[English] 日本語
Yorodumi
- PDB-2tmv: VISUALIZATION OF PROTEIN-NUCLEIC ACID INTERACTIONS IN A VIRUS. RE... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 2tmv
TitleVISUALIZATION OF PROTEIN-NUCLEIC ACID INTERACTIONS IN A VIRUS. REFINED STRUCTURE OF INTACT TOBACCO MOSAIC VIRUS AT 2.9 ANGSTROMS RESOLUTION BY X-RAY FIBER DIFFRACTION
Components
  • RNA (5'-R(P*GP*AP*A)-3')
  • TMV COAT PROTEIN
KeywordsVirus/RNA / VIRUS / Helical virus / Virus-RNA COMPLEX
Function / homologyTobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / Capsid protein / Capsid protein
Function and homology information
Biological speciesTobacco mosaic virus
MethodFIBER DIFFRACTION / Resolution: 2.9 Å
AuthorsStubbs, G. / Pattanayek, R. / Namba, K.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction.
Authors: Namba, K. / Pattanayek, R. / Stubbs, G.
#1: Journal: Science / Year: 1986
Title: Structure of Tobacco Mosaic Virus at 3.6 Angstroms Resolution. Implications for Assembly
Authors: Namba, K. / Stubbs, G.
#2: Journal: Biophys.J. / Year: 1986
Title: Application of Restrained Least-Squares Refinement to Fiber Diffraction from Macromolecular Assemblies
Authors: Stubbs, G. / Namba, K. / Makowski, L.
#3: Journal: Acta Crystallogr.,Sect.A / Year: 1985
Title: Solving the Phase Problem in Fiber Diffraction. Application to Tobacco Mosaic Virus at 3.6 Angstroms Resolution
Authors: Namba, K. / Stubbs, G.
#4: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of the RNA in Tobacco Mosaic Virus
Authors: Stubbs, G. / Stauffacher, C.
#5: Journal: Nature / Year: 1977
Title: Structure of RNA and RNA Binding Site in Tobacco Mosaic Virus from 4-Angstroms Map Calculated from X-Ray Fibre Diagrams
Authors: Stubbs, G. / Warren, S. / Holmes, K.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 15, 1988 / Release: Jan 9, 1989
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 9, 1989Structure modelrepositoryInitial release
1.1Mar 25, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Nov 29, 2017Structure modelDerived calculations / Otherpdbx_database_status / struct_conf / struct_conf_type_pdbx_database_status.process_site
Remark 650HELIX THE ENDS OF ALPHA HELICES ARE OFTEN DIFFICULT TO DEFINE AND IN SEVERAL CASES INCLUDE ONE TURN ...HELIX THE ENDS OF ALPHA HELICES ARE OFTEN DIFFICULT TO DEFINE AND IN SEVERAL CASES INCLUDE ONE TURN OF 3/10 HELIX.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: RNA (5'-R(P*GP*AP*A)-3')
P: TMV COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5043
Polymers18,4642
Non-polymers401
Water1,33374
1
R: RNA (5'-R(P*GP*AP*A)-3')
P: TMV COAT PROTEIN
hetero molecules
x 49


Theoretical massNumber of molelcules
Total (without water)906,704147
Polymers904,74098
Non-polymers1,96449
Water1,76598
TypeNameSymmetry operationNumber
helical symmetry operation49
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
Unit cell
γ
α
β
Length a, b, c (Å)1.000, 1.000, 1.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1
Atom site foot note1: SEE REMARK 7.
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 49 / Num. of operations: 49 / Rise per n subunits: 69 Å / Rotation per n subunits: 1080 °)
DetailsTMV IS A ROD-SHAPED VIRUS 3000 ANGSTROMS LONG AND 180 ANGSTROMS IN DIAMETER, WITH A CENTRAL HOLE OF DIAMETER 40 ANGSTROMS. APPROXIMATELY 2130 IDENTICAL PROTEIN SUBUNITS OF MOLECULAR WEIGHT 17500 FORM A RIGHT-HANDED HELIX OF PITCH 23 ANGSTROMS AND LENGTH 69 ANGTROMS WITH 49 SUBUNITS IN THREE TURNS. A SINGLE STRAND OF RNA FOLLOWS THE BASIC HELIX BETWEEN THE PROTEIN SUBUNITS AT A DISTANCE OF 40 ANGSTROMS. THERE ARE THREE NUCLEOTIDES BOUND TO EACH PROTEIN SUBUNIT.

-
Components

#1: RNA chain RNA (5'-R(P*GP*AP*A)-3')


Mass: 958.660 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein/peptide TMV COAT PROTEIN


Mass: 17505.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco mosaic virus / Strain: vulgare / References: UniProt: P03570, UniProt: P69687*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Calcium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O / Water
Nonpolymer detailsWATER MOLECULE 45 OCCUPIES A SITE BELIEVED TO BIND CALCIUM AT HIGHER CALCIUM CONCENTRATIONS.
Sequence detailsGENERATION OF DIFFERENT SUBUNITS IS MOST EASILY DONE IN POLAR COORDINATES. ASSUME THAT THE ...GENERATION OF DIFFERENT SUBUNITS IS MOST EASILY DONE IN POLAR COORDINATES. ASSUME THAT THE REFERENCE COORDINATES ARE FROM SUBUNIT NUMBER 0. CONVERT X(0) AND Y(0) TO POLAR COORDINATES R(0) AND PHI(0). PHI IS IN DEGREES. SUBUNIT N IS GENERATED BY R(N) = R(0) PHI(N) = PHI(0) + (3*360/49)*N Z(N) = Z(0) + (69/49)*N THEN CONVERT R(N) AND PHI(N) BACK TO CARTESIAN COORDINATES X(N) AND Y(N). THE LENGTH OF THE BASIC REPEAT UNIT IS 69.0 ANGSTROMS. THE NUMBER OF SUBUNITS IN THE BASIC REPEAT UNIT IS 49.

-
Experimental details

-
Experiment

ExperimentMethod: FIBER DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
Method: unknown

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.096 / Highest resolution: 2.9 Å
Details: THE STRUCTURE WAS DETERMINED BY FIBER DIFFRACTION USING MULTI-DIMENSIONAL ISOMORPHOUS REPLACEMENT WITH LAYER-LINE SPLITTING, SOLVENT FLATTENING REFINEMENT AND RESTRAINED LEAST SQUARES COORDINATE REFINEMENT. THE STRUCTURE INCLUDES 154 OF THE 158 AMINO ACIDS AND THREE RNA NUCLEOTIDES MODELLED AS GAA BUT REPRESENTING THE ENTIRE NUCLEIC ACID CONTENT.
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 67 1 74 1354
Refine LS restraints

Refinement-ID: FIBER DIFFRACTION

TypeDev idealDev ideal target
p_bond_d0.0110.02
p_angle_d0.0460.04
p_angle_deg
p_planar_d0.0440.05
p_hb_or_metal_coord
p_mcbond_it0.581
p_mcangle_it1.0611.5
p_scbond_it0.3051
p_scangle_it0.7281.5
p_plane_restr0.0090.02
p_chiral_restr0.1350.15
p_singtor_nbd0.2290.5
p_multtor_nbd0.4060.5
p_xhyhbond_nbd0.2880.5
p_xyhbond_nbd
p_planar_tor1.93
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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