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- PDB-1fou: CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29 -

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Basic information

Entry
Database: PDB / ID: 1fou
TitleCONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29
ComponentsUPPER COLLAR PROTEIN
KeywordsVIRAL PROTEIN / alpha-helical barrel
Function / homology
Function and homology information


viral procapsid / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / RNA binding
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #30 / Upper collar protein gp10 (connector protein) fold / Upper collar protein gp10 (connector protein) / Bacteriophage PHI-29 conector. Domain 3 / Portal protein Gp10 / Portal protein Gp10 superfamily / Phage Connector (GP10) / Crambin / Serum Albumin; Chain A, Domain 1 / Beta Barrel ...Serum Albumin; Chain A, Domain 1 - #30 / Upper collar protein gp10 (connector protein) fold / Upper collar protein gp10 (connector protein) / Bacteriophage PHI-29 conector. Domain 3 / Portal protein Gp10 / Portal protein Gp10 superfamily / Phage Connector (GP10) / Crambin / Serum Albumin; Chain A, Domain 1 / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsSimpson, A.A. / Tao, Y. / Leiman, P.G. / Badasso, M.O. / He, Y. / Jardine, P.J. / Olson, N.H. / Morais, M.C. / Grimes, S.N. / Anderson, D.L. ...Simpson, A.A. / Tao, Y. / Leiman, P.G. / Badasso, M.O. / He, Y. / Jardine, P.J. / Olson, N.H. / Morais, M.C. / Grimes, S.N. / Anderson, D.L. / Baker, T.S. / Rossmann, M.G.
CitationJournal: Nature / Year: 2000
Title: Structure of the bacteriophage phi29 DNA packaging motor.
Authors: A A Simpson / Y Tao / P G Leiman / M O Badasso / Y He / P J Jardine / N H Olson / M C Morais / S Grimes / D L Anderson / T S Baker / M G Rossmann /
Abstract: Motors generating mechanical force, powered by the hydrolysis of ATP, translocate double-stranded DNA into preformed capsids (proheads) of bacterial viruses and certain animal viruses. Here we ...Motors generating mechanical force, powered by the hydrolysis of ATP, translocate double-stranded DNA into preformed capsids (proheads) of bacterial viruses and certain animal viruses. Here we describe the motor that packages the double-stranded DNA of the Bacillus subtilis bacteriophage phi29 into a precursor capsid. We determined the structure of the head-tail connector--the central component of the phi29 DNA packaging motor--to 3.2 A resolution by means of X-ray crystallography. We then fitted the connector into the electron densities of the prohead and of the partially packaged prohead as determined using cryo-electron microscopy and image reconstruction analysis. Our results suggest that the prohead plus dodecameric connector, prohead RNA, viral ATPase and DNA comprise a rotary motor with the head-prohead RNA-ATPase complex acting as a stator, the DNA acting as a spindle, and the connector as a ball-race. The helical nature of the DNA converts the rotary action of the connector into translation of the DNA.
History
DepositionAug 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPPER COLLAR PROTEIN
B: UPPER COLLAR PROTEIN
C: UPPER COLLAR PROTEIN
D: UPPER COLLAR PROTEIN
E: UPPER COLLAR PROTEIN
F: UPPER COLLAR PROTEIN
G: UPPER COLLAR PROTEIN
H: UPPER COLLAR PROTEIN
I: UPPER COLLAR PROTEIN
J: UPPER COLLAR PROTEIN
K: UPPER COLLAR PROTEIN
L: UPPER COLLAR PROTEIN


Theoretical massNumber of molelcules
Total (without water)431,54712
Polymers431,54712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72370 Å2
ΔGint-354 kcal/mol
Surface area124490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.16, 169.24, 185.44
Angle α, β, γ (deg.)90, 114.1, 90
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Detailsthe biological entity is the same dodecamer found in the crystal assymetric unit

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Components

#1: Protein
UPPER COLLAR PROTEIN / GP 10 / CONNECTOR PROTEIN / LATE PROTEIN GP10 / P10 CONNECTOR PROTEIN


Mass: 35962.289 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Plasmid: PPC28D1 / Production host: Bacillus subtilis (bacteria) / References: UniProt: P04332

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30 % MPD, 0.05 M CaCl2, 0.1M Tris HCL, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion / Details: Badasso, M.O., (2000) Acta Crystallogr. D56, 1187.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-10 mg/mlprotein1drop
25 mMTris-HCl1drop
30.4 M1dropNaCl
40.1 MHEPES1drop
50.2 M1dropMgCl2
60.2 MMPD1reservoir
70.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.21→9 Å / Num. all: 78465 / Num. obs: 78035 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 21
Reflection shellResolution: 3.21→3.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.198 / Num. unique all: 2043 / % possible all: 100
Reflection
*PLUS
Highest resolution: 3.2 Å / Rmerge(I) obs: 0.065
Reflection shell
*PLUS

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Processing

Software
NameClassification
AMoREphasing
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementResolution: 3.2→9 Å / Cross valid method: THROUGHOUT / σ(F): 5 / Stereochemistry target values: Engh & Huber / Details: restrained least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.36 3898 5 %random
Rwork0.29 ---
all0.27 78465 --
obs0.27 78035 99.5 %-
Refinement stepCycle: LAST / Resolution: 3.2→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25272 0 0 0 25272
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_bond_d0.009
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 9 Å / σ(F): 5 / % reflection Rfree: 5 % / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.6

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