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

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Basic information

Entry
Database: PDB / ID: 8orv
TitleCrystal structure of monkeypox virus poxin in complex with the STING agonist MD1203
ComponentsMPXVgp165
KeywordsVIRAL PROTEIN / mpox / monkeypox / virus / poxin
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP binding / nuclease activity / 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-VZ6 / Poxin-Schlafen
Similarity search - Component
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionApr 17, 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

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Assembly

Deposited unit
A: MPXVgp165
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1712
Polymers22,5101
Non-polymers6611
Water4,612256
1
A: MPXVgp165
hetero molecules

A: MPXVgp165
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3434
Polymers45,0202
Non-polymers1,3232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2810 Å2
ΔGint-8 kcal/mol
Surface area17860 Å2
Unit cell
Length a, b, c (Å)54.128, 95.498, 93.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-448-

HOH

21A-468-

HOH

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Components

#1: Protein MPXVgp165


Mass: 22509.893 Da / Num. of mol.: 1
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-VZ6 / 9-[(1~{S},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-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: 661.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23F2N9O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 40% (v/v) PEG 300; 0.1M phosphate-citrate, pH 4.2

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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: Jan 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.65→46.74 Å / Num. obs: 29391 / % possible obs: 99.47 % / Redundancy: 12.9 % / Biso Wilson estimate: 24.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1307 / Rpim(I) all: 0.03743 / Rrim(I) all: 0.1361 / Net I/σ(I): 14.98
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 11.9 % / Rmerge(I) obs: 2.704 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 2841 / CC1/2: 0.508 / CC star: 0.821 / Rpim(I) all: 0.8001 / Rrim(I) all: 2.824 / % possible all: 97.76

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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: 1.65→46.74 Å / SU ML: 0.2955 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8417
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 1469 5 %random selection
Rwork0.1861 27913 --
obs0.188 29382 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.95 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 44 256 1820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071638
X-RAY DIFFRACTIONf_angle_d1.10362239
X-RAY DIFFRACTIONf_chiral_restr0.0695239
X-RAY DIFFRACTIONf_plane_restr0.01292
X-RAY DIFFRACTIONf_dihedral_angle_d12.223610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.710.56571420.5292698X-RAY DIFFRACTION97.76
1.71-1.780.39181460.3252767X-RAY DIFFRACTION99.86
1.78-1.860.25871450.23982758X-RAY DIFFRACTION99.9
1.86-1.960.23721460.21312777X-RAY DIFFRACTION99.69
1.96-2.080.22051470.20022782X-RAY DIFFRACTION99.86
2.08-2.240.21741450.18222766X-RAY DIFFRACTION99.76
2.24-2.460.21731480.1812802X-RAY DIFFRACTION99.56
2.46-2.820.25991470.18912799X-RAY DIFFRACTION99.8
2.82-3.550.21061470.17242818X-RAY DIFFRACTION99.4
3.55-46.740.18131560.14782946X-RAY DIFFRACTION99.33

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