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- PDB-1ifd: MODEL-BUILDING STUDIES OF INOVIRUS: GENETIC VARIATIONS ON A GEOME... -

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Basic information

Entry
Database: PDB / ID: 1ifd
TitleMODEL-BUILDING STUDIES OF INOVIRUS: GENETIC VARIATIONS ON A GEOMETRIC THEME
ComponentsINOVIRUSFf phages
KeywordsVIRUS / Helical virus
Function / homology
Function and homology information


helical viral capsid / host cell membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #80 / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage fd (virus)
MethodFIBER DIFFRACTION / Resolution: 4 Å
AuthorsMarvin, D.A.
Citation
Journal: Int.J.Biol.Macromol. / Year: 1990
Title: Model-building studies of Inovirus: genetic variations on a geometric theme.
Authors: Marvin, D.A.
#1: Journal: Int.J.Biol.Macromol. / Year: 1989
Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions
Authors: Marvin, D.A.
#2: Journal: J.Biosci. / Year: 1985
Title: Filamentous Bacterial Viruses
Authors: Marvin, D.A.
#3: Journal: Structural Molecular Biology / Year: 1982
Title: X-Ray Fiber Diffraction
Authors: Marvin, D.A. / Nave, C.
#4: Journal: Nature / Year: 1981
Title: Structure of the Protein and DNA in Fd Filamentous Bacterial Virus
Authors: Banner, D.W. / Nave, C. / Marvin, D.A.
#5: Journal: J.Mol.Biol. / Year: 1974
Title: Filamentous Bacterial Viruses Xii. Molecular Architecture of the Class I (Fd, If1, Ike) Virion
Authors: Marvin, D.A. / Pigram, W.J. / Wiseman, R.L. / Wachtel, E.J. / Marvin, F.J.
History
DepositionFeb 16, 1992Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOVIRUS


Theoretical massNumber of molelcules
Total (without water)5,2441
Polymers5,2441
Non-polymers00
Water0
1
A: INOVIRUS
x 55


Theoretical massNumber of molelcules
Total (without water)288,42055
Polymers288,42055
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation54
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
SymmetryHelical symmetry: (Circular symmetry: 5 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 55 / Rise per n subunits: 16 Å / Rotation per n subunits: -33.23 °)

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Components

#1: Protein/peptide INOVIRUS / Ff phages


Mass: 5244.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage fd (virus) / Genus: InovirusFf phages / Species: Enterobacteria phage M13 / Plasmid: M13 / References: UniProt: P69539
Source detailsINOVIRUS STRAIN FD WAS GROWN IN ESCHERICHIA COLI. THERE ARE TWO SYMMETRY CLASSES OF INOVIRUS. CLASS ...INOVIRUS STRAIN FD WAS GROWN IN ESCHERICHIA COLI. THERE ARE TWO SYMMETRY CLASSES OF INOVIRUS. CLASS I INCLUDES STRAINS FD, IF1 AND IKE. CLASS II INCLUDES STRAINS PF1 AND XF. STRAIN FD BELONGS TO THE FF GROUP WITHIN CLASS I. THE MEMBERS OF THE FF GROUP HAVE VIRTUALLY IDENTICAL COAT PROTEIN SEQUENCES AND ONLY SLIGHTLY DIFFERENT GENOME SEQUENCES. OTHER COMMONLY STUDIED FF STRAINS ARE F1, WHICH HAS THE SAME COAT PROTEIN SEQUENCE AS FD; AND M13, WHICH HAS AN ASP TO ASN EXCHANGE AT POSITION 12. THE COORDINATES OF THE M13 MODEL CAN BE DERIVED BY SUBSTITUTING ASN 12 FOR ASP 12 IN THE FD MODEL. MEMBERS OF THE FF GROUP GROW IN ESCHERICHIA COLI BACTERIA THAT CARRY THE F-FACTOR GENES. SOME OF THESE GENES ARE REQUIRED TO GENERATE THE F-PILI, WHICH ARE PROTEIN APPENDAGES THAT PROTRUDE FROM THE SURFACE OF THE BACTERIA AND ARE NECESSARY FOR ADSORPTION OF FD AS THE FIRST STEP IN INFECTION AND GROWTH.

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: fibre diffraction

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Data collection

Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: EREF / Classification: refinement
RefinementHighest resolution: 4 Å
Details: THE MODEL OF THE VIRION HELIX ASYMMETRIC UNIT IS AN ALPHA-HELIX APPROXIMATION TO THE STRUCTURE, SO THE ENTIRE MODEL IS ONE STRETCH OF GENTLY-CURVED HELIX. COORDINATES ARE GIVEN FOR A SINGLE ...Details: THE MODEL OF THE VIRION HELIX ASYMMETRIC UNIT IS AN ALPHA-HELIX APPROXIMATION TO THE STRUCTURE, SO THE ENTIRE MODEL IS ONE STRETCH OF GENTLY-CURVED HELIX. COORDINATES ARE GIVEN FOR A SINGLE ASYMMETRIC UNIT OF THE COAT PROTEIN ASSEMBLY. THE COMPLETE PROTEIN ASSEMBLY CONTAINS SEVERAL THOUSAND ASYMMETRIC UNITS; THE EXACT NUMBER DEPENDS ON THE LENGTH OF THE DNA. THE PROTEIN ASSEMBLY FORMS A CYLINDRICAL SHELL SURROUNDING A DNA CORE. THE DNA IS ABOUT 12% BY WEIGHT OF THE FD VIRION, AND PROBABLY HAS NO WELL-DEFINED STRUCTURE OTHER THAN THAT IMPOSED BY ITS SINGLE-STRANDED CIRCULAR TOPOLOGY: TWO OPPOSITELY DIRECTED DNA CHAINS RUN ALONG THE LENGTH OF THE VIRION TO COMPLETE THE CIRCLE. THE DNA MAY BE A LEFT-HANDED HELIX (SEE JRNL REFERENCE). THE TWO ENDS OF THE VIRION ARE CAPPED BY A FEW COPIES OF MINOR COAT PROTEINS, WHOSE STRUCTURE IS NOT KNOWN. THESE PROTEINS INTERACT WITH THE ENDS OF THE MAJOR COAT PROTEIN ASSEMBLY. THE N-TERMINAL END OF INOVIRUS HAS AN OPEN CUP SHAPE, AND THE C-TERMINAL END IS THE COMPLEMENT OF THIS, A POINTED ARROWHEAD SHAPE (SEE REFERENCES 1 AND 2). THE TWO ENDS OF THE FD ASSEMBLY CAN BE GENERATED BY OPERATING REPEATEDLY (SAY 10 - 20 TIMES) ON THE HELIX UNIT CELL CONTENTS (THE GROUP OF 5 ASYMMETRIC UNITS) WITH THE HELIX PARAMETERS, GIVING TWO DIFFERENT ENDS CONNECTED BY A SHORT SHAFT. SINCE THE MAJOR COAT PROTEIN SUBUNITS AT THE ENDS HAVE FEWER NEIGHBORS THAN THOSE IN THE CENTER OF THE ASSEMBLY, THEIR CONFORMATIONS ARE LESS CONSTRAINED AND MAY BE MODIFIED BY INTERACTION WITH THE MINOR COAT PROTEINS. THE HELIX UNIT CELL PARAMETERS ARE AFFECTED BY EXPERIMENTAL CONDITIONS SUCH AS HYDRATION, PH AND TEMPERATURE. BECAUSE OF THE OVERLAPPING INTERDIGITATED NATURE OF THE ASSEMBLY, EVEN SMALL CHANGES IN THE UNIT CELL PARAMETERS ARE ACCOMPANIED BY CHANGES IN THE SHAPE OF THE ASYMMETRIC UNIT. THESE CHANGES DO NOT ALTER THE PATTERN OF SIDE CHAIN INTERLOCKING BETWEEN NEIGHBORING ASYMMETRIC UNITS, BUT THEY CAN ALTER LOCAL NON-BONDED CONTACTS BY SEVERAL TENTHS OF AN ANGSTROM. THE DEPOSITORS DEFINE A CANONICAL HELIX UNIT CELL WITH PARAMETERS T = -33.23 DEGREES, P = 16.0 ANGSTROMS AND GIVE THE ATOMIC COORDINATES FOR THE ASYMMETRIC UNIT IN THIS UNIT CELL. TO DETERMINE THE COORDINATES OF THE ASYMMETRIC UNIT IN A NEW UNIT CELL WITH SLIGHTLY DIFFERENT PARAMETERS (T', P'), CONVERT FROM CARTESIAN COORDINATES TO CYLINDRICAL-POLAR COORDINATES AND USE EQUATION 5 OF THE JRNL REFERENCE. AN EQUIVALENT ALTERNATIVE METHOD IS TO APPLY A VARIABLE MATRIX THAT IS A FUNCTION OF THE Z COORDINATE OF THE ATOMS. DEFINE A SLEW COEFFICIENT S=(T'-T)/P; FOR EXAMPLE, FOR FD AT PH 2, T'=-36.0 DEGREES DEGREES, P'=16.15 ANGSTROMS AND S=-0.173 DEGREE/ANGSTROM. THEN, TO GENERATE THE SLEWED COORDINATES, APPLY THE MATRIX AND VECTOR (RECALCULATED FOR EACH ATOM): | COS(S*Z) -SIN(S*Z) 0 | | 0 | | SIN(S*Z) COS(S*Z) 0 | + | 0 | | 0 0 1 | | (P'/P)*Z | SLEWING THE COORDINATES IN THIS WAY GIVES RISE TO SMALL LOCAL DISTORTIONS IN COVALENT BOND LENGTHS AND BOND ANGLES, WHICH CAN BE CORRECTED BY A FEW CYCLES OF ENERGY MINIMIZATION. THE TEMPERATURE FACTOR WAS NOT REFINED AND IS GIVEN THE ARBITRARY VALUE OF 10.
Refinement stepCycle: LAST / Highest resolution: 4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms370 0 0 0 370
Refine LS restraints
Refine-IDTypeDev ideal
FIBER DIFFRACTIONo_bond_d0.004
FIBER DIFFRACTIONo_bond_d_na
FIBER DIFFRACTIONo_bond_d_prot
FIBER DIFFRACTIONo_angle_d
FIBER DIFFRACTIONo_angle_d_na
FIBER DIFFRACTIONo_angle_d_prot
FIBER DIFFRACTIONo_angle_deg
FIBER DIFFRACTIONo_angle_deg_na
FIBER DIFFRACTIONo_angle_deg_prot
FIBER DIFFRACTIONo_dihedral_angle_d
FIBER DIFFRACTIONo_dihedral_angle_d_na
FIBER DIFFRACTIONo_dihedral_angle_d_prot
FIBER DIFFRACTIONo_improper_angle_d
FIBER DIFFRACTIONo_improper_angle_d_na
FIBER DIFFRACTIONo_improper_angle_d_prot
FIBER DIFFRACTIONo_mcbond_it
FIBER DIFFRACTIONo_mcangle_it
FIBER DIFFRACTIONo_scbond_it
FIBER DIFFRACTIONo_scangle_it

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