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- PDB-1av6: VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M7G CAPPED RNA HEX... -

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Basic information

Entry
Database: PDB / ID: 1av6
TitleVACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M7G CAPPED RNA HEXAMER AND S-ADENOSYLHOMOCYSTEINE
Components
  • Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
  • RNA (5'-R(*GP*AP*AP*AP*AP*A)-3')
KeywordsTRANSFERASE/RNA / SINGLE-STRANDED RNA / METHYLTRANSFERASE / RNA CAP / POLY(A) POLYMERASE / VACCINIA / MRNA PROCESSING / TRANSCRIPTION / COMPLEX (TRANSFERASE-RNA) / TRANSFERASE-RNA complex
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
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / RNA / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesVaccinia virus WR
MethodX-RAY DIFFRACTION / MOLECULAR / Resolution: 2.8 Å
AuthorsHodel, A.E. / Gershon, P.D. / Quiocho, F.A.
CitationJournal: Mol.Cell / Year: 1998
Title: Structural basis for sequence-nonspecific recognition of 5'-capped mRNA by a cap-modifying enzyme.
Authors: Hodel, A.E. / Gershon, P.D. / Quiocho, F.A.
History
DepositionSep 26, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Derived calculations / Category: reflns / reflns_shell / struct_conn
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
B: RNA (5'-R(*GP*AP*AP*AP*AP*A)-3')
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4434
Polymers36,5192
Non-polymers9242
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.800, 64.600, 99.500
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: RNA chain RNA (5'-R(*GP*AP*AP*AP*AP*A)-3') / 5' CAPPED RNA HEXAMER


Mass: 1946.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#2: Protein Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase / Poly(A) polymerase regulatory subunit / Poly(A) polymerase small subunit / PAP-S / VP39


Mass: 34573.008 Da / Num. of mol.: 1 / Mutation: C-TERMINAL DELETION OF 26 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus WR / Genus: Orthopoxvirus / Strain: Western Reserve / Gene: PAPS, VACWR095, F9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: MUTATION:C-TERMINAL DELETION OF 26 RESIDUES / References: UniProt: P07617, methyltransferase cap1
#3: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#4: 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

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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: 2.77 Å3/Da / Density % sol: 56 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115-20 %PEG80001reservoir
20.1 Mcacodylate1reservoirpH7.0
30.125 Mammonium sulfate1reservoir
40.26 mMdelta C261drop
50.9 mMRNA1drop
61 mMAdoHcy1drop

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 15, 1997 / Details: GOBEL MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 9755 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 20
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Num. measured all: 22144 / Biso Wilson estimate: 27 Å2
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Redundancy: 2 % / Mean I/σ(I) obs: 6

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
SMARTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR
Starting model: PDB ENTRY 1VPT

1vpt


Resolution: 2.8→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: GROUP / Cross valid method: FREE-R / σ(F): 2
Details: SINGLE PHOSPHATE LINKS BETWEEN RESIDUES ARE PHOSPHOROTHIOATE, I.E., M7GPPPG-PS-A-PS-A-PS-A-PS-A-PS-A. PHOSPHOROTHIOLATES ARE LEFT AS PHOSPHATE IN THIS INITIAL DEPOSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 -5 %RANDOM
Rwork0.215 ---
obs0.215 9284 92 %-
Displacement parametersBiso mean: 13 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 130 58 0 2575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2

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