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- PDB-5noh: HRSV M2-1 core domain -

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Basic information

Entry
Database: PDB / ID: 5noh
TitleHRSV M2-1 core domain
ComponentsTranscription elongation factor M2-1
KeywordsTRANSCRIPTION / protein
Function / homology
Function and homology information


: / regulation of viral transcription / viral transcription / translation elongation factor activity / transcription antitermination / virion component / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding ...: / regulation of viral transcription / viral transcription / translation elongation factor activity / transcription antitermination / virion component / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / metal ion binding / cytoplasm
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
Protein M2-1 / Protein M2-1
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsJosts, I. / Almeida Hernandez, Y. / Molina, I.G. / de Prat-Gay, G. / Tidow, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
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 12, 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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription elongation factor M2-1
B: Transcription elongation factor M2-1


Theoretical massNumber of molelcules
Total (without water)23,1892
Polymers23,1892
Non-polymers00
Water3,171176
1
A: Transcription elongation factor M2-1


Theoretical massNumber of molelcules
Total (without water)11,5941
Polymers11,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription elongation factor M2-1


Theoretical massNumber of molelcules
Total (without water)11,5941
Polymers11,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.954, 69.241, 46.604
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcription elongation factor M2-1


Mass: 11594.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Gene: M2, DZ88_50545gpM2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059TDD0, UniProt: P04545*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, pH 7.5 1.4M Tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.6 Å / Num. obs: 21253 / % possible obs: 94.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 27.08 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.033 / Net I/σ(I): 12.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
Cootmodel building
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.6 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.1
RfactorNum. reflection% reflection
Rfree0.2103 1087 5.13 %
Rwork0.1694 --
obs0.1716 21206 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.62 Å2 / Biso mean: 37.8613 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.8→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 0 176 1794
Biso mean---45.34 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071624
X-RAY DIFFRACTIONf_angle_d0.8142189
X-RAY DIFFRACTIONf_chiral_restr0.033276
X-RAY DIFFRACTIONf_plane_restr0.003271
X-RAY DIFFRACTIONf_dihedral_angle_d13.239631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.8820.402880.30291961204973
1.882-1.98130.2931270.24882456258393
1.9813-2.10540.20651320.203526552787100
2.1054-2.2680.25511650.17552575274099
2.268-2.49620.24411480.170626412789100
2.4962-2.85730.24891330.17952646277999
2.8573-3.59970.19741450.16652600274598
3.5997-46.61960.16311490.13782585273496
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.44242.58270.97312.59211.32032.76120.0047-0.12310.22990.06240.00010.01130.03020.23010.01370.21340.0369-0.03960.29020.00170.222436.961419.36591.4809
23.142-3.65010.57915.5806-0.82830.6728-0.04590.1179-1.19120.06910.07851.38420.0788-0.5245-0.09570.2409-0.02920.02550.4477-0.00090.449715.809716.3522-6.9993
39.1046-5.8603-1.21235.64671.03531.9191-0.0270.03410.12350.1496-0.05090.1978-0.0708-0.17910.04850.2243-0.0152-0.0250.4085-0.00290.283621.179621.6086-10.6704
44.81723.8474-0.64453.6918-1.87393.2028-0.25940.26190.0111-0.52240.2585-0.45670.08720.3482-0.02940.17340.0148-0.01030.3336-0.01530.208438.615716.6222-11.6389
52.25880.93-3.17014.1731-1.28134.97880.0435-0.49050.62620.1223-0.1180.4648-0.0567-0.07680.03940.23520.0521-0.05810.4011-0.02680.320726.508123.025-0.8519
64.31381.9535-0.57693.275-1.75972.8404-0.0055-0.5675-0.0679-0.02680.0301-0.0616-0.1249-0.1375-0.02090.21210.05240.00490.2937-0.03690.22933.513228.496824.8436
77.3025-3.0646-0.96432.9418-0.19772.022-0.1089-0.28430.20150.13750.0992-0.3278-0.03650.43080.05740.2218-0.0303-0.03750.35240.01330.302751.315828.487514.1197
84.79051.0960.94812.7830.38953.2108-0.1480.0651-0.06-0.07420.14540.0048-0.0180.09610.00570.12650.01580.0410.1992-0.01570.181139.462427.55118.2522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )A1 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 45 )A34 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 68 )A46 - 68
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 81 )A69 - 81
5X-RAY DIFFRACTION5chain 'A' and (resid 82 through 103 )A82 - 103
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 32 )B1 - 32
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 68 )B33 - 68
8X-RAY DIFFRACTION8chain 'B' and (resid 69 through 103 )B69 - 103

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