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- PDB-2vdw: Guanosine N7 methyl-transferase sub-complex (D1-D12) of the vacci... -

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Basic information

Entry
Database: PDB / ID: 2vdw
TitleGuanosine N7 methyl-transferase sub-complex (D1-D12) of the vaccinia virus mRNA capping enzyme
Components
  • MRNA-CAPPING ENZYME SMALL SUBUNIT
  • VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE / S-ADENOSYL-L-METHIONINE / RNA METABOLISM / MRNA PROCESSING / METHYLTRANSFERASE / POXVIRUS / HYDROLASE / MRNA CAPPING / S-ADENOSYL HOMOCYSTEINE / D1-D12 HETERODIMER / METHYL-TRANSFERASE / MRNA CAPPING ENZYME / MULTIFUNCTIONAL ENZYME
Function / homology
Function and homology information


inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / virion component / DNA-templated transcription termination / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / virion component / DNA-templated transcription termination / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / GTP binding / RNA binding / metal ion binding
Similarity search - Function
Poxvirus mRNA capping enzyme, small subunit / mRNA-capping enzyme catalytic subunit, OB fold domain superfamily / mRNA-capping enzyme catalytic subunit, nucleotidyltransferase domain superfamily / mRNA-capping enzyme catalytic subunit, RNA triphosphatase domain superfamily / : / : / mRNA capping enzyme catalytic subunit, GTase, NTPase domain / mRNA-capping enzyme catalytic subunit, GTase, OB fold / Poxvirus mRNA capping enzyme, small subunit / Poxvirus mRNA capping enzyme, small subunit superfamily ...Poxvirus mRNA capping enzyme, small subunit / mRNA-capping enzyme catalytic subunit, OB fold domain superfamily / mRNA-capping enzyme catalytic subunit, nucleotidyltransferase domain superfamily / mRNA-capping enzyme catalytic subunit, RNA triphosphatase domain superfamily / : / : / mRNA capping enzyme catalytic subunit, GTase, NTPase domain / mRNA-capping enzyme catalytic subunit, GTase, OB fold / Poxvirus mRNA capping enzyme, small subunit / Poxvirus mRNA capping enzyme, small subunit superfamily / Poxvirus mRNA capping enzyme, small subunit / mRNA capping enzyme, large subunit, ATPase/guanylyltransferase, virus / mRNA capping enzyme catalytic subunit, RNA triphosphatase domain / mRNA (guanine-N(7))-methyltransferase domain / mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56) domain profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / mRNA-capping enzyme catalytic subunit / mRNA-capping enzyme regulatory subunit OPG124
Similarity search - Component
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsDe la Pena, M. / Kyrieleis, O.J.P. / Cusack, S.
CitationJournal: Embo J. / Year: 2007
Title: Structural Insights Into the Mechanism and Evolution of the Vaccinia Virus Mrna CAP N7 Methyl- Transferase.
Authors: De La Pena, M. / Kyrieleis, O.J.P. / Cusack, S.
History
DepositionOct 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT
B: MRNA-CAPPING ENZYME SMALL SUBUNIT
C: VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT
D: MRNA-CAPPING ENZYME SMALL SUBUNIT
E: VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT
F: MRNA-CAPPING ENZYME SMALL SUBUNIT
G: VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT
H: MRNA-CAPPING ENZYME SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,22323
Polymers272,6298
Non-polymers2,59415
Water00
1
A: VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT
B: MRNA-CAPPING ENZYME SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6384
Polymers68,1572
Non-polymers4802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-25.2 kcal/mol
Surface area30750 Å2
MethodPQS
2
C: VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT
D: MRNA-CAPPING ENZYME SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7345
Polymers68,1572
Non-polymers5773
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-25.4 kcal/mol
Surface area30900 Å2
MethodPQS
3
E: VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT
F: MRNA-CAPPING ENZYME SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8306
Polymers68,1572
Non-polymers6734
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-23.5 kcal/mol
Surface area30250 Å2
MethodPQS
4
G: VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT
H: MRNA-CAPPING ENZYME SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0228
Polymers68,1572
Non-polymers8656
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-23.3 kcal/mol
Surface area30800 Å2
MethodPQS
Unit cell
Length a, b, c (Å)60.890, 61.020, 225.780
Angle α, β, γ (deg.)94.22, 92.95, 108.26
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12E
22G
13B
23D
14H
24F
15H
25F
16B
26D
17A
27C
18B
28D
19B
29D
110F
210H
111F
211H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYVALVAL1AA563 - 66621 - 124
21GLYGLYVALVAL1CC563 - 66621 - 124
12GLYGLYARGARG1EE563 - 84421 - 302
22GLYGLYARGARG1GG563 - 84421 - 302
13METMETLYSLYS1BB1 - 881 - 88
23METMETLYSLYS1DD1 - 881 - 88
14THRTHRLEULEU1HH124 - 287124 - 287
24THRTHRLEULEU1FF124 - 287124 - 287
15METMETARGARG1HH1 - 921 - 92
25METMETARGARG1FF1 - 921 - 92
16THRTHRLEULEU1BB124 - 287124 - 287
26THRTHRLEULEU1DD124 - 287124 - 287
17LYSLYSARGARG1AA671 - 844129 - 302
27LYSLYSARGARG1CC671 - 844129 - 302
18ASPASPALAALA1BB97 - 10597 - 105
28ASPASPALAALA1DD97 - 10597 - 105
19LYSLYSASPASP1BB108 - 115108 - 115
29LYSLYSASPASP1DD108 - 115108 - 115
110ALAALASERSER1FF98 - 10498 - 104
210ALAALASERSER1HH98 - 10498 - 104
111ARGARGARGARG3FF106 - 114106 - 114
211ARGARGARGARG3HH106 - 114106 - 114

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

NCS oper:
IDCodeMatrixVector
1given(0.314267, -0.949334, -0.001133), (-0.949335, -0.314267, 1.7E-5), (-0.000372, 0.00107, -0.999999)-0.2583, -0.3616, -54.4296
2given(0.884017, -0.059359, 0.46367), (-0.016912, 0.987194, 0.158624), (-0.467148, -0.148068, 0.871693)-12.1819, 13.3997, -59.176
3given(0.336242, -0.819562, -0.463961), (-0.941718, -0.298057, -0.15598), (-0.010452, 0.489367, -0.872015)-37.6043, 4.6511, -106.4154

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Components

#1: Protein
VACCINIA VIRUS CAPPING ENZYME D1 SUBUNIT


Mass: 34760.551 Da / Num. of mol.: 4
Fragment: C-TERMINAL METHYL-TRANSFERASE DOMAIN, RESIDUES 545-844
Source method: isolated from a genetically manipulated source
Details: ADDITIONAL GLY-ALA PRECEDING ASP545 OF D1 / Source: (gene. exp.) VACCINIA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR(DE3) / Variant (production host): PLYSS / References: UniProt: P04298, mRNA guanylyltransferase
#2: Protein
MRNA-CAPPING ENZYME SMALL SUBUNIT / MRNA-GUANINE-N / 7- METHYLTRANSFERASE / MRNA CAP METHYLTRANSFERASE / VACCINIA VIRUS CAPPING ENZYME ...MRNA-GUANINE-N / 7- METHYLTRANSFERASE / MRNA CAP METHYLTRANSFERASE / VACCINIA VIRUS CAPPING ENZYME D12 SUBUNIT


Mass: 33396.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR(DE3) / Variant (production host): PLYSS
References: UniProt: P04318, mRNA (guanine-N7)-methyltransferase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
Nonpolymer detailsSULFATE ION (SO4): FROM CRYSTALLISATION MEDIUM
Sequence detailsADDITIONAL GA AT N-TERMINUS OF CONSTRUCT FROM CLEAVABLE HIS-TAG.

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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: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 6.5
Details: 10% PEG 4000, 0.1 M HEPES PH 6.5, 0.2 M LITHIUM SULPHATE, 0.3 M AMMONIUM SULPHATE, 5MM ADOHCY, 5MM GDP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.7→48.4 Å / Num. obs: 75699 / % possible obs: 89.7 % / Observed criterion σ(I): 0 / Redundancy: 1.87 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.31
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.94 / % possible all: 79.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.7→48.39 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.866 / SU B: 32.826 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3818 5 %RANDOM
Rwork0.223 ---
obs0.225 71880 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.04 Å2-0.05 Å2
2---1.34 Å2-0.18 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18637 0 159 0 18796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02219166
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213190
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.97525866
X-RAY DIFFRACTIONr_angle_other_deg0.851332084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51352260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05923.749891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.977153507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.70315120
X-RAY DIFFRACTIONr_chiral_restr0.0690.22899
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024022
X-RAY DIFFRACTIONr_nbd_refined0.2120.24007
X-RAY DIFFRACTIONr_nbd_other0.1840.213395
X-RAY DIFFRACTIONr_nbtor_refined0.1880.29327
X-RAY DIFFRACTIONr_nbtor_other0.0870.210518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2403
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4661.514790
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.551218542
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.87839320
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3494.57324
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
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1356tight positional0.020.05
2E3644tight positional0.020.05
3B1212tight positional0.020.05
4H2298tight positional0.020.05
5H1283tight positional0.020.05
6B2298tight positional0.020.05
7A2400tight positional0.020.05
8B88tight positional0.030.05
9B146tight positional0.020.05
10F69tight positional0.020.05
11F54tight positional0.030.05
11F116loose positional0.455
1A1356tight thermal0.050.5
2E3644tight thermal0.050.5
3B1212tight thermal0.040.5
4H2298tight thermal0.050.5
5H1283tight thermal0.050.5
6B2298tight thermal0.050.5
7A2400tight thermal0.050.5
8B88tight thermal0.060.5
9B146tight thermal0.030.5
10F69tight thermal0.070.5
11F54tight thermal0.070.5
11F116loose thermal0.5510
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.392 254
Rwork0.329 4727
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)
11.5526-0.6780.18271.9782-0.47393.21130.046-0.06370.0268-0.16870.0160.04650.0959-0.0934-0.0619-0.16790.00660.0015-0.25950.0069-0.18983.7523-11.001711.1943
22.84270.63050.02333.2864-0.4352.315-0.01930.0838-0.0126-0.2280.0697-0.0301-0.2539-0.1723-0.05040.00650.0766-0.0282-0.183-0.0126-0.2527-4.884111.3324-12.0077
32.2587-0.3577-0.30321.34360.14733.19850.0632-0.0934-0.0036-0.0676-0.00660.0242-0.11240.1273-0.0566-0.2674-0.05040.0147-0.168-0.014-0.18511.3466-0.3817-65.6226
42.59740.997-0.35013.2469-0.16562.55580.1684-0.13780.04960.201-0.09910.0894-0.073-0.3622-0.0693-0.232-0.01120.03520.0462-0.0407-0.2277-12.53710.772-42.4313
52.0146-0.94180.13313.1848-0.13812.815-0.1491-0.3124-0.15430.50080.25430.08630.2586-0.1979-0.10510.06390.05920.0313-0.12120.03-0.1422-17.8061-35.316964.3779
63.58390.6621.3312.01970.14262.9178-0.02790.05040.22450.10260.0502-0.0208-0.3280.0378-0.0223-0.08580.08050.0336-0.2582-0.0088-0.1989-15.5632-9.386244.1314
73.9953-0.48950.2141.55050.22722.94230.12310.57660.1501-0.223-0.0474-0.0792-0.26480.2633-0.0757-0.1633-0.03710.03380.05780.0509-0.126327.50727.3338-118.5753
81.5320.0536-0.18543.78641.07072.7326-0.06620.0481-0.06450.00660.08510.17450.1512-0.2322-0.0189-0.30290.00830.0158-0.03650.0221-0.19273.975217.6592-98.4558
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A545 - 844
2X-RAY DIFFRACTION2B1 - 287
3X-RAY DIFFRACTION3C545 - 844
4X-RAY DIFFRACTION4D1 - 287
5X-RAY DIFFRACTION5E545 - 844
6X-RAY DIFFRACTION6F1 - 287
7X-RAY DIFFRACTION7G545 - 844
8X-RAY DIFFRACTION8H1 - 287

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