[English] 日本語
Yorodumi
- PDB-6cj6: Structure of the poxvirus protein F9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cj6
TitleStructure of the poxvirus protein F9
ComponentsProtein F9
KeywordsVIRAL PROTEIN / entry fusion complex associated protein
Function / homology
Function and homology information


membrane => GO:0016020 / viral envelope / virion membrane
Similarity search - Function
Virion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses
Similarity search - Domain/homology
ETHANOL / Chem-ETE / 2-ETHOXYETHANOL / METHANOL / 1,3-PROPANDIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / S-1,2-PROPANEDIOL / Protein F9
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsDiesterbeck, U.S. / Gittis, A.G. / Garboczi, D.N. / Moss, B.
CitationJournal: Sci Rep / Year: 2018
Title: The 2.1 angstrom structure of protein F9 and its comparison to L1, two components of the conserved poxvirus entry-fusion complex.
Authors: Diesterbeck, U.S. / Gittis, A.G. / Garboczi, D.N. / Moss, B.
History
DepositionFeb 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein F9
B: Protein F9
C: Protein F9
D: Protein F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,217183
Polymers78,5434
Non-polymers13,675179
Water3,891216
1
A: Protein F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,16452
Polymers19,6361
Non-polymers3,52851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,26937
Polymers19,6361
Non-polymers2,63336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,06043
Polymers19,6361
Non-polymers3,42442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein F9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,72551
Polymers19,6361
Non-polymers4,08950
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.450, 75.080, 136.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Protein F9


Mass: 19635.631 Da / Num. of mol.: 4 / Fragment: residues 1-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Western Reserve)
Strain: Western Reserve / Gene: VACWR048, F9L / Production host: Escherichia coli (E. coli) / References: UniProt: P24361

-
Non-polymers , 15 types, 395 molecules

#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O2
#8: Chemical...
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: C2H6O
#9: Chemical...
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: CH4O
#10: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O2
#11: Chemical
ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2
#12: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20O5
#13: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#14: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL, PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#15: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown from a solution containing 25% PEG 8000, 10% ethanol, 1-5% cocktail mixture of low molecular alcohols, 30% sucrose at pH 8.5 buffered with Tris in the presence of 50mM ...Details: Crystals were grown from a solution containing 25% PEG 8000, 10% ethanol, 1-5% cocktail mixture of low molecular alcohols, 30% sucrose at pH 8.5 buffered with Tris in the presence of 50mM NaCl. The protein concentration was 10mg/ml

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→38.86 Å / Num. obs: 37485 / % possible obs: 93.83 % / Redundancy: 8.7 % / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 1884 / % possible all: 67

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.86 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 32.59
RfactorNum. reflection% reflection
Rfree0.2685 2000 5.34 %
Rwork0.2257 --
obs0.2279 37485 93.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4927 0 898 216 6041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145744
X-RAY DIFFRACTIONf_angle_d1.7287377
X-RAY DIFFRACTIONf_dihedral_angle_d18.6051955
X-RAY DIFFRACTIONf_chiral_restr0.06818
X-RAY DIFFRACTIONf_plane_restr0.02895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.38171010.35181783X-RAY DIFFRACTION67
2.1525-2.21070.35651130.31472017X-RAY DIFFRACTION75
2.2107-2.27570.36651250.2942223X-RAY DIFFRACTION84
2.2757-2.34910.28661370.26572429X-RAY DIFFRACTION91
2.3491-2.43310.30261500.26952653X-RAY DIFFRACTION98
2.4331-2.53050.3061470.25412627X-RAY DIFFRACTION99
2.5305-2.64560.36441500.26142659X-RAY DIFFRACTION99
2.6456-2.78510.3461510.2382672X-RAY DIFFRACTION99
2.7851-2.95950.24941510.23492684X-RAY DIFFRACTION100
2.9595-3.18790.27171510.22482683X-RAY DIFFRACTION100
3.1879-3.50860.24431530.20082701X-RAY DIFFRACTION100
3.5086-4.01580.20611530.19412728X-RAY DIFFRACTION100
4.0158-5.05770.22911570.18382769X-RAY DIFFRACTION100
5.0577-38.86670.26861610.22682857X-RAY DIFFRACTION99

+
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://pdbjlvh1.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