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- PDB-3s24: Crystal structure of human mRNA guanylyltransferase -

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Basic information

Entry
Database: PDB / ID: 3s24
TitleCrystal structure of human mRNA guanylyltransferase
ComponentsmRNA-capping enzyme
KeywordsHYDROLASE / TRANSFERASE / Capping enzyme / CE / HCE / GTASE / M7GPPPN CAP / GT/DNA ligase fold / transcription factor Spt5 / CTD
Function / homology
Function and homology information


RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / phosphoprotein phosphatase activity / 7-methylguanosine mRNA capping ...RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / phosphoprotein phosphatase activity / 7-methylguanosine mRNA capping / RNA processing / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
mRNA Capping Enzyme; Chain / mRNA Capping Enzyme; domain 3 / 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 ...mRNA Capping Enzyme; Chain / mRNA Capping Enzyme; domain 3 / 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 profile. / Dual specificity protein phosphatase domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Nucleic acid-binding proteins / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0137 Å
AuthorsDas, K. / Chu, C. / Thyminski, J.R. / Bauman, J.D. / Guan, R. / Qiu, W. / Montelione, G.T. / Arnold, E. / Shatkin, A.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of the guanylyltransferase domain of human mRNA capping enzyme.
Authors: Chu, C. / Das, K. / Tyminski, J.R. / Bauman, J.D. / Guan, R. / Qiu, W. / Montelione, G.T. / Arnold, E. / Shatkin, A.J.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: 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_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_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: mRNA-capping enzyme
D: mRNA-capping enzyme
E: mRNA-capping enzyme
G: mRNA-capping enzyme
F: mRNA-capping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,40312
Polymers279,9237
Non-polymers4805
Water00
1
A: mRNA-capping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3735
Polymers39,9891
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mRNA-capping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0852
Polymers39,9891
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mRNA-capping enzyme


Theoretical massNumber of molelcules
Total (without water)39,9891
Polymers39,9891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mRNA-capping enzyme


Theoretical massNumber of molelcules
Total (without water)39,9891
Polymers39,9891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: mRNA-capping enzyme


Theoretical massNumber of molelcules
Total (without water)39,9891
Polymers39,9891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
G: mRNA-capping enzyme


Theoretical massNumber of molelcules
Total (without water)39,9891
Polymers39,9891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: mRNA-capping enzyme


Theoretical massNumber of molelcules
Total (without water)39,9891
Polymers39,9891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.121, 104.658, 149.571
Angle α, β, γ (deg.)90.00, 94.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
mRNA-capping enzyme / HCAP1 / HCE / Polynucleotide 5'-triphosphatase / mRNA 5'capping / TPase / mRNA guanylyltransferase / GTase


Mass: 39988.984 Da / Num. of mol.: 7 / Fragment: UNP Residues 229-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNGTT, CAP1A / Plasmid: pET20b / Production host: Escherichia coli (E. coli)
References: UniProt: O60942, polynucleotide 5'-phosphatase, mRNA guanylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.7 M ammonium sulfate, 10% glucose, 5 mM 2-mercaptoethanol, 5 mM MgCl2, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2009
RadiationMonochromator: tungsten-boron-carbide multilayer flms grown on silicon
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 53410 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 1.2 / Num. unique all: 4128 / % possible all: 74.8

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CKN

1ckn


Resolution: 3.0137→35.427 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 33.13 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2724 5.1 %RANDOM
Rwork0.2578 ---
all0.2598 56119 --
obs0.2598 53386 95.13 %-
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.474 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-72.6435 Å2-0 Å2-12.9999 Å2
2--56.5821 Å20 Å2
3---49.5149 Å2
Refinement stepCycle: LAST / Resolution: 3.0137→35.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18362 0 25 0 18387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01118775
X-RAY DIFFRACTIONf_angle_d1.43425300
X-RAY DIFFRACTIONf_dihedral_angle_d17.3067185
X-RAY DIFFRACTIONf_chiral_restr0.1072712
X-RAY DIFFRACTIONf_plane_restr0.0063284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0137-3.12130.42971900.39083737X-RAY DIFFRACTION71
3.1213-3.24620.40352590.34714686X-RAY DIFFRACTION88
3.2462-3.39390.3772540.32495090X-RAY DIFFRACTION96
3.3939-3.57260.34242660.30555249X-RAY DIFFRACTION99
3.5726-3.79620.322750.28685263X-RAY DIFFRACTION99
3.7962-4.08890.27473070.26635262X-RAY DIFFRACTION100
4.0889-4.49970.28482940.23765308X-RAY DIFFRACTION100
4.4997-5.14910.27922950.21855311X-RAY DIFFRACTION100
5.1491-6.48090.33862780.26515359X-RAY DIFFRACTION100
6.4809-35.42930.24963060.235397X-RAY DIFFRACTION99

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