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- PDB-4ckc: Vaccinia virus capping enzyme complexed with SAH (monoclinic form) -

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Basic information

Entry
Database: PDB / ID: 4ckc
TitleVaccinia virus capping enzyme complexed with SAH (monoclinic form)
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 / 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 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
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: 2.9 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)261,2756
Polymers260,5074
Non-polymers7692
Water1,47782
1
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 area2950 Å2
ΔGint-18.4 kcal/mol
Surface area49470 Å2
MethodPISA
2
D: MRNA-CAPPING ENZYME CATALYTIC SUBUNIT
E: 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 area2940 Å2
ΔGint-17.9 kcal/mol
Surface area49550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.710, 200.260, 128.100
Angle α, β, γ (deg.)90.00, 102.18, 90.00
Int Tables number4
Space group name H-MP1211
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
1121A222 - 317
2121D222 - 317
1221A325 - 407
2221D325 - 407
1321A415 - 530
2321D415 - 530
1131A544 - 728
2131D544 - 728
1231A735 - 844
2231D735 - 844
1141B1 - 118
2141E1 - 118
1241B125 - 287
2241E125 - 287

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999962, 0.008424, 0.002388), (-0.008459, 0.999854, 0.014856), (-0.002263, -0.014876, 0.999887)-13.01567, 12.8167, 61.41864
3given(1), (1), (1)
4given(0.999966, 0.007853, 0.002531), (-0.007879, 0.999914, 0.010507), (-0.002448, -0.010527, 0.999942)-13.04113, 12.77359, 61.70205
5given(1), (1), (1)
6given(0.999987, 0.002763, 0.004267), (-0.00275, 0.999992, -0.002915), (-0.004275, 0.002903, 0.999987)-13.256, 12.76998, 62.18256
7given(1), (1), (1)
8given(0.999999, 0.001687, -0.000356), (-0.001691, 0.999943, -0.01058), (0.000338, 0.010581, 0.999944)-13.31697, 12.71205, 62.29103

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsS-ADENOSYL-L-HOMOCYSTEINE (SAH): CO-CRYSTALLISED LIGAND

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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: 3.04 Å3/Da / Density % sol: 59.6 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN SOLUTION AT 4 MG/ML IN 40 MM TRIS-HCL, PH 8.0, 200 MM NACL, 5 MM DTT WITH 5 MM ADOMET. RESERVOIR SOLUTION: 0.1 M TRIS-HCL, PH 7.5, 0.2 M LICL, 0.2M (NH4)2SO4, 15% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 62825 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 1.88 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.05
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.13 / % possible all: 81.1

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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: 2.9→125 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.865 / SU B: 52.269 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.29706 3174 5.1 %RANDOM
Rwork0.25485 ---
obs0.25697 59652 93.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.427 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20.52 Å2
2---3.01 Å20 Å2
3---3.98 Å2
Refinement stepCycle: LAST / Resolution: 2.9→125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17909 0 52 82 18043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01918348
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217819
X-RAY DIFFRACTIONr_angle_refined_deg1.011.97224802
X-RAY DIFFRACTIONr_angle_other_deg0.699341080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34152199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47824.318829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.218153403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2531594
X-RAY DIFFRACTIONr_chiral_restr0.0550.22833
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0220244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024134
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_it0.781.7498832
X-RAY DIFFRACTIONr_mcbond_other0.781.7498831
X-RAY DIFFRACTIONr_mcangle_it1.4692.61711019
X-RAY DIFFRACTIONr_mcangle_other1.4692.61711020
X-RAY DIFFRACTIONr_scbond_it0.3821.759516
X-RAY DIFFRACTIONr_scbond_other0.3821.759516
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8092.60513784
X-RAY DIFFRACTIONr_long_range_B_refined2.46813.10320133
X-RAY DIFFRACTIONr_long_range_B_other2.46813.10420131
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 / Type: tight thermal / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A33945.73
2A47277.76
3A47432.74
4B45935.37
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 204 -
Rwork0.366 3861 -
obs--82.32 %
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)
11.2762-0.78290.89960.7349-0.50491.12660.30660.28660.0592-0.092-0.2366-0.2670.21420.2071-0.06990.2670.22210.01720.31670.10570.36380.931-65.59454.185
21.4407-0.81060.84860.5806-0.70661.79230.32520.0809-0.1272-0.2021-0.1833-0.07340.16720.2979-0.14190.27510.15860.04150.23160.16170.342814.604-78.201-8.365
31.1025-0.41430.54631.0796-0.90611.72110.12910.17430.1036-0.1947-0.17620.39130.18180.35490.04710.17850.0453-0.06370.18210.04460.326-23.11-45.94643.083
41.60340.29170.31831.3544-0.3380.40470.0674-0.1220.05720.0837-0.01150.0210.0168-0.0421-0.0560.1852-0.04550.00970.20080.09010.2533-11.588-13.28459.679
51.73870.41420.28041.4072-0.07970.25860.0602-0.3013-0.07210.0993-0.0244-0.0735-0.0501-0.0559-0.03590.1962-0.00120.02260.22040.0110.17861.754-26.066-2.402
60.5091-0.25130.10031.6281-0.7411.35240.0523-0.1086-0.0485-0.2686-0.12440.31730.06460.12530.07220.18380.0331-0.04110.05720.03670.426-9.577-58.675-19.171
71.65790.2194-0.91562.23991.19431.30260.06780.02040.1126-0.1301-0.00510.0407-0.10510.0169-0.06270.1387-0.046-0.06390.17290.10250.324112.355.0145.42
81.11950.1608-0.95942.77741.46481.86580.1550.01840.1733-0.0657-0.0116-0.0503-0.0740.021-0.14340.18970.02370.00040.135-0.01970.196725.682-7.842-16.783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 221
2X-RAY DIFFRACTION2D1 - 221
3X-RAY DIFFRACTION3A222 - 529
4X-RAY DIFFRACTION4A544 - 844
5X-RAY DIFFRACTION4A1845
6X-RAY DIFFRACTION5D544 - 844
7X-RAY DIFFRACTION5D1845
8X-RAY DIFFRACTION6D222 - 530
9X-RAY DIFFRACTION7B1 - 287
10X-RAY DIFFRACTION8E1 - 287

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