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- PDB-6vag: Crystal structure of the oligomerization domain of phosphoprotein... -

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Basic information

Entry
Database: PDB / ID: 6vag
TitleCrystal structure of the oligomerization domain of phosphoprotein from parainfluenza virus 5
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / Paramyxovirus / Phosphoprotein / Oligomerization domain
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / Phosphoprotein
Function and homology information
Biological speciesParainfluenza virus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAggarwal, M. / Abdella, R. / He, Y. / Lamb, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation.
Authors: Ryan Abdella / Megha Aggarwal / Takashi Okura / Robert A Lamb / Yuan He /
Abstract: Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a ...Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a template for the polymerase complex, composed of the large protein (L) and the homo-tetrameric phosphoprotein (P). The ∼250-kDa L possesses all enzymatic activities necessary for its function but requires P in vivo. Structural information is available for individual P domains from different paramyxoviruses, but how P interacts with L and how that affects the activity of L is largely unknown due to the lack of high-resolution structures of this complex in this viral family. In this study we determined the structure of the L-P complex from parainfluenza virus 5 (PIV5) at 4.3-Å resolution using cryoelectron microscopy, as well as the oligomerization domain (OD) of P at 1.4-Å resolution using X-ray crystallography. P-OD associates with the RNA-dependent RNA polymerase domain of L and protrudes away from it, while the X domain of one chain of P is bound near the L nucleotide entry site. The methyltransferase (MTase) domain and the C-terminal domain (CTD) of L adopt a unique conformation, positioning the MTase active site immediately above the poly-ribonucleotidyltransferase domain and near the likely exit site for the product RNA 5' end. Our study reveals a potential mechanism that mononegavirus polymerases may employ to switch between transcription and genome replication. This knowledge will assist in the design and development of antivirals against paramyxoviruses.
History
DepositionDec 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 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: Phosphoprotein
B: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5395
Polymers23,2632
Non-polymers2763
Water1,838102
1
A: Phosphoprotein
B: Phosphoprotein
hetero molecules

A: Phosphoprotein
B: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,07810
Polymers46,5254
Non-polymers5536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14640 Å2
ΔGint-143 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.893, 36.048, 140.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-437-

HOH

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Components

#1: Protein Phosphoprotein / Protein P


Mass: 11631.290 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parainfluenza virus 5 (strain W3) / Strain: W3 / Gene: P/V / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P11208
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.62 Å3/Da / Density % sol: 23.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MIB buffer (malonic acid, imidazone, boric acid), pH 6.0 and 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 28002 / % possible obs: 90.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.73 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 38.12
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.08 / Num. unique obs: 1239 / CC1/2: 0.774 / CC star: 0.934

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
PHASERphasing
AMPLEphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ideal helices

Resolution: 1.4→23.34 Å / SU ML: 0.1307 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.5125
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1797 1360 4.86 %
Rwork0.1546 26610 -
obs0.1559 27970 90.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.94 Å2
Refinement stepCycle: LAST / Resolution: 1.4→23.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 18 102 1224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491167
X-RAY DIFFRACTIONf_angle_d0.69251582
X-RAY DIFFRACTIONf_chiral_restr0.0498203
X-RAY DIFFRACTIONf_plane_restr0.0029205
X-RAY DIFFRACTIONf_dihedral_angle_d2.8396720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.24881150.19532297X-RAY DIFFRACTION79.71
1.45-1.510.22111340.15862329X-RAY DIFFRACTION80.99
1.51-1.580.18521310.14122367X-RAY DIFFRACTION82.72
1.58-1.660.18421270.12732462X-RAY DIFFRACTION85.02
1.66-1.760.16461090.12482577X-RAY DIFFRACTION89.12
1.76-1.90.16861260.12932721X-RAY DIFFRACTION92.62
1.9-2.090.15841400.13582831X-RAY DIFFRACTION97.41
2.09-2.390.16291560.12692923X-RAY DIFFRACTION99.42
2.39-3.020.16241580.15682992X-RAY DIFFRACTION99.78
3.02-23.340.19781640.18253111X-RAY DIFFRACTION98.97

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