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- PDB-1vtm: STRUCTURE OF THE U2 STRAIN OF TOBACCO MOSAIC VIRUS REFINED AT 3.5... -

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Basic information

Entry
Database: PDB / ID: 1vtm
TitleSTRUCTURE OF THE U2 STRAIN OF TOBACCO MOSAIC VIRUS REFINED AT 3.5 ANGSTROMS RESOLUTION USING X-RAY FIBER DIFFRACTION
Components
  • Coat protein
  • RNA (5'-R(P*GP*AP*A)-3')
KeywordsVirus/RNA / VIRUS / Helical virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


helical viral capsid / structural molecule activity
Similarity search - Function
Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / Capsid protein
Similarity search - Component
Biological speciesTobacco mild green mosaic virus
MethodFIBER DIFFRACTION / Resolution: 3.5 Å
AuthorsStubbs, G. / Pattanayek, R.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Structure of the U2 strain of tobacco mosaic virus refined at 3.5 A resolution using X-ray fiber diffraction.
Authors: Pattanayek, R. / Stubbs, G.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1993
Title: Molecular Dynamics in Refinement Against Fiber Diffraction Data
Authors: Wang, H. / 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.
History
DepositionMar 30, 1992Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: RNA (5'-R(P*GP*AP*A)-3')
P: Coat protein


Theoretical massNumber of molelcules
Total (without water)18,4262
Polymers18,4262
Non-polymers00
Water1448
1
R: RNA (5'-R(P*GP*AP*A)-3')
P: Coat protein
x 49


Theoretical massNumber of molelcules
Total (without water)902,87398
Polymers902,87398
Non-polymers00
Water1,76598
TypeNameSymmetry operationNumber
helical symmetry operation48
identity operation1_555x,y,z1
2


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


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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: GLN P 99 - PRO P 100 OMEGA = 251.92 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
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 °)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW REPRESENTS HELICAL SYMMETRY WITH THE HELIX AXIS ON THE Z AXIS. THERE ARE 49 SUBUNITS IN 3 TURNS OF THE HELIX. THE FULL (49 SUBUNIT) HELICAL REPEAT IS 69 ANGSTROMS.

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Components

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


Mass: 958.660 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (gene. exp.) Tobacco mild green mosaic virus (TMGMV)
Strain: U2 / Gene: CP
#2: Protein Coat protein


Mass: 17467.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P03579
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONCERNING THE APPARENT SEQUENCE DISCREPANCY: THE AUTHORS USED THE SEQUENCE REPORTED BY ALTSCHUH ET ...CONCERNING THE APPARENT SEQUENCE DISCREPANCY: THE AUTHORS USED THE SEQUENCE REPORTED BY ALTSCHUH ET AL., J. MOL. BIOL. (1987) 193, 693-707 RATHER THAN THAT FOUND IN SWISS-PROT ENTRY COAT_TMGMV. THE AUTHORS' VIRUS STOCKS WERE CLOSELY RELATED TO THE ALTSCHUH STOCKS. THE AUTHORS STATE THAT THE DIFFERENCES ARE NOT PARTICULARLY IMPORTANT STRUCTURALLY AND WERE TOO SMALL FOR THEIR MAP TO RESOLVE.

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: unknown

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.5→10 Å / Rfactor obs: 0.096
Details: THIS STRUCTURE WAS DETERMINED FROM FIBER DIFFRACTION DATA BY MOLECULAR REPLACEMENT FROM TMV, PROTEIN DATA BANK ENTRY 2TMV. U2 HAS 72 PER CENT SEQUENCE HOMOLOGY WITH TMV. THIS STRUCTURE ...Details: THIS STRUCTURE WAS DETERMINED FROM FIBER DIFFRACTION DATA BY MOLECULAR REPLACEMENT FROM TMV, PROTEIN DATA BANK ENTRY 2TMV. U2 HAS 72 PER CENT SEQUENCE HOMOLOGY WITH TMV. THIS STRUCTURE INCLUDES ALL 158 AMINO ACIDS AND 3 RNA NUCLEOTIDES, MODELED AS GAA BUT REPRESENTING THE ENTIRE GENOME. THERE IS ONE SMALL SHEET IN THIS STRUCTURE BUT IT IS TOO IRREGULAR TO INCLUDE.
Refinement stepCycle: LAST / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 67 0 8 1307
Refine LS restraints
Refine-IDTypeDev ideal
FIBER DIFFRACTIONp_bond_d0.019
FIBER DIFFRACTIONp_angle_d4.1
FIBER DIFFRACTIONp_angle_deg
FIBER DIFFRACTIONp_planar_d
FIBER DIFFRACTIONp_hb_or_metal_coord
FIBER DIFFRACTIONp_mcbond_it
FIBER DIFFRACTIONp_mcangle_it
FIBER DIFFRACTIONp_scbond_it
FIBER DIFFRACTIONp_scangle_it
FIBER DIFFRACTIONp_plane_restr
FIBER DIFFRACTIONp_chiral_restr
FIBER DIFFRACTIONp_singtor_nbd
FIBER DIFFRACTIONp_multtor_nbd
FIBER DIFFRACTIONp_xhyhbond_nbd
FIBER DIFFRACTIONp_xyhbond_nbd
FIBER DIFFRACTIONp_planar_tor
FIBER DIFFRACTIONp_staggered_tor
FIBER DIFFRACTIONp_orthonormal_tor
FIBER DIFFRACTIONp_transverse_tor
FIBER DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.096
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg4.1
X-RAY DIFFRACTIONp_dihedral_angle_d25
X-RAY DIFFRACTIONp_dihedral_angle_deg1.9
LS refinement shell
*PLUS
Highest resolution: 3.53 Å / Lowest resolution: 3.77 Å / Total num. of bins used: 7 / Rfactor obs: 0.171

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