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- PDB-1jsz: Crystal Structure Analysis of N7,9-dimethylguanine-VP39 complex -

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Basic information

Entry
Database: PDB / ID: 1jsz
TitleCrystal Structure Analysis of N7,9-dimethylguanine-VP39 complex
ComponentsVP39
KeywordsTRANSFERASE / VP39 / mRNA Cap-binding protein / methyltransferase
Function / homology
Function and homology information


regulation of mRNA 3'-end processing / 7-methylguanosine mRNA capping / virion component / methylation / methyltransferase cap1 / methyltransferase cap1 activity / RNA binding
Similarity search - Function
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. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7,9-DIMETHYLGUANINE / S-ADENOSYL-L-HOMOCYSTEINE / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.93 Å
AuthorsHu, G. / Oguro, A. / Gershon, P.D. / Quiocho, F.A.
CitationJournal: Biochemistry / Year: 2002
Title: The "cap-binding slot" of an mRNA cap-binding protein: quantitative effects of aromatic side chain choice in the double-stacking sandwich with cap.
Authors: Hu, G. / Oguro, A. / Li, C. / Gershon, P.D. / Quiocho, F.A.
History
DepositionAug 19, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: VP39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4903
Polymers35,9211
Non-polymers5692
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.300, 67.700, 79.600
Angle α, β, γ (deg.)90.00, 118.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein VP39 / POLY(A) POLYMERASE REGULATORY SUBUNIT


Mass: 35921.438 Da / Num. of mol.: 1 / Fragment: residues 1-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Production host: Escherichia coli (E. coli)
References: UniProt: P07617, polynucleotide adenylyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-NDM / 7,9-DIMETHYLGUANINE


Mass: 184.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 8000, sodium citrate, ammonium sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: unknown
Details: Hodel, A.E., (1996) Cell(Cambridge,Mass.), 85, 247.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG800011
20.125 M11AmSO4
30.1 Mcitrate11

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: CCD / Date: Jan 1, 1999 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 23277 / Num. obs: 22339 / % possible obs: 73.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.93→1.99 Å / % possible all: 50
Reflection
*PLUS
Rmerge(I) obs: 0.081

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
SAINT(SIEMENS)data reduction
SAINT(SIEMENS)data scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.93→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2301 10.9697 %random
Rwork0.21 ---
all0.224 23266 --
obs0.214 20976 --
Refinement stepCycle: LAST / Resolution: 1.93→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 39 166 2607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.58
X-RAY DIFFRACTIONx_dihedral_angle_d24.38
X-RAY DIFFRACTIONx_improper_angle_d1.36
LS refinement shellResolution: 1.93→1.99 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.36 12 -
Rwork0.32 --
obs-140 50 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor all: 0.224 / Rfactor obs: 0.214 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.38
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36
LS refinement shell
*PLUS
Rfactor Rfree: 0.36 / Rfactor Rwork: 0.32

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