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- PDB-2l9j: hRSV M2-1 core domain structure -

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Basic information

Entry
Database: PDB / ID: 2l9j
TitlehRSV M2-1 core domain structure
ComponentsMatrix protein 2-1
KeywordsViral protein / Transcription / PROCESSIVITY / TRANSCRIPTION CO-FACTOR / RNA BINDING PROTEIN / RESPIRATORY SYNCYTIAL VIRUS (RSV)
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 / structural molecule activity ...: / regulation of viral transcription / viral transcription / translation elongation factor activity / transcription antitermination / virion component / host cell cytoplasm / structural constituent of virion / 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) / 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
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsDubosclard, V. / Blondot, M. / Bontems, F. / Eleouet, J. / Sizun, C.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structure and functional analysis of the RNA- and viral phosphoprotein-binding domain of respiratory syncytial virus M2-1 protein.
Authors: Blondot, M.L. / Dubosclard, V. / Fix, J. / Lassoued, S. / Aumont-Nicaise, M. / Bontems, F. / Eleouet, J.F. / Sizun, C.
History
DepositionFeb 12, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein 2-1


Theoretical massNumber of molelcules
Total (without water)13,5141
Polymers13,5141
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Matrix protein 2-1 / M2-1


Mass: 13514.423 Da / Num. of mol.: 1 / Fragment: core domain, residues 58-177 / Mutation: L120P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Strain: Long / Production host: Escherichia coli (E. coli) / References: UniProt: Q4KRW3, UniProt: P04545*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1322D 1H-13C HSQC
1423D (H)CCH-TOCSY
1523D CCH-TOCSY
1623D (H)CCH-TOCSY aromatic
1723D 1H-13C NOESY
1832D 1H-15N HSQC IPAP
1942D 1H-15N HSQC IPAP
11053D HNCO
11153D HNCA
11253D HN(CA)CB
11353D CBCA(CO)NH
11452D (HB)CB(CGCD)HD

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Sample preparation

Details
Solution-IDContentsSolvent system
10.120 mM [U-100% 15N] M2-1-1, 50 mM sodium phosphate-2, 150 mM sodium chloride-3, 1 mM DTT-4, 93% H2O/7% D2O93% H2O/7% D2O
20.1 mM [U-100% 13C] M2-1-5, 50 mM sodium phosphate-6, 150 mM sodium chloride-7, 1 mM DTT-8, 100% D2O100% D2O
30.2 mM [U-100% 15N] M2-1-9, 50 mM sodium phosphate-10, 150 mM sodium chloride-11, 1 mM DTT-12, 0.055 v/v c12e5-13, 0.017 v/v Hexanol-14, 93% H2O/7% D2O93% H2O/7% D2O
40.12 mM [U-100% 15N] M2-1-15, 50 mM sodium phosphate-16, 150 mM sodium chloride-17, 1 mM DTT-18, 6 % acrylamide/bisacryamide-19, 93% H2O/7% D2O93% H2O/7% D2O
50.120 mM [U-100% 13C; U-100% 15N] M2-1-20, 50 mM sodium phosphate-21, 150 mM sodium chloride-22, 1 mM DTT-23, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
120 uMM2-1-1[U-100% 15N]1
50 mMsodium phosphate-21
150 mMsodium chloride-31
1 mMDTT-41
0.1 mMM2-1-5[U-100% 13C]2
50 mMsodium phosphate-62
150 mMsodium chloride-72
1 mMDTT-82
0.2 mMM2-1-9[U-100% 15N]3
50 mMsodium phosphate-103
150 mMsodium chloride-113
1 mMDTT-123
0.055 v/vc12e5-133
0.017 v/vHexanol-143
0.12 mMM2-1-15[U-100% 15N]4
50 mMsodium phosphate-164
150 mMsodium chloride-174
1 mMDTT-184
6 %acrylamide/bisacryamide-194
120 uMM2-1-20[U-100% 13C; U-100% 15N]5
50 mMsodium phosphate-215
150 mMsodium chloride-225
1 mMDTT-235
Sample conditionsIonic strength: 150 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANA2Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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