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- PDB-6g0y: X-ray structure of M-21 protein complex -

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Basic information

Entry
Database: PDB / ID: 6g0y
TitleX-ray structure of M-21 protein complex
Components
  • Matrix M2-1
  • Phosphoprotein
KeywordsVIRAL PROTEIN / HRSV / antitermination / transcription / replication
Function / homology
Function and homology information


: / regulation of viral transcription / viral transcription / viral life cycle / transcription antitermination / virion component / : / host cell cytoplasm / RNA-dependent RNA polymerase activity / host cell nucleus ...: / regulation of viral transcription / viral transcription / viral life cycle / transcription antitermination / virion component / : / host cell cytoplasm / RNA-dependent RNA polymerase activity / host cell nucleus / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Pneumovirus matrix protein 2 (M2), zinc-binding domain / Pneumovirus matrix 2-1 / Pneumovirus matrix protein 2 (M2) / Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Pneumovirus matrix protein 2 (M2), zinc-binding domain / Pneumovirus matrix 2-1 / Pneumovirus matrix protein 2 (M2) / Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphoprotein / Protein M2-1
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsEdwards, T.A. / Barr, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)RG-IMCB-100571 United Kingdom
CitationJournal: Mbio / Year: 2018
Title: The Structure of the Human Respiratory Syncytial Virus M2-1 Protein Bound to the Interaction Domain of the Phosphoprotein P Defines the Orientation of the Complex.
Authors: Selvaraj, M. / Yegambaram, K. / Todd, E.J.A.A. / Richard, C.A. / Dods, R.L. / Pangratiou, G.M. / Trinh, C.H. / Moul, S.L. / Murphy, J.C. / Mankouri, J. / Eleouet, J.F. / Barr, J.N. / Edwards, T.A.
History
DepositionMar 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Matrix M2-1
A: Matrix M2-1
C: Matrix M2-1
E: Matrix M2-1
H: Phosphoprotein
G: Phosphoprotein
J: Phosphoprotein
I: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,80912
Polymers98,5488
Non-polymers2624
Water4,125229
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Gel filtration and crystal structure of M2-1 showed that it forms a tight homotetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19270 Å2
ΔGint-94 kcal/mol
Surface area34660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.555, 116.524, 72.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Matrix M2-1 / Envelope-associated 22 kDa protein


Mass: 22190.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Gene: M2-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04545
#2: Protein/peptide
Phosphoprotein / / Protein P


Mass: 2446.617 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Human respiratory syncytial virus A (strain A2)
References: UniProt: P03421
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: The crystals are small rods.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: The crystallisation plate was incluabed in 20 degree celcius for crystal growth. The reservoir had 500 micro litre of 20% PEG-MME 2000, 0.1M TRis (pH 8.5), 0.2M trimethylamine N-oxide. The ...Details: The crystallisation plate was incluabed in 20 degree celcius for crystal growth. The reservoir had 500 micro litre of 20% PEG-MME 2000, 0.1M TRis (pH 8.5), 0.2M trimethylamine N-oxide. The 2microlitre protein-peptide sample was mixed with 1ul of reservoir solution and placed in the cover slip for hanging drop set up

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.42→74.35 Å / Num. obs: 32012 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 45.2 Å2 / CC1/2: 0.9 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.06 / Rrim(I) all: 0.16 / Net I/av σ(I): 2.2 / Net I/σ(I): 9.5
Reflection shellResolution: 2.42→2.48 Å / Redundancy: 13 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2309 / CC1/2: 0.5 / Rpim(I) all: 0.39 / Rrim(I) all: 1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→74.35 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.457 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28035 1498 4.8 %RANDOM
Rwork0.21986 ---
obs0.22282 29906 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.935 Å2
Baniso -1Baniso -2Baniso -3
1--3.51 Å20 Å20 Å2
2--0.96 Å20 Å2
3---2.56 Å2
Refinement stepCycle: 1 / Resolution: 2.42→74.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 4 229 6023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195875
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9637898
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5455703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.6724.259270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.847151157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8661540
X-RAY DIFFRACTIONr_chiral_restr0.1240.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214253
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4645.5972845
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.9198.3753537
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5955.8793029
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.81675.5868855
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: 2.419→2.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 105 -
Rwork0.411 2080 -
obs--94.84 %

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