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- PDB-2ga9: Crystal Structure of the Heterodimeric Vaccinia Virus Polyadenyla... -

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Basic information

Entry
Database: PDB / ID: 2ga9
TitleCrystal Structure of the Heterodimeric Vaccinia Virus Polyadenylate Polymerase with Bound ATP-gamma-S
Components
  • Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
  • Poly(A) polymerase catalytic subunit
KeywordsTRANSFERASE / polyadenylate polymerase / nucleotidyltransferase / poxvirus / heterodimer / processivity
Function / homology
Function and homology information


regulation of mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / mRNA processing / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding ...regulation of mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / mRNA processing / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Poxvirus poly(A) polymerase, N domain / Poxvirus poly(A) polymerase, nucleotidyltransferase domain / Poly(A) polymerase catalytic subunit, Poxviridae / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase, catalytic subunit, C-terminal / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal / Poly(A) polymerase catalytic subunit superfamily / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal domain superfamily / Poxvirus poly(A) polymerase, nucleotidyltransferase domain superfamily / Poxvirus poly(A) polymerase nucleotidyltransferase domain ...Poxvirus poly(A) polymerase, N domain / Poxvirus poly(A) polymerase, nucleotidyltransferase domain / Poly(A) polymerase catalytic subunit, Poxviridae / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase, catalytic subunit, C-terminal / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal / Poly(A) polymerase catalytic subunit superfamily / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal domain superfamily / Poxvirus poly(A) polymerase, nucleotidyltransferase domain superfamily / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase C-terminal domain / Poxvirus poly(A) polymerase N-terminal domain / mRNA methyltransferase-like / Poxvirus/kinetoplastid-type cap-specific nucleoside 2-O-methyltransferase / Poxvirus cap-specific nucleoside 2-O-methyltransferase / Poly A polymerase regulatory subunit / Poxvirus/kinetoplastid-type ribose 2'-O-methyltransferase (EC 2.1.1.57) family profile. / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Beta Polymerase; domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase / Poly(A) polymerase catalytic subunit
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsMoure, C.M. / Bowman, B.R. / Gershon, P.D. / Quiocho, F.A.
CitationJournal: Mol.Cell / Year: 2006
Title: Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: insights into ATP selectivity and processivity.
Authors: Moure, C.M. / Bowman, B.R. / Gershon, P.D. / Quiocho, F.A.
History
DepositionMar 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2012Group: Non-polymer description / Other
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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_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_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_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
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
D: Poly(A) polymerase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1046
Polymers88,9782
Non-polymers1,1274
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.050, 91.690, 133.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase / PolyA / polymerase regulatory subunit / PolyA / polymerase small subunit / PAP-S / VP39


Mass: 34588.961 Da / Num. of mol.: 1 / Mutation: R140A K142A R143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P07617, methyltransferase cap1
#2: Protein Poly(A) polymerase catalytic subunit / PolyA / polymerase large subunit / PAP-L / VP55


Mass: 54388.844 Da / Num. of mol.: 1 / Mutation: L36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta
References: UniProt: P23371, polynucleotide adenylyltransferase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: 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.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 20% PEG 4000, 0.240 M CaCl2, 5% glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(11) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 38285 / Num. obs: 38285 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.3→2.38 Å / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementResolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1819 4.7 %RANDOM
Rwork0.222 ---
all0.225 38228 --
obs0.225 36590 93.8 %-
Solvent computationBsol: 35.436 Å2
Displacement parametersBiso mean: 33.885 Å2
Baniso -1Baniso -2Baniso -3
1--2.611 Å20 Å20 Å2
2--2.284 Å20 Å2
3---0.328 Å2
Refine analyzeLuzzati coordinate error obs: 0.2959 Å / Luzzati d res low obs: 2.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6009 0 64 260 6333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008414
X-RAY DIFFRACTIONc_angle_deg1.61662
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.3079 140 -
Rwork0.2617 --
obs-2973 77.45 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2sap.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water.param

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