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- PDB-3wry: Crystal structure of helicase complex 2 -

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Basic information

Entry
Database: PDB / ID: 3wry
TitleCrystal structure of helicase complex 2
Components
  • Replicase large subunit
  • Tm-1 protein
KeywordsTRANSFERASE / alpha/beta domain / Helicase
Function / homology
Function and homology information


modulation by host of viral RNA genome replication / mRNA methyltransferase activity / RNA processing / catalytic activity / Transferases; Transferring one-carbon groups; Methyltransferases / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase ...modulation by host of viral RNA genome replication / mRNA methyltransferase activity / RNA processing / catalytic activity / Transferases; Transferring one-carbon groups; Methyltransferases / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / protein homodimerization activity / ATP hydrolysis activity / RNA binding / ATP binding
Similarity search - Function
Beta-Lactamase - #420 / Uncharacterised protein family UPF0261, NC domain / : / Uncharacterised protein family UPF0261, NN domain / UPF0261 domain / Uncharacterised protein family (UPF0261) / TIM-barrel domain, IGPS-like / Phosphoenolpyruvate hydrolase-like / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain ...Beta-Lactamase - #420 / Uncharacterised protein family UPF0261, NC domain / : / Uncharacterised protein family UPF0261, NN domain / UPF0261 domain / Uncharacterised protein family (UPF0261) / TIM-barrel domain, IGPS-like / Phosphoenolpyruvate hydrolase-like / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Beta-Lactamase / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Aldolase-type TIM barrel / P-loop containing nucleotide triphosphate hydrolases / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ToMV resistance protein Tm-1(GCR237) / Replicase large subunit
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Tomato mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMatsumura, H. / Katoh, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1
Authors: Ishibashi, K. / Kezuka, Y. / Kobayashi, C. / Kato, M. / Inoue, T. / Nonaka, T. / Ishikawa, M. / Matsumura, H. / Katoh, E.
History
DepositionFeb 27, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 8, 2017Group: Source and taxonomy / Structure summary / Category: entity / entity_name_com / entity_src_gen
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type
Revision 1.3Mar 20, 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 / struct_conn / 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 / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tm-1 protein
B: Tm-1 protein
C: Replicase large subunit
D: Replicase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,51913
Polymers193,2934
Non-polymers2,2269
Water13,133729
1
A: Tm-1 protein
C: Replicase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7426
Polymers96,6462
Non-polymers1,0954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-42 kcal/mol
Surface area36480 Å2
MethodPISA
2
B: Tm-1 protein
D: Replicase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7777
Polymers96,6462
Non-polymers1,1315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-55 kcal/mol
Surface area36900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.981, 133.550, 195.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Tm-1 protein / Resistance protein


Mass: 46145.445 Da / Num. of mol.: 2 / Mutation: T91I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: Tm-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A7M6E7
#2: Protein Replicase large subunit / 183 kDa protein / RNA-directed RNA polymerase


Mass: 50500.984 Da / Num. of mol.: 2 / Fragment: UNP residues 666-1116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato mosaic virus (strain L) / Strain: L / Production host: Escherichia coli (E. coli)
References: UniProt: P03587, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, RNA-directed RNA polymerase, RNA helicase

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Non-polymers , 4 types, 738 molecules

#3: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.2M L-proline, 0.1M HEPES-KOH, pH7.0, 11%(w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→33.75 Å / Num. all: 99309 / Num. obs: 99309 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.5 Å2
Reflection shellResolution: 2.3→2.34 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100966.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4771 5.1 %RANDOM
Rwork0.202 ---
all0.204 99309 --
obs0.202 94449 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1986 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.02 Å20 Å20 Å2
2---0.41 Å20 Å2
3---7.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13082 0 129 729 13940
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 711 5 %
Rwork0.262 13635 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5tm1hel.paramtm1hel.top

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