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- PDB-3rtx: Crystal structure of mammalian capping enzyme (Mce1) and Pol II C... -

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Basic information

Entry
Database: PDB / ID: 3rtx
TitleCrystal structure of mammalian capping enzyme (Mce1) and Pol II CTD complex
Components
  • RNA Polymerase II C-terminal domain
  • mRNA-capping enzyme
KeywordsTRANSFERASE / Guanylyltransferase / RNA Polymerase II CTD / lysyl-N-GMP / Nucleus / mRNA capping
Function / homology
Function and homology information


RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / inorganic triphosphate phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / 7-methylguanosine mRNA capping / dephosphorylation / mRNA guanylyltransferase activity ...RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / inorganic triphosphate phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / 7-methylguanosine mRNA capping / dephosphorylation / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding / ATP binding / nucleus
Similarity search - Function
Dna Ligase; domain 1 - #430 / mRNA capping enzyme, bifunctional / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / DNA ligase/mRNA capping enzyme / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain ...Dna Ligase; domain 1 - #430 / mRNA capping enzyme, bifunctional / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / DNA ligase/mRNA capping enzyme / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Dna Ligase; domain 1 / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANINE / mRNA-capping enzyme
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsGhosh, A. / Lima, C.D.
CitationJournal: Mol.Cell / Year: 2011
Title: Structural insights to how mammalian capping enzyme reads the CTD code.
Authors: Ghosh, A. / Shuman, S. / Lima, C.D.
History
DepositionMay 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: mRNA-capping enzyme
B: mRNA-capping enzyme
C: RNA Polymerase II C-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3975
Polymers81,0953
Non-polymers3022
Water2,198122
1
A: mRNA-capping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5842
Polymers39,4331
Non-polymers1511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mRNA-capping enzyme
C: RNA Polymerase II C-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8133
Polymers41,6622
Non-polymers1511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-7 kcal/mol
Surface area14780 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-14 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.980, 114.750, 150.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein mRNA-capping enzyme / HCE / MCE1 / Polynucleotide 5'-triphosphatase / TPase / mRNA 5'-triphosphatase / mRNA ...HCE / MCE1 / Polynucleotide 5'-triphosphatase / TPase / mRNA 5'-triphosphatase / mRNA guanylyltransferase / GTP--RNA guanylyltransferase / GTase


Mass: 39432.590 Da / Num. of mol.: 2 / Fragment: GTase domain (UNP residues 226-567)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Gene: Cap1a, MCE1, Rngtt / Plasmid: TOPO-ADAPTED PET28B-SMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O55236, mRNA guanylyltransferase
#2: Protein/peptide RNA Polymerase II C-terminal domain


Mass: 2229.766 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic phosphorylated peptide derived from the C-terminal domain of RNA polymerase II
#3: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 6% PEG-3350, 100 mM HEPES, 3% dioxane and 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2008 / Details: Cryo-Cooled Si(111) double crystal
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 17720 / % possible obs: 93 % / Observed criterion σ(I): -1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.062 / Χ2: 0.956 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.92.50.21914340.772182.1
2.9-3.022.70.18514740.771183.4
3.02-3.153.30.15915650.88189.9
3.15-3.323.80.12316600.913193.3
3.32-3.534.30.10216540.945194.4
3.53-3.84.90.08117140.964195.6
3.8-4.185.60.0616890.887196.5
4.18-4.796.30.04917440.918197.5
4.79-6.036.20.04917860.885198.1
6.03-506.80.04318551.227198

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNS1.3refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NTase domain of CGT1

Resolution: 2.81→50 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 3762173 / 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
Rfree0.28 905 5.1 %RANDOM
Rwork0.224 ---
obs-17661 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.7591 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 144.24 Å2 / Biso mean: 58.6375 Å2 / Biso min: 17.65 Å2
Baniso -1Baniso -2Baniso -3
1--15.83 Å20 Å20 Å2
2--29 Å20 Å2
3----13.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 22 122 4388
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it2.472.5
X-RAY DIFFRACTIONc_mcangle_it4.123
X-RAY DIFFRACTIONc_scbond_it4.013.5
X-RAY DIFFRACTIONc_scangle_it5.944
LS refinement shellResolution: 2.81→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 134 5.1 %
Rwork0.33 2513 -
all-2647 -
obs--90 %
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 DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6sep2.parsep2.top
X-RAY DIFFRACTION75ga.par5ga.top

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