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- PDB-3cpe: Crystal Structure of T4 gp17 -

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Basic information

Entry
Database: PDB / ID: 3cpe
TitleCrystal Structure of T4 gp17
ComponentsDNA packaging protein Gp17
KeywordsHYDROLASE / large terminase / Alternative initiation / ATP-binding / DNA-binding / Nuclease / Nucleotide-binding
Function / homology
Function and homology information


viral terminase, large subunit / DNA nuclease activity / viral genome packaging / viral procapsid maturation / viral DNA genome packaging / nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity ...viral terminase, large subunit / DNA nuclease activity / viral genome packaging / viral procapsid maturation / viral DNA genome packaging / nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Nucleotidyltransferase; domain 5 - #240 / Terminase, large subunit, gp17-like / Terminase, large subunit gp17-like, C-terminal / Terminase RNaseH-like domain / Terminase large subunit, T4likevirus-type, N-terminal / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich ...Nucleotidyltransferase; domain 5 - #240 / Terminase, large subunit, gp17-like / Terminase, large subunit gp17-like, C-terminal / Terminase RNaseH-like domain / Terminase large subunit, T4likevirus-type, N-terminal / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Terminase, large subunit
Similarity search - Component
Biological speciesBacteriophage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsSun, S. / Rossmann, M.G.
CitationJournal: Cell / Year: 2008
Title: The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.
Authors: Siyang Sun / Kiran Kondabagil / Bonnie Draper / Tanfis I Alam / Valorie D Bowman / Zhihong Zhang / Shylaja Hegde / Andrei Fokine / Michael G Rossmann / Venigalla B Rao /
Abstract: Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The ...Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The structure consists of an N-terminal ATPase domain, which provides energy for compacting DNA, and a C-terminal nuclease domain, which terminates packaging. We show that another function of the C-terminal domain is to translocate the genome into the procapsid. The two domains are in close contact in the crystal structure, representing a "tensed state." A cryo-electron microscopy reconstruction of the T4 procapsid complexed with gp17 shows that the packaging motor is a pentamer and that the domains within each monomer are spatially separated, representing a "relaxed state." These structures suggest a mechanism, supported by mutational and other data, in which electrostatic forces drive the DNA packaging by alternating between tensed and relaxed states. Similar mechanisms may occur in other molecular motors.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _software.classification ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA packaging protein Gp17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0234
Polymers67,8101
Non-polymers2133
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.587, 119.587, 226.301
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

21A-663-

HOH

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Components

#1: Protein DNA packaging protein Gp17 / Terminase


Mass: 67809.719 Da / Num. of mol.: 1 / Fragment: residues 1-567 / Mutation: D255E, E256D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage T4 (virus) / Gene: 17 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P17312
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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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: 3.44 Å3/Da / Density % sol: 64.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2M Na/K phosphate, 0.1M CAPS, pH 6.0, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 24326 / Num. obs: 23617 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 74.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 23.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2308 / Rsym value: 0.349 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å46.88 Å
Translation3 Å46.88 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2O0H and 3C6H

2o0h

3c6h


Resolution: 2.8→46.88 Å / FOM work R set: 0.748 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1207 5 %RANDOM
Rwork0.25 ---
all0.25 24326 --
obs0.25 23560 96.9 %-
Solvent computationBsol: 45.024 Å2
Displacement parametersBiso mean: 65.782 Å2
Baniso -1Baniso -2Baniso -3
1-10.956 Å20 Å20 Å2
2--10.956 Å20 Å2
3----21.912 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4467 0 11 167 4645
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061.5
X-RAY DIFFRACTIONc_angle_d1.12
X-RAY DIFFRACTIONc_dihedral_angle_d25.62
X-RAY DIFFRACTIONc_improper_angle_d1.342.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.41 203 -
Rwork0.336 --
obs-3900 98.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water.param

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