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- PDB-2tmv: VISUALIZATION OF PROTEIN-NUCLEIC ACID INTERACTIONS IN A VIRUS. RE... -

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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 / homology
Function and homology information


helical viral capsid / structural molecule activity / identical protein binding
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 / Capsid protein
Similarity search - Component
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.
History
DepositionSep 15, 1988Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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.

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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: 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 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: 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.

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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
#2: Protein 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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.

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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

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 ...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
Refine-IDTypeDev idealDev ideal target
FIBER DIFFRACTIONp_bond_d0.0110.02
FIBER DIFFRACTIONp_angle_d0.0460.04
FIBER DIFFRACTIONp_angle_deg
FIBER DIFFRACTIONp_planar_d0.0440.05
FIBER DIFFRACTIONp_hb_or_metal_coord
FIBER DIFFRACTIONp_mcbond_it0.581
FIBER DIFFRACTIONp_mcangle_it1.0611.5
FIBER DIFFRACTIONp_scbond_it0.3051
FIBER DIFFRACTIONp_scangle_it0.7281.5
FIBER DIFFRACTIONp_plane_restr0.0090.02
FIBER DIFFRACTIONp_chiral_restr0.1350.15
FIBER DIFFRACTIONp_singtor_nbd0.2290.5
FIBER DIFFRACTIONp_multtor_nbd0.4060.5
FIBER DIFFRACTIONp_xhyhbond_nbd0.2880.5
FIBER DIFFRACTIONp_xyhbond_nbd
FIBER DIFFRACTIONp_planar_tor1.93
FIBER DIFFRACTIONp_staggered_tor
FIBER DIFFRACTIONp_orthonormal_tor
FIBER DIFFRACTIONp_transverse_tor
FIBER DIFFRACTIONp_special_tor

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