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- PDB-5nkx: HRSV M2-1 core domain, P3221 crystal form -

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Basic information

Entry
Database: PDB / ID: 5nkx
TitleHRSV M2-1 core domain, P3221 crystal form
ComponentsM2-1
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


regulation of viral transcription / viral transcription / translation elongation factor activity / transcription antitermination / virion component / host cell cytoplasm / structural constituent of virion / host cell nucleus / 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) / 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
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00008687185 Å
AuthorsAlmeida Hernandez, Y. / Josts, I. / Molina, I.G. / de Pray-Gay, G. / Tidow, H.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structure and stability of the Human respiratory syncytial virus M RNA-binding core domain reveals a compact and cooperative folding unit.
Authors: Ivana G Molina / Inokentijs Josts / Yasser Almeida Hernandez / Sebastian Esperante / Mariano Salgueiro / Maria M Garcia Alai / Gonzalo de Prat-Gay / Henning Tidow /
Abstract: Human syncytial respiratory virus is a nonsegmented negative-strand RNA virus with serious implications for respiratory disease in infants, and has recently been reclassified into a new family, ...Human syncytial respiratory virus is a nonsegmented negative-strand RNA virus with serious implications for respiratory disease in infants, and has recently been reclassified into a new family, Pneumoviridae. One of the main reasons for this classification is the unique presence of a transcriptional antiterminator, called M. The puzzling mechanism of action of M, which is a rarity among antiterminators in viruses and is part of the RNA polymerase complex, relies on dissecting the structure and function of this multidomain tetramer. The RNA-binding activity is located in a monomeric globular `core' domain, a high-resolution crystal structure of which is now presented. The structure reveals a compact domain which is superimposable on the full-length M tetramer, with additional electron density for the C-terminal tail that was not observed in the previous models. Moreover, its folding stability was determined through chemical denaturation, which shows that the secondary and tertiary structure unfold concomitantly, which is indicative of a two-state equilibrium. These results constitute a further step in the understanding of this unique RNA-binding domain, for which there is no sequence or structural counterpart outside this virus family, in addition to its implications in transcription regulation and its likeliness as an antiviral target.
History
DepositionApr 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: M2-1
B: M2-1


Theoretical massNumber of molelcules
Total (without water)25,3612
Polymers25,3612
Non-polymers00
Water3,405189
1
A: M2-1


Theoretical massNumber of molelcules
Total (without water)12,6811
Polymers12,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: M2-1


Theoretical massNumber of molelcules
Total (without water)12,6811
Polymers12,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.949, 91.949, 97.799
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-289-

HOH

21B-291-

HOH

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Components

#1: Protein M2-1 / Matrix protein 2-1 / Transcription elongation factor M2-1


Mass: 12680.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Gene: M2-1, M2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4KRW3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 4.71 Å3/Da / Density % sol: 73.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4M SODIUM MALONATE

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.7→48.9 Å / Num. obs: 52178 / % possible obs: 97.6 % / Redundancy: 9.4 % / Biso Wilson estimate: 36.0833907196 Å2 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.073 / Net I/σ(I): 6.5
Reflection shellResolution: 1.7→8.97 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C3E

4c3e


Resolution: 2.00008687185→45.9745 Å / SU ML: 0.258524136178 / Cross valid method: FREE R-VALUE / σ(F): 1.34056912212 / Phase error: 24.0263873939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228983235859 1641 5.01282991202 %
Rwork0.189825351995 31095 -
obs0.191709571525 32736 99.9969453524 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.914782771 Å2
Refinement stepCycle: LAST / Resolution: 2.00008687185→45.9745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 0 189 1835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002748127766161683
X-RAY DIFFRACTIONf_angle_d0.5333230104362280
X-RAY DIFFRACTIONf_chiral_restr0.0384091766767290
X-RAY DIFFRACTIONf_plane_restr0.00261089408136286
X-RAY DIFFRACTIONf_dihedral_angle_d5.026576536041472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05890.3343387386531290.3602851329012541X-RAY DIFFRACTION100
2.0589-2.12540.3675754906821690.3279378354672524X-RAY DIFFRACTION100
2.1254-2.20140.3338819228481270.2925829855252560X-RAY DIFFRACTION100
2.2014-2.28950.2912627803241280.268512112162568X-RAY DIFFRACTION100
2.2895-2.39370.2774489640461600.2454597075282545X-RAY DIFFRACTION100
2.3937-2.51990.2729906160431430.2314047534882559X-RAY DIFFRACTION100
2.5199-2.67770.2761220586381220.2253239189212586X-RAY DIFFRACTION100
2.6777-2.88450.2634584322811340.2042611823142608X-RAY DIFFRACTION100
2.8845-3.17470.2046899136281190.1874735415962614X-RAY DIFFRACTION100
3.1747-3.63390.197018268331280.1623512737592616X-RAY DIFFRACTION100
3.6339-4.57770.1825704325511240.1338343647932641X-RAY DIFFRACTION99.9638467101
4.5777-45.98660.1943222013931580.1588676621842733X-RAY DIFFRACTION100

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