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- PDB-6pzq: Structure of the human respiratory syncytial virus M2-1 protein i... -

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Basic information

Entry
Database: PDB / ID: 6pzq
TitleStructure of the human respiratory syncytial virus M2-1 protein in complex with a short positive-sense gene-end RNA
Components
  • Matrix M2-1
  • RNA (5'-R(P*GP*UP*UP*AP*AP*U)-3')
KeywordsMETAL BINDING PROTEIN/RNA / HRSV M2-1 RNA complex / RNA BINDING PROTEIN / METAL BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


: / regulation of viral transcription / viral transcription / transcription antitermination / virion component / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
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.
Similarity search - Domain/homology
Biological speciesHuman respiratory syncytial virus A
Human respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.703 Å
AuthorsGao, Y. / Cao, D. / Liang, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01GM130950 United States
CitationJournal: Structure / Year: 2020
Title: Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA.
Authors: Gao, Y. / Cao, D. / Pawnikar, S. / John, K.P. / Ahn, H.M. / Hill, S. / Ha, J.M. / Parikh, P. / Ogilvie, C. / Swain, A. / Yang, A. / Bell, A. / Salazar, A. / Miao, Y. / Liang, B.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 2023Group: 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
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: Matrix M2-1
B: Matrix M2-1
C: Matrix M2-1
D: Matrix M2-1
I: RNA (5'-R(P*GP*UP*UP*AP*AP*U)-3')
J: RNA (5'-R(P*GP*UP*UP*AP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,54010
Polymers93,2786
Non-polymers2624
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.750, 94.750, 199.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 22216.404 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 (E. coli) / References: UniProt: P04545
#2: RNA chain RNA (5'-R(P*GP*UP*UP*AP*AP*U)-3')


Mass: 2206.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human respiratory syncytial virus A2
#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.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.703→94.75 Å / Num. obs: 25701 / % possible obs: 99.8 % / Redundancy: 24.3 % / Biso Wilson estimate: 89.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.027 / Rrim(I) all: 0.132 / Net I/σ(I): 13.3
Reflection shellResolution: 2.703→2.85 Å / Redundancy: 26 % / Num. unique obs: 3673 / Rpim(I) all: 0.39 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C3B

4c3b


Resolution: 2.703→63.517 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 1279 5 %
Rwork0.2249 24312 -
obs0.2281 25591 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.15 Å2 / Biso mean: 104.4578 Å2 / Biso min: 36.64 Å2
Refinement stepCycle: final / Resolution: 2.703→63.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 272 4 14 5329
Biso mean--99.23 70.53 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175422
X-RAY DIFFRACTIONf_angle_d1.477348
X-RAY DIFFRACTIONf_chiral_restr0.071850
X-RAY DIFFRACTIONf_plane_restr0.009884
X-RAY DIFFRACTIONf_dihedral_angle_d18.0983335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.703-2.81130.38971390.30542637100
2.8113-2.93920.36451390.28852652100
2.9392-3.09420.39251400.27412654100
3.0942-3.2880.33751400.26762657100
3.288-3.54190.39441410.26972686100
3.5419-3.89830.3061410.22422681100
3.8983-4.46220.22941440.19042723100
4.4622-5.62140.27131450.2023274099
5.6214-63.5170.26421500.223288299

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