[English] 日本語
Yorodumi
- PDB-8xif: The crystal structure of the AEP domain of VACV D5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xif
TitleThe crystal structure of the AEP domain of VACV D5
ComponentsUncoating factor OPG117
KeywordsREPLICATION / primase / VACV
Function / homology
Function and homology information


: / DNA replication, synthesis of primer / viral DNA genome replication / ribonucleoside triphosphate phosphatase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / ATP binding
Similarity search - Function
DNA primase/nucleoside triphosphatase, C-terminal / Poxvirus D5 protein-like / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PYROPHOSPHATE / Uncoating factor OPG117
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsGan, J. / Zhang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2024
Title: Structural and functional insights into the helicase protein E5 of Mpox virus.
Authors: Weizhen Zhang / Yusong Liu / Mengquan Yang / Jie Yang / Zhiwei Shao / Yanqing Gao / Xinran Jiang / Ruixue Cui / Yixi Zhang / Xin Zhao / Qiyuan Shao / Chulei Cao / Huili Li / Linxi Li / Hehua ...Authors: Weizhen Zhang / Yusong Liu / Mengquan Yang / Jie Yang / Zhiwei Shao / Yanqing Gao / Xinran Jiang / Ruixue Cui / Yixi Zhang / Xin Zhao / Qiyuan Shao / Chulei Cao / Huili Li / Linxi Li / Hehua Liu / Haishan Gao / Jianhua Gan /
Abstract: Mpox virus (MPXV) can cause mpox in humans. Due to its quick and wide spread in the past two years, mpox has turned into a significant public health concern. Helicase E5 is a multi-domain protein; ...Mpox virus (MPXV) can cause mpox in humans. Due to its quick and wide spread in the past two years, mpox has turned into a significant public health concern. Helicase E5 is a multi-domain protein; its primer synthesis and DNA unwinding activity are required for genome uncoating and DNA replication of MPXV. However, the in vitro DNA unwinding activity has never been demonstrated. Here, we report the structural and biochemical studies of MPXV E5, showing that the full-length protein adopts an auto-inhibited conformation. Truncation of the N-terminus can recover the in vitro unwinding activity of E5 towards the forked DNA. Further structural analysis reveals that MPXV E5 shares a conserved mechanism in DNA unwinding and primer synthesis with the homologous proteins. These findings not only advance our understanding on the function of MPXV E5, but also provide a solid basis for the development of anti-poxvirus drugs.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Jul 10, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncoating factor OPG117
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1814
Polymers25,9541
Non-polymers2273
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-26 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.470, 56.620, 74.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Uncoating factor OPG117


Mass: 25954.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: OPG117, VACWR110, D5R / Production host: Escherichia coli (E. coli)
References: UniProt: P04305, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.39→28.31 Å / Num. obs: 45138 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.029 / Rrim(I) all: 0.102 / Net I/σ(I): 13.8
Reflection shellResolution: 1.39→1.42 Å / Redundancy: 13 % / Rmerge(I) obs: 0.098 / Num. unique obs: 45138 / CC1/2: 0.998

-
Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→28.31 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 2283 5.06 %
Rwork0.1791 --
obs0.18 45138 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 11 172 1986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081853
X-RAY DIFFRACTIONf_angle_d1.0482517
X-RAY DIFFRACTIONf_dihedral_angle_d6.779253
X-RAY DIFFRACTIONf_chiral_restr0.09292
X-RAY DIFFRACTIONf_plane_restr0.012326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.37441580.34572639X-RAY DIFFRACTION100
1.42-1.450.34741340.29912663X-RAY DIFFRACTION100
1.45-1.490.27781570.2642625X-RAY DIFFRACTION100
1.49-1.530.25461230.23422649X-RAY DIFFRACTION100
1.53-1.570.22091460.20342645X-RAY DIFFRACTION100
1.57-1.630.24831350.1912638X-RAY DIFFRACTION100
1.63-1.680.19651330.18472651X-RAY DIFFRACTION100
1.68-1.750.18161610.17872649X-RAY DIFFRACTION100
1.75-1.830.20181270.17742677X-RAY DIFFRACTION100
1.83-1.930.21611570.17962633X-RAY DIFFRACTION100
1.93-2.050.20521360.17132696X-RAY DIFFRACTION100
2.05-2.210.2011370.16972686X-RAY DIFFRACTION100
2.21-2.430.20271410.17962688X-RAY DIFFRACTION100
2.43-2.780.20611430.1842709X-RAY DIFFRACTION100
2.78-3.50.2131360.17412769X-RAY DIFFRACTION100
3.5-28.310.15331590.15752838X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 13.4521 Å / Origin y: 8.5366 Å / Origin z: 15.8979 Å
111213212223313233
T0.1385 Å20.0143 Å2-0.0083 Å2-0.1478 Å20.0144 Å2--0.1565 Å2
L0.8748 °20.2597 °2-0.144 °2-0.9475 °20.2643 °2--1.6586 °2
S-0.0059 Å °0.0062 Å °0.0359 Å °0.0015 Å °0.0547 Å °0.0128 Å °0.0166 Å °-0.0034 Å °-0.0489 Å °
Refinement TLS groupSelection details: all

+
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