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- PDB-2c46: CRYSTAL STRUCTURE OF THE HUMAN RNA guanylyltransferase and 5'- ph... -

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Basic information

Entry
Database: PDB / ID: 2c46
TitleCRYSTAL STRUCTURE OF THE HUMAN RNA guanylyltransferase and 5'- phosphatase
ComponentsMRNA CAPPING ENZYMEMRNA guanylyltransferase
KeywordsTRANSFERASE / PHOSPHATASE / HYDROLASE / MRNA PROCESSING / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE
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 / protein tyrosine/serine/threonine 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 / 7-methylguanosine mRNA capping ...RNA guanylyltransferase activity / inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / protein tyrosine/serine/threonine 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 / 7-methylguanosine mRNA capping / RNA processing / dephosphorylation / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
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 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily ...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 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDebreczeni, J. / Johansson, C. / Longman, E. / Gileadi, O. / SavitskySmee, P. / Smee, C. / Bunkoczi, G. / Ugochukwu, E. / von Delft, F. / Sundstrom, M. ...Debreczeni, J. / Johansson, C. / Longman, E. / Gileadi, O. / SavitskySmee, P. / Smee, C. / Bunkoczi, G. / Ugochukwu, E. / von Delft, F. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of the Human RNA Guanylyltransferase and 5'-Phosphatase
Authors: Debreczeni, J. / Johansson, C. / Longman, E. / Gileadi, O. / Savitskysmee, P. / Smee, C. / Bunkoczi, G. / Ugochukwu, E. / von Delft, F. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C. / Edwards, A. / Knapp, S.
History
DepositionOct 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 5, 2012Group: Database references / Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)110,7534
Polymers110,7534
Non-polymers00
Water8,287460
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MRNA CAPPING ENZYME


Theoretical massNumber of molelcules
Total (without water)27,6881
Polymers27,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: MRNA CAPPING ENZYME


Theoretical massNumber of molelcules
Total (without water)27,6881
Polymers27,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: MRNA CAPPING ENZYME


Theoretical massNumber of molelcules
Total (without water)27,6881
Polymers27,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: MRNA CAPPING ENZYME


Theoretical massNumber of molelcules
Total (without water)27,6881
Polymers27,6881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 161.600, 60.700
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.25252, -0.00603, -0.96757), (-0.01609, -0.99987, 0.00203), (-0.96746, 0.01506, -0.25258)10.41836, -31.93671, 8.84349
2given(0.24694, 0.00835, 0.96899), (0.01351, 0.99984, -0.01206), (-0.96894, 0.01607, 0.24679)4.83173, 39.30937, 12.57283
3given(0.86098, 0.01896, 0.50829), (0.02088, -0.99978, 0.00194), (0.50822, 0.00894, -0.86118)0.60225, -72.99242, 0.5283

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Components

#1: Protein
MRNA CAPPING ENZYME / MRNA guanylyltransferase / HUMAN RNA GUANYLYLTRANSFERASE AND 5'-PHOSPHATASE / HCE / HCAP1


Mass: 27688.188 Da / Num. of mol.: 4 / Fragment: TPASE REGION, RESIDUES 1-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O60942, mRNA guanylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL MHHHHHHSSGVDLGTENLYFQS IS AN UNCLEAVED HIS TAG CLONING ARTEFACT

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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: 44.6 %
Crystal growDetails: 2 M POTASSIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.6→47.9 Å / Num. obs: 133485 / % possible obs: 90.4 % / Observed criterion σ(I): 3 / Redundancy: 3.79 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.29
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.71 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I9S

1i9s


Resolution: 1.6→80.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.64 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 6714 5 %RANDOM
Rwork0.204 ---
obs0.206 126725 90.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0.12 Å2
2--0.82 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→80.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6215 0 0 460 6675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226442
X-RAY DIFFRACTIONr_bond_other_d0.0020.025720
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9658753
X-RAY DIFFRACTIONr_angle_other_deg0.892313283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78423.694314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.109151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7921547
X-RAY DIFFRACTIONr_chiral_restr0.1020.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021352
X-RAY DIFFRACTIONr_nbd_refined0.2040.21373
X-RAY DIFFRACTIONr_nbd_other0.1790.25673
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23181
X-RAY DIFFRACTIONr_nbtor_other0.0820.23557
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1070.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.54047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08326372
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.61232715
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4214.52374
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.362 437
Rwork0.301 8334
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.18810.00340.92121.718-0.66832.86030.04020.0364-0.0089-0.0632-0.01610.14830.0087-0.052-0.0241-0.2276-0.0183-0.002-0.1592-0.0154-0.1664-19.2616-53.4159-9.1112
21.8683-0.660.17641.564-0.35725.0489-0.04080.03490.07080.1425-0.0625-0.0159-0.04270.0080.1033-0.2502-0.0142-0.0078-0.2172-0.0103-0.1444-6.026822.409228.6762
31.8958-0.2824-0.82663.1508-0.12424.0111-0.0530.0174-0.1114-0.0998-0.1013-0.15690.11940.07220.15440.0774-0.02890.0104-0.1844-0.0053-0.0873-9.1667-14.327627.9593
42.24840.8635-0.15833.2288-0.50243.57890.0944-0.00720.17320.2569-0.10230.3505-0.2168-0.07030.00780.0788-0.01410.1005-0.1165-0.0456-0.0364-15.3408-20.7059-0.8801
54.2065-0.4641-1.85983.40540.06612.25720.3218-0.02720.56250.1513-0.00431.0316-0.437-0.8827-0.31750.15620.09440.10760.2298-0.01740.4365-31.1919-18.0438-2.8708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 199
2X-RAY DIFFRACTION2B20 - 199
3X-RAY DIFFRACTION3C19 - 199
4X-RAY DIFFRACTION4D29 - 56
5X-RAY DIFFRACTION4D120 - 200
6X-RAY DIFFRACTION5D59 - 113

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