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- PDB-8xy1: Crystal structure of MPXV P1 protein -

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Basic information

Entry
Database: PDB / ID: 8xy1
TitleCrystal structure of MPXV P1 protein
ComponentsProtein OPG035
KeywordsVIRAL PROTEIN / MPXV / P1
Function / homologyOrthopoxvirus, Protein N1 / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / symbiont-mediated perturbation of host apoptosis / symbiont-mediated perturbation of host defense response / symbiont-mediated suppression of host NF-kappaB cascade / Protein OPG035
Function and homology information
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.575 Å
AuthorsNi, X.C. / Lei, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF0702004 China
CitationJournal: Emerg Microbes Infect / Year: 2025
Title: Structural insights into MPXV P1 protein and its orthologs reveal conformational dynamics and a conserved antiviral pocket.
Authors: Ni, X. / Wang, Y. / Fan, X. / Yu, J. / Lei, J.
History
DepositionJan 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein OPG035
B: Protein OPG035
F: Protein OPG035
E: Protein OPG035
C: Protein OPG035
D: Protein OPG035


Theoretical massNumber of molelcules
Total (without water)96,9926
Polymers96,9926
Non-polymers00
Water2,036113
1
A: Protein OPG035
B: Protein OPG035


Theoretical massNumber of molelcules
Total (without water)32,3312
Polymers32,3312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-2 kcal/mol
Surface area11660 Å2
MethodPISA
2
F: Protein OPG035
E: Protein OPG035


Theoretical massNumber of molelcules
Total (without water)32,3312
Polymers32,3312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-1 kcal/mol
Surface area11650 Å2
MethodPISA
3
C: Protein OPG035
D: Protein OPG035


Theoretical massNumber of molelcules
Total (without water)32,3312
Polymers32,3312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-0 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.417, 114.417, 126.789
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein
Protein OPG035 / Protein N1


Mass: 16165.386 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG035, P1L, MPXVgp023 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.8 M Succinic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979152 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979152 Å / Relative weight: 1
ReflectionResolution: 2.57→99.09 Å / Num. obs: 30914 / % possible obs: 100 % / Redundancy: 16 % / CC1/2: 0.998 / Net I/σ(I): 10.9
Reflection shellResolution: 2.57→2.71 Å / Num. unique obs: 4468 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I39

2i39


Resolution: 2.575→99 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.247 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.542 / ESU R Free: 0.286
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2418 1489 4.84 %
Rwork0.1961 29274 -
all0.198 --
obs-30763 99.46 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.587 Å2
Baniso -1Baniso -2Baniso -3
1-0.752 Å20.376 Å20 Å2
2--0.752 Å2-0 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 2.575→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5840 0 0 113 5953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135961
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175659
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.6438042
X-RAY DIFFRACTIONr_angle_other_deg1.3711.59413049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3465705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40821.123383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.255151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1951567
X-RAY DIFFRACTIONr_chiral_restr0.0880.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021360
X-RAY DIFFRACTIONr_nbd_refined0.2110.21184
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.25023
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22963
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22809
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.24
X-RAY DIFFRACTIONr_nbd_other0.2330.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0450.21
X-RAY DIFFRACTIONr_mcbond_it4.7124.9022814
X-RAY DIFFRACTIONr_mcbond_other4.7094.9012813
X-RAY DIFFRACTIONr_mcangle_it6.7757.3523509
X-RAY DIFFRACTIONr_mcangle_other6.7757.3543510
X-RAY DIFFRACTIONr_scbond_it6.6045.7213147
X-RAY DIFFRACTIONr_scbond_other6.6035.7233148
X-RAY DIFFRACTIONr_scangle_it10.0098.2464529
X-RAY DIFFRACTIONr_scangle_other10.0088.2484530
X-RAY DIFFRACTIONr_lrange_it11.99455.5376701
X-RAY DIFFRACTIONr_lrange_other11.99855.5446695
X-RAY DIFFRACTIONr_ncsr_local_group_10.0720.053753
X-RAY DIFFRACTIONr_ncsr_local_group_20.0590.053864
X-RAY DIFFRACTIONr_ncsr_local_group_30.0950.053754
X-RAY DIFFRACTIONr_ncsr_local_group_40.0640.053842
X-RAY DIFFRACTIONr_ncsr_local_group_50.0880.053735
X-RAY DIFFRACTIONr_ncsr_local_group_60.0830.053789
X-RAY DIFFRACTIONr_ncsr_local_group_70.0870.053796
X-RAY DIFFRACTIONr_ncsr_local_group_80.0810.053747
X-RAY DIFFRACTIONr_ncsr_local_group_90.0760.053852
X-RAY DIFFRACTIONr_ncsr_local_group_100.0880.053808
X-RAY DIFFRACTIONr_ncsr_local_group_110.0670.053850
X-RAY DIFFRACTIONr_ncsr_local_group_120.0850.053799
X-RAY DIFFRACTIONr_ncsr_local_group_130.0910.053769
X-RAY DIFFRACTIONr_ncsr_local_group_140.0810.053808
X-RAY DIFFRACTIONr_ncsr_local_group_150.0910.053735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.575-2.6420.323890.2752178X-RAY DIFFRACTION99.9559
2.642-2.7140.361170.2662080X-RAY DIFFRACTION100
2.714-2.7930.249930.2642045X-RAY DIFFRACTION100
2.793-2.8790.2991010.2531987X-RAY DIFFRACTION100
2.879-2.9730.27930.2161894X-RAY DIFFRACTION100
2.973-3.0770.2791070.2191861X-RAY DIFFRACTION100
3.077-3.1930.286960.2181789X-RAY DIFFRACTION100
3.193-3.3240.297850.2041725X-RAY DIFFRACTION100
3.324-3.4710.264890.1911668X-RAY DIFFRACTION100
3.471-3.6410.241770.2091521X-RAY DIFFRACTION95.976
3.641-3.8370.29870.2671431X-RAY DIFFRACTION94.9937
3.837-4.070.234750.1781442X-RAY DIFFRACTION99.9341
4.07-4.350.163830.1511332X-RAY DIFFRACTION99.9294
4.35-4.6990.183510.1461282X-RAY DIFFRACTION100
4.699-5.1460.197570.1541185X-RAY DIFFRACTION99.9195
5.146-5.7530.288520.1591059X-RAY DIFFRACTION100
5.753-6.640.19540.174946X-RAY DIFFRACTION100
6.64-8.1270.205400.157820X-RAY DIFFRACTION100
8.127-11.470.194260.129650X-RAY DIFFRACTION99.8523
11.47-990.142170.26379X-RAY DIFFRACTION96.3504

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