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- PDB-2vqp: Structure of the matrix protein from human Respiratory Syncytial Virus -

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Basic information

Entry
Database: PDB / ID: 2vqp
TitleStructure of the matrix protein from human Respiratory Syncytial Virus
ComponentsMATRIX PROTEIN
KeywordsVIRAL PROTEIN / VIRAL MATRIX PROTEIN / PERIPHERAL MEMBRANE PROTEIN / RSV / VIRION / MATRIX PROTEIN / ENVELOPE PROTEIN
Function / homology
Function and homology information


Translation of respiratory syncytial virus mRNAs / viral tegument / virion assembly / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / host cell cytoplasm / structural constituent of virion / viral envelope ...Translation of respiratory syncytial virus mRNAs / viral tegument / virion assembly / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / host cell cytoplasm / structural constituent of virion / viral envelope / host cell nucleus / host cell plasma membrane / membrane
Similarity search - Function
HRSV-S2 matrix protein, N-terminal domain / Pneumovirus matrix protein / Pneumovirus matrix, N-terminal / Pneumovirus matrix protein / Topoisomerase I; domain 3 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Matrix protein / Matrix protein
Similarity search - Component
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.6 Å
AuthorsMoney, V.A. / McPhee, H.K. / Sanderson, J.M. / Yeo, R.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Surface Features of a Mononegavirales Matrix Protein Indicate Sites of Membrane Interaction.
Authors: Money, V.A. / Mcphee, H.K. / Mosely, J.A. / Sanderson, J.M. / Yeo, R.P.
History
DepositionMar 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MATRIX PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,57113
Polymers28,8871
Non-polymers68312
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.299, 78.697, 66.018
Angle α, β, γ (deg.)90.00, 96.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MATRIX PROTEIN


Mass: 28887.496 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS / Strain: A2 / Plasmid: PETM254R / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (CODON PLUS) / References: UniProt: P03419, UniProt: P0DOE7*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET254 IN DATABASE ENTRY IS ARG254 IN THE PDB FILE DUE TO A MUTATION

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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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7
Details: MOTHER LIQUOR OF BETWEEN 45% AND 65% V/V TACSIMATE PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 7, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→65.65 Å / Num. obs: 35218 / % possible obs: 96.2 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.4
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.5 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 1.6→65.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.824 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1730 5 %RANDOM
Rwork0.18 ---
obs0.182 32606 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20.05 Å2
2--0.53 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→65.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 0 45 186 2222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222142
X-RAY DIFFRACTIONr_bond_other_d0.0060.021428
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9882910
X-RAY DIFFRACTIONr_angle_other_deg0.95733554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71125.31679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35315397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.439157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02377
X-RAY DIFFRACTIONr_nbd_refined0.2210.2370
X-RAY DIFFRACTIONr_nbd_other0.1920.21451
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21038
X-RAY DIFFRACTIONr_nbtor_other0.0870.21103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3441.51374
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76822183
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8363862
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0984.5714
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 147
Rwork0.261 2328

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