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- PDB-1t6o: Nucleocapsid-binding domain of the measles virus P protein (amino... -

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Basic information

Entry
Database: PDB / ID: 1t6o
TitleNucleocapsid-binding domain of the measles virus P protein (amino acids 457-507) in complex with amino acids 486-505 of the measles virus N protein
Components
  • (phosphoprotein) x 2
  • linker
KeywordsVIRAL PROTEIN / four helix bundle
Function / homology
Function and homology information


helical viral capsid / viral genome replication / viral nucleocapsid / molecular adaptor activity / host cell cytoplasm / ribonucleoprotein complex / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / Phosphoprotein / Nucleoprotein
Similarity search - Component
Biological speciesMeasles virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKingston, R.L. / Hamel, D.J. / Gay, L.S. / Dahlquist, F.W. / Matthews, B.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural basis for the attachment of a paramyxoviral polymerase to its template.
Authors: Kingston, R.L. / Hamel, D.J. / Gay, L.S. / Dahlquist, F.W. / Matthews, B.W.
#1: Journal: To be Published
Title: Characterization of nucleocapsid binding by the measles and the mumps virus phosphoprotein
Authors: Kingston, R.L. / Baase, W.A. / Gay, L.S.
History
DepositionMay 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Structure of a chimeric molecule encompassing amino acids 457-507 of measles P and 486-505 ...SEQUENCE Structure of a chimeric molecule encompassing amino acids 457-507 of measles P and 486-505 of measles N. They are connected by a flexible 8 amino acid linker (GS)4, which is largely disordered in the crystal structure. The asymmetric unit of the crystal contains the P moiety from one molecule (chain A) bound to the N moiety of a different molecule (Chain B). Link record between chain A and L is not provided since the part of the chain L which is linked to chain A is missing from the coordinates due to lack of electron density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phosphoprotein
L: linker
B: phosphoprotein


Theoretical massNumber of molelcules
Total (without water)8,6483
Polymers8,6483
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.226, 42.226, 81.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein phosphoprotein


Mass: 5891.055 Da / Num. of mol.: 1 / Fragment: residues 457-507 / Mutation: P458G
Source method: isolated from a genetically manipulated source
Details: Chimeric molecule encompassing amino acids 457-507 of measles P (chain A) and 486-505 of measles N (chain B). They are connected by a flexible 8 amino acid linker (GS)4 (chain L)
Source: (gene. exp.) Measles virus / Genus: Morbillivirus / Strain: Moraten vaccine strain / Gene: P/V / Plasmid: pET41a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star(DE3) / References: GenBank: 9181875, UniProt: Q77M42*PLUS
#2: Protein/peptide linker


Mass: 594.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic linker
#3: Protein/peptide phosphoprotein


Mass: 2162.453 Da / Num. of mol.: 1 / Fragment: residues 486-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus / Genus: Morbillivirus / Strain: Moraten vaccine strain / Gene: N / Plasmid: pET41a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star(DE3) / References: GenBank: 9181874, UniProt: Q77M43*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 9.1
Details: 0.2M AMPSO/KOH buffer, 0.5 - 1.0 M Ammonium sulfate, pH 9.1, VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 4, 2004
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 5306 / Num. obs: 5306 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.03 Å / % possible all: 96.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OKS.pdb

1oks


Resolution: 2→25 Å / Isotropic thermal model: Individual Isotropic B / Cross valid method: test set omitted from all refinement / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 307 -RANDOM
Rwork0.23 ---
all0.232 5306 --
obs0.232 5306 97.5 %-
Solvent computationSolvent model: Moews & Kretsinger / Bsol: 300 Å2 / ksol: 0.85 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.884 Å20 Å20 Å2
2---2.884 Å20 Å2
3---5.768 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms548 0 0 28 576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.004827
X-RAY DIFFRACTIONt_angle_deg0.84607
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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