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- PDB-4ckb: Vaccinia virus capping enzyme complexed with GTP and SAH -

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Basic information

Entry
Database: PDB / ID: 4ckb
TitleVaccinia virus capping enzyme complexed with GTP and SAH
Components
  • MRNA-CAPPING ENZYME CATALYTIC SUBUNIT
  • MRNA-CAPPING ENZYME REGULATORY SUBUNIT
KeywordsTRANSFERASE/HYDROLASE / TRANSFERASE-HYDROLASE COMPLEX / TRIFUNCTIONAL VACCINIA VIRUS MRNA CAPPING 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
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #830 / mRNA Triphosphatase Cet1; Chain A - #20 / D-amino Acid Aminotransferase; Chain A, domain 1 - #140 / 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 ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #830 / mRNA Triphosphatase Cet1; Chain A - #20 / D-amino Acid Aminotransferase; Chain A, domain 1 - #140 / 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 / mRNA capping enzyme, large subunit, ATPase/guanylyltransferase, virus / mRNA capping enzyme catalytic subunit, RNA triphosphatase domain / Poxvirus mRNA capping enzyme, small subunit / Poxvirus mRNA capping enzyme, small subunit superfamily / Poxvirus mRNA capping enzyme, small subunit / mRNA Triphosphatase Cet1; Chain A / 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. / D-amino Acid Aminotransferase; Chain A, domain 1 / Vaccinia Virus protein VP39 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Barrel / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKyrieleis, O.J.P. / Chang, J. / de la Pena, M. / Shuman, S. / Cusack, S.
CitationJournal: Structure / Year: 2014
Title: Crystal Structure of Vaccinia Virus Mrna Capping Enzyme Provides Insights Into the Mechanism and Evolution of the Capping Apparatus.
Authors: Kyrieleis, O.J.P. / Chang, J. / De La Pena, M. / Shuman, S. / Cusack, S.
History
DepositionJan 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MRNA-CAPPING ENZYME CATALYTIC SUBUNIT
B: MRNA-CAPPING ENZYME REGULATORY SUBUNIT
D: MRNA-CAPPING ENZYME CATALYTIC SUBUNIT
E: MRNA-CAPPING ENZYME REGULATORY SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,7997
Polymers260,5074
Non-polymers1,2923
Water45025
1
D: MRNA-CAPPING ENZYME CATALYTIC SUBUNIT
E: MRNA-CAPPING ENZYME REGULATORY SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1614
Polymers130,2532
Non-polymers9082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-19.4 kcal/mol
Surface area48160 Å2
MethodPISA
2
A: MRNA-CAPPING ENZYME CATALYTIC SUBUNIT
B: MRNA-CAPPING ENZYME REGULATORY SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,6383
Polymers130,2532
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-19.4 kcal/mol
Surface area48400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.340, 197.730, 61.110
Angle α, β, γ (deg.)90.13, 109.27, 94.05
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D
13A
23D
14B
24E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 197
2111D1 - 197
1211A204 - 221
2211D204 - 221
1122A222 - 320
2122D222 - 320
1222A324 - 407
2222D324 - 407
1322A413 - 527
2322D413 - 527
1131A544 - 728
2131D544 - 728
1231A735 - 844
2231D735 - 844
1141B1 - 287
2141E1 - 287

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.986259, -0.164926, 0.009643), (-0.164909, 0.986306, 0.002518), (-0.009926, 0.000893, -0.99995)-60.19046, 89.11481, 18.4209
3given(1), (1), (1)
4given(-0.986536, -0.163521, 0.002881), (-0.163523, 0.986539, -0.000399), (-0.002777, -0.000864, -0.999996)-60.11407, 89.28198, 18.62575
5given(1), (1), (1)
6given(-0.992491, -0.122202, -0.005247), (-0.12223, 0.992488, 0.00522), (0.004569, 0.005822, -0.999973)-57.46082, 91.51631, 19.42024
7given(1), (1), (1)
8given(-0.991299, -0.131421, 0.007444), (-0.131426, 0.991326, -0.00016), (-0.007358, -0.001137, -0.999972)-58.36908, 90.97787, 18.37049

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Components

#1: Protein MRNA-CAPPING ENZYME CATALYTIC SUBUNIT / VIRUS TERMINATION FACTOR LARGE SUBUNIT / VTF LARGE SUBUNIT / MRNA-CAPPING ENZYME 97 KDA SUBUNIT / ...VIRUS TERMINATION FACTOR LARGE SUBUNIT / VTF LARGE SUBUNIT / MRNA-CAPPING ENZYME 97 KDA SUBUNIT / MRNA-CAPPING ENZYME D1 SUBUNIT / MRNA-CAPPING ENZYME LARGE SUBUNIT / POLYNUCLEOTIDE 5'-TRIPHOSPHATASE / MRNA 5'-TRIPHOSPHATASE / TPASE / MRNA GUANYLYLTRANSFERASE / GTP--RNA GUANYLYLTRANSFERASE / GTASE / MRNA (GUANINE-N(7)-)-METHYLTRANSFERASE / MRNA CAP METHYLTRANSFERASE


Mass: 96856.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS
References: UniProt: P04298, polynucleotide 5'-phosphatase, mRNA guanylyltransferase, mRNA (guanine-N7)-methyltransferase
#2: Protein MRNA-CAPPING ENZYME REGULATORY SUBUNIT / VIRUS TERMINATION FACTOR SMALL SUBUNIT / VTF SMALL SUBUNIT / MRNA-CAPPING ENZYME 33 KDA SUBUNIT / ...VIRUS TERMINATION FACTOR SMALL SUBUNIT / VTF SMALL SUBUNIT / MRNA-CAPPING ENZYME 33 KDA SUBUNIT / MRNA-CAPPING ENZYME D12 SUBUNIT / MRNA-CAPPING ENZYME SMALL SUBUNIT


Mass: 33396.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS / References: UniProt: P04318
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.7 Å3/Da / Density % sol: 54.4 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN SOLUTION AT 4 MG/ML IN 40 MM TRIS-HCL, PH 8.0, 200 MM NACL, 5 MM DTT WITH 100 MM GTP, 5 MM MANGANESE CHLORIDE, AND 5 MM ADOMET. RESERVOIR SOLUTION 0.1 M CITRIC ACID, PH 6.5, 1.2 M LICL, 6% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 62966 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.37 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.75
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.31 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.43 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VDW

2vdw


Resolution: 2.8→49.2 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 44.995 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25477 3184 5.1 %RANDOM
Rwork0.20889 ---
obs0.21118 59782 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.694 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å2-0.98 Å23.06 Å2
2---4.25 Å2-0.64 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17754 0 84 25 17863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01918193
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217671
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.97624596
X-RAY DIFFRACTIONr_angle_other_deg0.7340744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21752176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23824.375816
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.935153372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3591592
X-RAY DIFFRACTIONr_chiral_restr0.0610.22816
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024065
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9154.5388755
X-RAY DIFFRACTIONr_mcbond_other1.9154.5388754
X-RAY DIFFRACTIONr_mcangle_it3.3476.79710914
X-RAY DIFFRACTIONr_mcangle_other3.3476.79710915
X-RAY DIFFRACTIONr_scbond_it1.7354.7059438
X-RAY DIFFRACTIONr_scbond_other1.7314.6989426
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0766.96213663
X-RAY DIFFRACTIONr_long_range_B_refined5.57234.97320022
X-RAY DIFFRACTIONr_long_range_B_other5.55634.9520015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21A3027medium positional0.020.5
22D3027medium positional0.020.5
11A3377tight thermal14.480.5
12D3377tight thermal14.480.5
21A1744tight thermal12.430.5
22D1744tight thermal12.430.5
31A4587tight thermal7.250.5
32D4587tight thermal7.250.5
41B4630tight thermal15.430.5
42E4630tight thermal15.430.5
21A3027medium thermal12.612
22D3027medium thermal12.612
LS refinement shellResolution: 2.804→2.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 212 -
Rwork0.364 4316 -
obs--93.92 %
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)
10.50450.44530.44651.47710.820.6033-0.11430.03630.02730.28580.06750.1266-0.0909-00.04680.72760.10320.21520.1109-0.08150.2315-14.29768.70320.045
21.53730.03550.45330.2652-0.461.24090.01850.03890.0704-0.1183-0.0685-0.0177-0.01690.02860.05010.29350.0252-0.02010.31980.07830.3349-41.841-27.643-1.313
30.55330.09440.04911.05740.3070.58830.17210.1020.057-0.2308-0.04080.0137-0.0648-0.0696-0.13130.55440.02510.06450.13140.00270.212-15.52949.792-6.266
40.13770.0626-0.37941.6199-0.25771.80430.0885-0.0442-0.1035-0.0158-0.0028-0.0563-0.32830.165-0.08560.3099-0.0501-0.00410.3573-0.02660.2661-2.4817.5559.584
50.4104-0.462-0.78421.45120.49081.9941-0.15720.0954-0.19190.1525-0.25980.23120.0259-0.06080.4170.3458-0.10360.14070.1556-0.07550.4179-45.566-80.1679.18
61.6418-0.07630.04820.405-0.35520.57850.0742-0.196-0.15060.0446-0.05230.0142-0.03860.0369-0.02190.216-0.012-0.05130.3640.0260.3408-37.423-46.19624.944
71.8642-1.058-0.29011.2461-0.4290.8986-0.04130.0934-0.11010.0730.0102-0.0335-0.0484-0.1720.03110.2540.0342-0.04860.404-0.01660.2477-21.733-2.14727.539
80.73780.3796-0.23382.06910.85521.25120.0625-0.11120.172-0.1174-0.203-0.11020.21870.30590.14050.4150.04030.28210.27460.07080.3311-24.146-97.131-8.895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 221
2X-RAY DIFFRACTION2D1 - 221
3X-RAY DIFFRACTION3A222 - 528
4X-RAY DIFFRACTION4A544 - 844
5X-RAY DIFFRACTION4A1845
6X-RAY DIFFRACTION5D544 - 844
7X-RAY DIFFRACTION5D1845
8X-RAY DIFFRACTION6D222 - 528
9X-RAY DIFFRACTION6D1846
10X-RAY DIFFRACTION7B1 - 287
11X-RAY DIFFRACTION8E1 - 287

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