[English] 日本語
Yorodumi
- PDB-1f15: CUCUMBER MOSAIC VIRUS (STRAIN FNY) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f15
TitleCUCUMBER MOSAIC VIRUS (STRAIN FNY)
ComponentsCOAT PROTEIN
KeywordsVIRUS / beta barrel / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity
Similarity search - Function
Cucumovirus coat protein, subunit A / Cucumovirus coat protein / Cucumovirus coat protein, subunit A superfamily / Cucumovirus coat protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCucumber mosaic virus (cucumber mosaic cucumovirus)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsSmith, T.J. / Chase, E. / Schmidt, T. / Perry, K.
CitationJournal: J.Virol. / Year: 2000
Title: The structure of cucumber mosaic virus and comparison to cowpea chlorotic mottle virus.
Authors: Smith, T.J. / Chase, E. / Schmidt, T. / Perry, K.L.
History
DepositionMay 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)72,5303
Polymers72,5303
Non-polymers00
Water0
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)4,351,791180
Polymers4,351,791180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 5


  • icosahedral pentamer
  • 363 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)362,64915
Polymers362,64915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 6


  • icosahedral 23 hexamer
  • 435 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)435,17918
Polymers435,17918
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 5


  • crystal asymmetric unit, crystal frame
  • 363 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)362,64915
Polymers362,64915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)336, 336, 336
Angle α, β, γ (deg.)90, 90, 90
Int Tables number208
Space group name H-MP4232
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)

-
Components

#1: Protein COAT PROTEIN


Mass: 24176.617 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cucumber mosaic virus (strain FNY) / Genus: Cucumovirus / Species: Cucumber mosaic virus / Strain: FNY / References: UniProt: P69466

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Sodium formate, sodium acetate, PEG 8000, cyclohexyl-pentyl-D-maltoside, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 Msodium formate1reservoir
20.1 Msodium acetate1reservoirpH4.6
30.05-0.125 %PEG80001reservoir
41 Msodium formate1drop
50.05 Msodium acetate1drop
60.025-0.0625 %PEG80001drop
74 mMTris1drop
80.8 mg/mlprotein1drop
92.4 mMCYMAL-51drop

-
Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.131 / % possible all: 18.6
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / % possible obs: 57 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 18.6 %

-
Processing

Software
NameVersionClassification
RAVEmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RAVEphasing
RefinementResolution: 3.2→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.246 288647
all-288647
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4200 0 0 0 4200
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.247 / Rfactor Rwork: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

+
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