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- PDB-5oiy: Structure of the HMPV P oligomerization domain at 2.2 A -

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Basic information

Entry
Database: PDB / ID: 5oiy
TitleStructure of the HMPV P oligomerization domain at 2.2 A
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / Phosphoprotein / P protein / Mononegavirales / Viral replication / Tetramerization
Function / homologyPhosphoprotein, pneumoviral / Pneumovirus phosphoprotein / RNA-dependent RNA polymerase activity / Phosphoprotein
Function and homology information
Biological speciesHuman metapneumovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsRenner, M. / Paesen, G.C. / Grison, C.M. / Granier, S. / Grimes, J.M. / Leyrat, C.
Funding support United Kingdom, France, 4items
OrganizationGrant numberCountry
Wellcome Trust204703/Z/16/Z United Kingdom
European UnionFP7/2007-2013 United Kingdom
Medical Research Council (United Kingdom)MR/L017709/1 United Kingdom
Labex EpiGenMedANR-10-LABX-12-01 France
CitationJournal: Sci Rep / Year: 2017
Title: Structural dissection of human metapneumovirus phosphoprotein using small angle x-ray scattering.
Authors: Renner, M. / Paesen, G.C. / Grison, C.M. / Granier, S. / Grimes, J.M. / Leyrat, C.
History
DepositionJul 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,0648
Polymers106,0648
Non-polymers00
Water1,20767
1
A: Phosphoprotein
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)53,0324
Polymers53,0324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-50 kcal/mol
Surface area6130 Å2
MethodPISA
2
E: Phosphoprotein
F: Phosphoprotein
G: Phosphoprotein
H: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)53,0324
Polymers53,0324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-48 kcal/mol
Surface area6150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.847, 45.437, 116.808
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: Protein
Phosphoprotein /


Mass: 13257.938 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta2 / References: UniProt: Q91KZ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 3350, 200 mM MgCl, and 100 mM Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→42.4 Å / Num. obs: 10774 / % possible obs: 98.71 % / Redundancy: 12.2 % / Biso Wilson estimate: 33.87 Å2 / Net I/σ(I): 11.89

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Processing

Software
NameClassification
PHENIXrefinement
xia2data reduction
Cootmodel building
PHASERphasing
RefinementResolution: 2.2→42.4 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2654 --
Rwork0.2479 --
obs-10636 98.71 %
Refinement stepCycle: LAST / Resolution: 2.2→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 0 67 1653

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