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- PDB-8p44: Crystal structure of monkeypox virus poxin in complex with the ST... -

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Basic information

Entry
Database: PDB / ID: 8p44
TitleCrystal structure of monkeypox virus poxin in complex with the STING agonist MD1202D
ComponentsMPXVgp165
KeywordsVIRAL PROTEIN / mpox / monkeypox / virus / poxin
Function / homology
Function and homology information


nuclease activity / 2',3'-cyclic GMP-AMP binding / symbiont-mediated suppression of host innate immune response
Similarity search - Function
Poxin, virus / Schlafen family / Orthopoxvirus B3 protein / Poxviridae B3 protein / Schlafen, AlbA_2 domain / Schlafen, AlbA_2 domain superfamily / Schlafen, AlbA_2
Similarity search - Domain/homology
Chem-WY8 / Poxin-Schlafen
Similarity search - Component
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDuchoslav, V. / Klima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Fluorinated cGAMP analogs, which act as STING agonists and are not cleavable by poxins: Structural basis of their function.
Authors: Klima, M. / Dejmek, M. / Duchoslav, V. / Eisenreichova, A. / Sala, M. / Chalupsky, K. / Chalupska, D. / Novotna, B. / Birkus, G. / Nencka, R. / Boura, E.
History
DepositionMay 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MPXVgp165
B: MPXVgp165
C: MPXVgp165
D: MPXVgp165
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8148
Polymers90,0404
Non-polymers2,7744
Water10,647591
1
A: MPXVgp165
B: MPXVgp165
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4074
Polymers45,0202
Non-polymers1,3872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MPXVgp165
D: MPXVgp165
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4074
Polymers45,0202
Non-polymers1,3872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.212, 91.222, 93.098
Angle α, β, γ (deg.)90.000, 90.030, 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
MPXVgp165


Mass: 22509.893 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: MPXV-M5312_HM12_Rivers-164 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7H0DNF0
#2: Chemical
ChemComp-WY8 / 9-[(1~{S},3~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one


Mass: 693.537 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H23F2N9O8P2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM ammonium nitrate, 20% w/v PEG 3.350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.93→46.86 Å / Num. obs: 66736 / % possible obs: 97.86 % / Redundancy: 7 % / Biso Wilson estimate: 26.56 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.2053 / Rpim(I) all: 0.08302 / Rrim(I) all: 0.2217 / Net I/σ(I): 8.17
Reflection shellResolution: 1.93→1.999 Å / Redundancy: 7.1 % / Rmerge(I) obs: 2.153 / Mean I/σ(I) obs: 1 / Num. unique obs: 6613 / CC1/2: 0.502 / CC star: 0.818 / Rpim(I) all: 0.862 / Rrim(I) all: 2.321 / % possible all: 97.66

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Processing

Software
NameVersionClassification
XDSxdsapp v3.1.9data reduction
XDSxdsapp v3.1.9data scaling
PHASER2.8.3phasing
Coot0.9.8.7model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→46.86 Å / SU ML: 0.2711 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.5253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 3329 5 %random selection
Rwork0.2223 63308 --
obs0.2243 66637 97.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.4 Å2
Refinement stepCycle: LAST / Resolution: 1.93→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 176 591 6841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616470
X-RAY DIFFRACTIONf_angle_d0.74368837
X-RAY DIFFRACTIONf_chiral_restr0.0525947
X-RAY DIFFRACTIONf_plane_restr0.00621149
X-RAY DIFFRACTIONf_dihedral_angle_d12.03542395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.960.35461340.31962566X-RAY DIFFRACTION97.33
1.96-1.990.37931390.30462649X-RAY DIFFRACTION98.17
1.99-2.020.32421380.30032637X-RAY DIFFRACTION97.71
2.02-2.050.35131360.30192590X-RAY DIFFRACTION98.06
2.05-2.090.3541400.29292666X-RAY DIFFRACTION97.57
2.09-2.120.31991380.27942606X-RAY DIFFRACTION97.97
2.12-2.170.30831390.27172671X-RAY DIFFRACTION97.47
2.17-2.210.29451320.252501X-RAY DIFFRACTION93.8
2.21-2.260.35841380.25162620X-RAY DIFFRACTION98.39
2.26-2.310.26541390.24722628X-RAY DIFFRACTION98.5
2.31-2.370.2791400.24892656X-RAY DIFFRACTION98.35
2.37-2.430.28881380.24642630X-RAY DIFFRACTION98.26
2.43-2.50.26561400.23582652X-RAY DIFFRACTION98.52
2.5-2.580.26581410.24062687X-RAY DIFFRACTION98.47
2.58-2.680.29251380.23012613X-RAY DIFFRACTION98.64
2.68-2.780.26681390.22162651X-RAY DIFFRACTION98.2
2.78-2.910.25221360.21762572X-RAY DIFFRACTION95.25
2.91-3.060.28971400.21812696X-RAY DIFFRACTION99.4
3.06-3.260.22481410.2032669X-RAY DIFFRACTION99.12
3.26-3.510.22091410.19262677X-RAY DIFFRACTION99.3
3.51-3.860.21571410.18332693X-RAY DIFFRACTION98.71
3.86-4.420.22231370.18692595X-RAY DIFFRACTION95.96
4.42-5.560.22551420.18432697X-RAY DIFFRACTION99.34
5.56-46.860.25061420.23442686X-RAY DIFFRACTION96.45

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