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- PDB-8btj: Murine cytomegalovirus protein M35 -

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Basic information

Entry
Database: PDB / ID: 8btj
TitleMurine cytomegalovirus protein M35
ComponentsProtein M35
KeywordsSTRUCTURAL PROTEIN / CMV / M35 / virus protein / NFKB mediated transcription
Function / homologyHerpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25) / Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25) / host cell nucleus / (R,R)-2,3-BUTANEDIOL / MALONATE ION / Protein M35
Function and homology information
Biological speciesMuromegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsSchmelz, S. / Van den Heuvel, J. / Blankenfeldt, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2023
Title: The Cytomegalovirus M35 Protein Directly Binds to the Interferon-beta Enhancer and Modulates Transcription of Ifnb1 and Other IRF3-Driven Genes.
Authors: Schwanke, H. / Goncalves Magalhaes, V. / Schmelz, S. / Wyler, E. / Hennig, T. / Gunther, T. / Grundhoff, A. / Dolken, L. / Landthaler, M. / van Ham, M. / Jansch, L. / Bussow, K. / van den ...Authors: Schwanke, H. / Goncalves Magalhaes, V. / Schmelz, S. / Wyler, E. / Hennig, T. / Gunther, T. / Grundhoff, A. / Dolken, L. / Landthaler, M. / van Ham, M. / Jansch, L. / Bussow, K. / van den Heuvel, J. / Blankenfeldt, W. / Friedel, C.C. / Erhard, F. / Brinkmann, M.M.
History
DepositionNov 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein M35
B: Protein M35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,67313
Polymers101,6702
Non-polymers1,00311
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-10 kcal/mol
Surface area33830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.090, 130.711, 67.827
Angle α, β, γ (deg.)90.000, 101.260, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Protein M35


Mass: 50834.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Muromegalovirus / Gene: M35 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8E1G1
#2: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.1M Na2 Malon, 0.1 M HEPES pH 7.0, 0.5 % (v/v) Jeffamine ED-2001 protein conc: 3.6mg/ml cryoprotectant: 12 (v/v) (2R,3R) -(-)-2,3-Butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.94→66.52 Å / Num. obs: 50243 / % possible obs: 92 % / Redundancy: 10.6 % / Biso Wilson estimate: 29.79 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.047 / Net I/σ(I): 11.6
Reflection shellResolution: 1.94→2.151 Å / Num. unique obs: 2513 / CC1/2: 0.581 / Rpim(I) all: 0.488

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Processing

Software
NameVersionClassification
PHENIX1.20-4459refinement
AutoProcessdata scaling
STARANISOdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→57.95 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2261 2543 5.06 %
Rwork0.1739 47683 -
obs0.1765 50226 67.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.96 Å2
Refinement stepCycle: LAST / Resolution: 1.94→57.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6353 0 67 299 6719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01236691
X-RAY DIFFRACTIONf_angle_d1.24249088
X-RAY DIFFRACTIONf_chiral_restr0.05971053
X-RAY DIFFRACTIONf_plane_restr0.02291173
X-RAY DIFFRACTIONf_dihedral_angle_d6.5214926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.980.218630.292441X-RAY DIFFRACTION1.08
1.98-2.020.4647150.2682251X-RAY DIFFRACTION6.52
2.02-2.060.288190.2619452X-RAY DIFFRACTION12.32
2.07-2.110.3555460.2398730X-RAY DIFFRACTION23.47
2.11-2.170.2813690.21421361X-RAY DIFFRACTION35.07
2.17-2.230.27471220.21481876X-RAY DIFFRACTION48.78
2.23-2.290.28051080.2411951X-RAY DIFFRACTION50.16
2.29-2.360.25491720.20622905X-RAY DIFFRACTION74.72
2.36-2.450.25971650.20633254X-RAY DIFFRACTION83.23
2.45-2.550.23571950.19383589X-RAY DIFFRACTION92.84
2.55-2.660.25891890.20353915X-RAY DIFFRACTION99.73
2.66-2.80.27452200.19983908X-RAY DIFFRACTION99.9
2.8-2.980.25472200.18543888X-RAY DIFFRACTION99.95
2.98-3.210.21212150.17753885X-RAY DIFFRACTION100
3.21-3.530.23992100.16873924X-RAY DIFFRACTION100
3.53-4.040.22361560.1393846X-RAY DIFFRACTION97.49
4.04-5.090.18172000.13723946X-RAY DIFFRACTION99.9
5.09-57.950.19472190.18013961X-RAY DIFFRACTION99.83

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