[English] 日本語
Yorodumi
- PDB-1tnv: CRYSTAL STRUCTURAL ANALYSIS OF TOBACCO NECROSIS VIRUS (TNV) AT 5 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tnv
TitleCRYSTAL STRUCTURAL ANALYSIS OF TOBACCO NECROSIS VIRUS (TNV) AT 5 ANGSTROMS RESOLUTION
Components
  • TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
  • TOBACCO NECROSIS VIRUS (SUBUNIT VP3)
KeywordsVIRUS / Icosahedral virus
Biological speciesunidentified tobacco necrosis virus
MethodX-RAY DIFFRACTION / Resolution: 5 Å
AuthorsTsukihara, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystal structural analysis of tobacco necrosis virus at 5 A resolution.
Authors: Bando, M. / Morimoto, Y. / Sato, T. / Tsukihara, T.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Symmetry and Subunit Arrangement of Tobacco Necrosis Virus
Authors: Tsukihara, T. / Yokota, Y. / Koyama, T. / Fukuyama, K. / Matsubara, H.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Tobacco Necrosis Virus
Authors: Fukuyama, K. / Hirota, S. / Tsukihara, T.
History
DepositionMar 11, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
B: TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
C: TOBACCO NECROSIS VIRUS (SUBUNIT VP3)


Theoretical massNumber of molelcules
Total (without water)49,5853
Polymers49,5853
Non-polymers00
Water00
1
A: TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
B: TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
C: TOBACCO NECROSIS VIRUS (SUBUNIT VP3)
x 60


Theoretical massNumber of molelcules
Total (without water)2,975,100180
Polymers2,975,100180
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: TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
B: TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
C: TOBACCO NECROSIS VIRUS (SUBUNIT VP3)
x 5


  • icosahedral pentamer
  • 248 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)247,92515
Polymers247,92515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
B: TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
C: TOBACCO NECROSIS VIRUS (SUBUNIT VP3)
x 6


  • icosahedral 23 hexamer
  • 298 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)297,51018
Polymers297,51018
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
B: TOBACCO NECROSIS VIRUS (SUBUNIT VP1)
C: TOBACCO NECROSIS VIRUS (SUBUNIT VP3)
x 5


  • crystal asymmetric unit, crystal frame
  • 248 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)247,92515
Polymers247,92515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)338.000, 338.000, 338.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
Atom site foot note1: UNK B 111 - UNK B 112 OMEGA = 211.95 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
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 TOBACCO NECROSIS VIRUS (SUBUNIT VP1)


Mass: 15847.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) unidentified tobacco necrosis virus / Genus: Necrovirus / Organ: BEAN
#2: Protein TOBACCO NECROSIS VIRUS (SUBUNIT VP3)


Mass: 17889.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unidentified tobacco necrosis virus / Genus: Necrovirus / Organ: BEAN
Sequence detailsTHE PRIMARY SEQUENCE OF TNV IS NOT YET KNOWN; THEREFORE ALL RESIDUES WERE MODELED AS GLY AND ARE ...THE PRIMARY SEQUENCE OF TNV IS NOT YET KNOWN; THEREFORE ALL RESIDUES WERE MODELED AS GLY AND ARE REPRESENTED HERE AS UNK, ACCORDING TO PDB CONVENTION. THE SECONDARY STRUCTURES WERE NAMED FOLLOWING THE NOMENCLATURE FOR SOUTHERN BEAN MOSAIC VIRUS (HERMODSON ET AL., 1982).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
pH: 6 / Method: microdialysis
Components of the solutions
*PLUS
Conc.: 0.4 M / Common name: sodium phosphate

-
Data collection

Reflection
*PLUS
Highest resolution: 5 Å / Lowest resolution: 100 Å / Num. all: 29161 / Num. obs: 24127 / Observed criterion σ(F): 5 / Num. measured all: 90251 / Rmerge(I) obs: 0.115
Reflection shell
*PLUS
Highest resolution: 5 Å / Lowest resolution: 6 Å / Num. possible: 12028 / Num. measured obs: 9515

-
Processing

SoftwareName: NCS / Classification: refinement
RefinementHighest resolution: 5 Å
Refinement stepCycle: LAST / Highest resolution: 5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 0 0 2328
Software
*PLUS
Name: NCS / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.184 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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