[English] 日本語
Yorodumi
- PDB-8gp6: Structure of the vaccinia virus A16/G9 sub-complex from the ortho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gp6
TitleStructure of the vaccinia virus A16/G9 sub-complex from the orthopoxvirus entry-fusion complex
Components
  • Myristoylated protein G9Myristoylation
  • Virion membrane protein A16
KeywordsVIRAL PROTEIN / the components of entry-fusion complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / helicase activity / DNA-templated transcription termination / hydrolase activity / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / virion membrane / DNA binding / ATP binding / membrane
Similarity search - Function
Pox virus entry-fusion-complex G9/A16 / Pox virus entry-fusion-complex G9/A16
Similarity search - Domain/homology
Entry-fusion complex protein OPG094 / Virion membrane protein OPG143
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLu, G.W. / Yang, F.L. / Lin, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Emerg Microbes Infect / Year: 2023
Title: Structural basis of poxvirus A16/G9 binding for sub-complex formation.
Authors: Yang, F. / Lin, S. / Chen, Z. / Yue, D. / Yang, M. / He, B. / Cao, Y. / Dong, H. / Li, J. / Zhao, Q. / Lu, G.
History
DepositionAug 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Myristoylated protein G9
A: Virion membrane protein A16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8963
Polymers77,8042
Non-polymers921
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-24 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.275, 122.008, 123.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Myristoylated protein G9 / Myristoylation / Protein F1


Mass: 37514.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Western Reserve)
Strain: Western Reserve / Gene: VACWR087, G9R / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P07611
#2: Protein Virion membrane protein A16


Mass: 40289.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Western Reserve)
Strain: Western Reserve / Gene: VACWR136, A16L / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P16710
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 4% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.1 M Citric acid pH 3.5, 20% w/v Polyethylene glycol 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18033 / % possible obs: 99.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 26.7
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 3.58 / Num. unique obs: 1175 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold 2

Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.904 / SU B: 16.85 / SU ML: 0.336 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 859 4.8 %RANDOM
Rwork0.2426 ---
obs0.2441 17023 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.79 Å2 / Biso mean: 68.3 Å2 / Biso min: 37.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å20 Å2
2--5.53 Å2-0 Å2
3----8.03 Å2
Refinement stepCycle: final / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 6 0 4462
Biso mean--69.75 --
Num. residues----546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194595
X-RAY DIFFRACTIONr_bond_other_d0.0020.024171
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9476220
X-RAY DIFFRACTIONr_angle_other_deg1.1139645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5715544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2423.84237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.38815788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0581532
X-RAY DIFFRACTIONr_chiral_restr0.0970.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215205
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021109
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 50 -
Rwork0.324 1239 -
all-1289 -
obs--99.69 %

+
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