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

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Basic information

Entry
Database: PDB / ID: 5dhv
TitleHIV-1 Rev NTD dimers with variable crossing angles
Components
  • (Anti-Rev Antibody Fab single-chain variable fragment, heavy ...) x 2
  • Anti-Rev Antibody Fab single-chain variable fragment, light chain
  • Protein Rev
KeywordsIMMUNE 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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
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 1.2Aug 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 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 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
A: Anti-Rev Antibody Fab single-chain variable fragment, heavy chain
B: Anti-Rev Antibody Fab single-chain variable fragment, light chain
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
N: Protein Rev
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8758
Polymers64,8046
Non-polymers712
Water3,153175
1
A: Anti-Rev Antibody Fab single-chain variable fragment, heavy chain
B: Anti-Rev Antibody Fab single-chain variable fragment, light chain
N: Protein Rev
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8524
Polymers32,8173
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-31 kcal/mol
Surface area14490 Å2
MethodPISA
2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0234
Polymers31,9883
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-29 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.895, 81.869, 98.809
Angle α, β, γ (deg.)90.00, 101.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules MN

#4: Protein Protein Rev


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 Anti-Rev Antibody Fab single-chain variable fragment, heavy chain


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)
#2: Antibody Anti-Rev Antibody Fab single-chain variable fragment, light chain


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 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)

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Non-polymers , 2 types, 177 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.25 %
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: I24 / Wavelength: 0.9779 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: 0.9779 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.3→2.4 Å / Redundancy: 5 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
HKL-2000data scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X7L

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1542 5.04 %RANDOM
Rwork0.1878 ---
obs0.1897 30568 100 %-
Displacement parametersBiso mean: 60.47 Å2
Baniso -1Baniso -2Baniso -3
1--7.7264 Å20 Å24.4338 Å2
2--4.0491 Å20 Å2
3---3.6773 Å2
Refine analyzeLuzzati coordinate error obs: 0.353 Å
Refinement stepCycle: 1 / Resolution: 2.3→20.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4474 0 2 175 4651
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014588HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.156244HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1518SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes677HARMONIC5
X-RAY DIFFRACTIONt_it4588HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion19.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion608SEMIHARMONIC5
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_contact5005SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2793 122 4.12 %
Rwork0.225 2842 -
all0.2271 2964 -
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)
13.58520.2511-1.89413.6224-2.80215.23780.0791-0.04790.33280.8175-0.569-0.5907-0.66710.45330.490.1776-0.0941-0.2719-0.4645-0.0675-0.265326.929534.59719.999
20.4381-0.17620.61356.17393.15823.4160.159-0.1160.0170.4855-0.27940.09920.5581-0.06770.1204-0.0025-0.036-0.1388-0.5211-0.0026-0.473420.95569.99178.3
31.50340.61431.19244.99140.84853.6529-0.1006-0.0870.3265-0.9216-0.38081.4724-0.3575-0.71430.48150.10560.1184-0.4459-0.4399-0.1971-0.07459.1524.9418-1.4405
41.0579-0.70131.07735.1221-0.36433.5530.04420.3306-0.1247-0.65940.04110.0170.18880.2157-0.0853-0.2013-0.0317-0.1331-0.4552-0.0238-0.4513.2259-4.343741.1392
51.5233-0.17431.15255.2486-0.30352.4407-0.05260.01150.0586-0.08480.09830.7919-0.0954-0.2565-0.0456-0.3374-0.0161-0.0795-0.46630.0483-0.34710.719211.301148.0696
63.57161.7141.96188.57262.21614.7025-0.1049-0.14220.07921.16630.4856-1.00060.02610.6013-0.38070.03830.051-0.2626-0.3545-0.0667-0.307120.2874-0.677466.6413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ N|8 - N|65 }
2X-RAY DIFFRACTION2{ A|1 - A|123 }
3X-RAY DIFFRACTION3{ B|1 - B|110 }
4X-RAY DIFFRACTION4{ H|1 - H|115 }
5X-RAY DIFFRACTION5{ L|1 - L|110 }
6X-RAY DIFFRACTION6{ M|5 - M|65 }

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