[English] 日本語
Yorodumi
- PDB-8xy2: Crystal structure of MPXV P1 protein S87P mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xy2
TitleCrystal structure of MPXV P1 protein S87P mutant
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 defense response / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host NF-kappaB cascade / Protein OPG035
Function and homology information
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,7024
Polymers64,7024
Non-polymers00
Water7,062392
1
B: Protein OPG035
A: Protein OPG035


Theoretical massNumber of molelcules
Total (without water)32,3512
Polymers32,3512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-2 kcal/mol
Surface area11180 Å2
MethodPISA
2
C: Protein OPG035
D: Protein OPG035


Theoretical massNumber of molelcules
Total (without water)32,3512
Polymers32,3512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-0 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.366, 155.500, 131.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Protein OPG035 / Protein N1


Mass: 16175.423 Da / Num. of mol.: 4 / Mutation: S87P
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.: 392 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 14.4% w/v PEG 8000, 80 mM Sodium cacodylate/ Hydrochloric acid pH 6.5, 160 mM Calcium acetate, 20% v/v Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.24→43.91 Å / Num. obs: 29804 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 2.24→2.31 Å / Num. unique obs: 2712 / CC1/2: 0.949

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XY1

8xy1


Resolution: 2.24→42.461 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.132 / SU ML: 0.209 / Cross valid method: FREE R-VALUE / ESU R: 0.308 / ESU R Free: 0.241
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2718 1502 5.044 %
Rwork0.2186 28274 -
all0.221 --
obs-29776 99.923 %
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: 40.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.581 Å20 Å2-0 Å2
2---0.975 Å20 Å2
3----2.605 Å2
Refinement stepCycle: LAST / Resolution: 2.24→42.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 0 392 4267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133949
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173757
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6465332
X-RAY DIFFRACTIONr_angle_other_deg1.3691.5938665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2221.146253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31215749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4241544
X-RAY DIFFRACTIONr_chiral_restr0.0860.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02893
X-RAY DIFFRACTIONr_nbd_refined0.2120.2896
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23688
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21975
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21831
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1590.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0870.212
X-RAY DIFFRACTIONr_nbd_other0.1920.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.210
X-RAY DIFFRACTIONr_mcbond_it3.8474.0581854
X-RAY DIFFRACTIONr_mcbond_other3.8454.0571853
X-RAY DIFFRACTIONr_mcangle_it5.4216.0732311
X-RAY DIFFRACTIONr_mcangle_other5.426.0742312
X-RAY DIFFRACTIONr_scbond_it4.594.482095
X-RAY DIFFRACTIONr_scbond_other4.5894.4822096
X-RAY DIFFRACTIONr_scangle_it6.8046.5453020
X-RAY DIFFRACTIONr_scangle_other6.8036.5473021
X-RAY DIFFRACTIONr_lrange_it8.42946.6974688
X-RAY DIFFRACTIONr_lrange_other8.40246.484621
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.053816
X-RAY DIFFRACTIONr_ncsr_local_group_20.1020.053716
X-RAY DIFFRACTIONr_ncsr_local_group_30.0980.053818
X-RAY DIFFRACTIONr_ncsr_local_group_40.0870.053774
X-RAY DIFFRACTIONr_ncsr_local_group_50.0770.053821
X-RAY DIFFRACTIONr_ncsr_local_group_60.0780.053779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.2980.371190.322060X-RAY DIFFRACTION99.8168
2.298-2.3610.3551000.2992031X-RAY DIFFRACTION99.9062
2.361-2.4290.3871210.2991903X-RAY DIFFRACTION99.9506
2.429-2.5040.4221050.2991905X-RAY DIFFRACTION100
2.504-2.5860.321910.281853X-RAY DIFFRACTION99.9486
2.586-2.6770.322980.2591790X-RAY DIFFRACTION100
2.677-2.7780.292950.221723X-RAY DIFFRACTION100
2.778-2.8910.287890.2171651X-RAY DIFFRACTION100
2.891-3.0190.312890.2271581X-RAY DIFFRACTION100
3.019-3.1670.263770.231548X-RAY DIFFRACTION99.9385
3.167-3.3380.291810.2331455X-RAY DIFFRACTION99.9349
3.338-3.540.244710.2131389X-RAY DIFFRACTION99.8632
3.54-3.7830.227600.191321X-RAY DIFFRACTION100
3.783-4.0860.223540.1821221X-RAY DIFFRACTION100
4.086-4.4740.221500.1681123X-RAY DIFFRACTION100
4.474-50.209540.1471038X-RAY DIFFRACTION99.9085
5-5.770.221570.189904X-RAY DIFFRACTION100
5.77-7.0570.315400.225785X-RAY DIFFRACTION99.8789
7.057-9.940.161350.176621X-RAY DIFFRACTION99.8478
9.94-42.460.281160.247373X-RAY DIFFRACTION97.9849

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more