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- PDB-7yny: Crystal structure of baculovirus LEF-3 from Helicoverpa armigera ... -

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Basic information

Entry
Database: PDB / ID: 7yny
TitleCrystal structure of baculovirus LEF-3 from Helicoverpa armigera nucleopolyhedrovirus
ComponentsLef3
KeywordsDNA BINDING PROTEIN / ssDNA / SSB / Baculovirus / Replication
Function / homologyNucleopolyhedrovirus late expression factor 3 / Nucleopolyhedrovirus late expression factor 3 (LEF-3) / regulation of DNA-templated transcription / DNA binding / Lef3
Function and homology information
Biological speciesHelicoverpa armigera nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsYin, J. / Li, Z. / Cao, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507200 China
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Structural transitions during the cooperative assembly of baculovirus single-stranded DNA-binding protein on ssDNA.
Authors: Jiayi Yin / Yan Fu / Guibo Rao / Zhiqiang Li / Kexing Tian / Tingting Chong / Kai Kuang / Manli Wang / Zhihong Hu / Sheng Cao /
Abstract: Single-stranded DNA-binding proteins (SSBs) interact with single-stranded DNA (ssDNA) to form filamentous structures with various degrees of cooperativity, as a result of intermolecular interactions ...Single-stranded DNA-binding proteins (SSBs) interact with single-stranded DNA (ssDNA) to form filamentous structures with various degrees of cooperativity, as a result of intermolecular interactions between neighboring SSB subunits on ssDNA. However, it is still challenging to perform structural studies on SSB-ssDNA filaments at high resolution using the most studied SSB models, largely due to the intrinsic flexibility of these nucleoprotein complexes. In this study, HaLEF-3, an SSB protein from Helicoverpa armigera nucleopolyhedrovirus, was used for in vitro assembly of SSB-ssDNA filaments, which were structurally studied at atomic resolution using cryo-electron microscopy. Combined with the crystal structure of ssDNA-free HaLEF-3 octamers, our results revealed that the three-dimensional rearrangement of HaLEF-3 induced by an internal hinge-bending movement is essential for the formation of helical SSB-ssDNA complexes, while the contacting interface between adjacent HaLEF-3 subunits remains basically intact. We proposed a local cooperative SSB-ssDNA binding model, in which, triggered by exposure to oligonucleotides, HaLEF-3 molecules undergo ring-to-helix transition to initiate continuous SSB-SSB interactions along ssDNA. Unique structural features revealed by the assembly of HaLEF-3 on ssDNA suggest that HaLEF-3 may represent a new class of SSB.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lef3
B: Lef3
C: Lef3
D: Lef3
E: Lef3
F: Lef3
G: Lef3
H: Lef3


Theoretical massNumber of molelcules
Total (without water)381,1028
Polymers381,1028
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34700 Å2
ΔGint-123 kcal/mol
Surface area110270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.059, 117.738, 128.473
Angle α, β, γ (deg.)90.000, 108.119, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Lef3


Mass: 47637.707 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicoverpa armigera nucleopolyhedrovirus
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q91BW6

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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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1,200 mM sodium phosphate monobasic, 800 mM potassium phosphate dibasic, 100 mM CAPS/NaOH, pH 10.5, 200 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.51→48.52 Å / Num. obs: 44026 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 133.56 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.28
Reflection shellResolution: 3.51→3.64 Å / Rmerge(I) obs: 0.737 / Num. unique obs: 4203

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASERphasing
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: our cryoEM model

Resolution: 3.51→48.52 Å / SU ML: 0.5849 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.5101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2872 2201 5 %
Rwork0.236 41808 -
obs0.2386 44009 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 137.21 Å2
Refinement stepCycle: LAST / Resolution: 3.51→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21644 0 0 0 21644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002921989
X-RAY DIFFRACTIONf_angle_d0.67429661
X-RAY DIFFRACTIONf_chiral_restr0.04813355
X-RAY DIFFRACTIONf_plane_restr0.00273789
X-RAY DIFFRACTIONf_dihedral_angle_d8.3742897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.51-3.590.45081270.40532403X-RAY DIFFRACTION91.83
3.59-3.670.41911380.36252635X-RAY DIFFRACTION99.75
3.67-3.770.35871370.34912589X-RAY DIFFRACTION99.71
3.77-3.870.35071380.3112624X-RAY DIFFRACTION99.71
3.87-3.980.361370.3062608X-RAY DIFFRACTION99.78
3.98-4.110.35721360.30132599X-RAY DIFFRACTION99.74
4.11-4.260.33841380.29652623X-RAY DIFFRACTION99.89
4.26-4.430.3341390.25692635X-RAY DIFFRACTION99.57
4.43-4.630.2941370.23352610X-RAY DIFFRACTION99.82
4.63-4.870.26251370.21662603X-RAY DIFFRACTION99.75
4.87-5.180.29421380.22822616X-RAY DIFFRACTION99.75
5.18-5.580.27291390.22752635X-RAY DIFFRACTION99.78
5.58-6.140.30121390.2592640X-RAY DIFFRACTION99.89
6.14-7.020.3331390.24882636X-RAY DIFFRACTION99.78
7.02-8.840.24571390.21062654X-RAY DIFFRACTION99.71
8.84-48.520.20581430.15912698X-RAY DIFFRACTION99.09

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