rev Antibody Fab single-chain variable fragment, light chain,Anti-Rev Antibody Fab single-chain variable fragment, heavy chain
C: Protein Rev


Theoretical massNumber of molelcules
Total (without water)34,2072
Polymers34,2072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-3 kcal/mol
Surface area13930 Å2
MethodPISA
2
L: Anti-Rev Antibody Fab single-chain variable fragment, light chain,Anti-Rev Antibody Fab single-chain variable fragment, heavy chain
M: Protein Rev


Theoretical massNumber of molelcules
Total (without water)34,2072
Polymers34,2072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-4 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.528, 87.101, 166.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26456.133 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)
#2: Protein Protein Rev / ART/TRS / Anti-repression transactivator / Regulator of expression of viral proteins


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: P69718, UniProt: P04616*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.68 %
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

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 14917 / % possible obs: 99.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 80.69 Å2 / Net I/σ(I): 10.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.1 / % possible all: 99.2

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Processing

SoftwareName: BUSTER / Version: 2.9.2 / Classification: refinement
RefinementResolution: 2.9→46.84 Å / Cor.coef. Fo:Fc: 0.8839 / Cor.coef. Fo:Fc free: 0.8587 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 750 5.03 %RANDOM
Rwork0.2459 ---
obs0.2473 14917 100 %-
Displacement parametersBiso mean: 70.11 Å2
Baniso -1Baniso -2Baniso -3
1--7.9128 Å20 Å20 Å2
2--12.9291 Å20 Å2
3----5.0163 Å2
Refine analyzeLuzzati coordinate error obs: 0.507 Å
Refinement stepCycle: 1 / Resolution: 2.9→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4381 0 0 0 4381
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014492HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.216126HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1448SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes665HARMONIC5
X-RAY DIFFRACTIONt_it4492HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion21.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion606SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4873SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.1 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3155 146 5.51 %
Rwork0.2345 2503 -
all0.2388 2649 -
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)
100.0702-0.83941.1221-0.56315.8928-0.10780.03050.0168-0.08680.0143-0.0352-0.0342-0.1210.09350.0662-0.00580.0671-0.0405-0.0334-0.0566-30.9525-8.413610.4561
22.03141.24020.3324.35361.55491.6480.0317-0.1130.1644-0.18410.0275-0.3595-0.54420.4296-0.05910.304-0.1520.152-0.12310.0105-0.0876-17.44167.06513.9945
34.0468-1.61642.80933.7785-0.70093.3141-0.2545-0.22670.1138-0.54420.21770.10840.3416-0.34420.03680.2042-0.1520.0365-0.0638-0.0624-0.1657-34.3051-6.5325-14.6749
41.2870.0503-0.42664.78721.06631.06340.0465-0.01910.03770.0355-0.05780.1077-0.04990.00650.01120.0734-0.01110.03-0.1111-0.00160.00411.098-10.78437.9904
50.9515-0.4459-0.58834.2175-0.07381.3695-0.0006-0.14730.01380.4538-0.0740.5442-0.00890.00110.07450.0113-0.0580.1228-0.17490.02060.1407-11.5414-25.199746.8093
64.6071-2.91041.48494.7766-1.89133.15180.09830.0299-0.1105-0.5408-0.1404-0.16770.21740.32150.04210.13290.00890.0618-0.0774-0.0206-0.0985.7535-31.362925.3436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B|1 - B|110 }
2X-RAY DIFFRACTION2{ B|111 - B|231 }
3X-RAY DIFFRACTION3{ C|5 - C|65 }
4X-RAY DIFFRACTION4{ L|1 - L|110 }
5X-RAY DIFFRACTION5{ L|111 - L|227 }
6X-RAY DIFFRACTION6{ M|5 - M|65 }

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