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- PDB-4cke: Vaccinia virus capping enzyme complexed with SAH in P1 form -

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Basic information

Entry
Database: PDB / ID: 4cke
TitleVaccinia virus capping enzyme complexed with SAH in P1 form
Components
  • MRNA-CAPPING ENZYME CATALYTIC SUBUNIT
  • MRNA-CAPPING ENZYME REGULATORY SUBUNIT
KeywordsTRANSFERASE / TRIFUNCTIONAL VACCINIA VIRUS MRNA CAPPING ENZYME GUANINE-N7-METHYLTRANSFERASE (MTASE)
Function / homology
Function and homology information


inorganic triphosphate phosphatase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / DNA-templated transcription termination / virion component / 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 / DNA-templated transcription termination / virion component / 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 / mRNA capping enzyme, large subunit, ATPase/guanylyltransferase, virus / Poxvirus mRNA capping enzyme, small subunit superfamily / Poxvirus mRNA capping enzyme, small subunit / mRNA capping enzyme catalytic subunit, RNA triphosphatase domain / mRNA Triphosphatase Cet1; Chain A / mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7))-methyltransferase domain / 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 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 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. 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
Water1,36976
1
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 area2990 Å2
ΔGint-18.8 kcal/mol
Surface area49230 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 area2980 Å2
ΔGint-18.7 kcal/mol
Surface area49090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.130, 62.020, 198.500
Angle α, β, γ (deg.)90.01, 85.53, 71.69
Int Tables number1
Space group name H-MP1

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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 / MRNA 5-TRIPHOSPHATASE / TPASE / GTP--RNA GUANYLYLTRANSFERASE / GTASE / MRNA CAP METHYLTRANSFERASE / VACCINIA CAPPING ENZYME D1 SUBUNIT


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 / VACCINIA CAPPING ENZYME D12 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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.8 Å3/Da / Density % sol: 56.1 % / Description: NONE
Crystal growTemperature: 293 K / pH: 6
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, 1 MM MGCL2 AND 2 MM M7GPPPG. RESERVOIR SOLUTION CONTAINS 0.1 M MES, PH 6.0, 1 M LICL, 10% PEG6000 AT 20 C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 57928 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 43.05 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.42
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.73 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VDW

2vdw


Resolution: 2.9→41.813 Å / SU ML: 0.5 / σ(F): 1.99 / Phase error: 31.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 2920 5 %
Rwork0.2552 --
obs0.2571 57927 94.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→41.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17644 0 52 76 17772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318072
X-RAY DIFFRACTIONf_angle_d0.79624428
X-RAY DIFFRACTIONf_dihedral_angle_d15.1476794
X-RAY DIFFRACTIONf_chiral_restr0.032798
X-RAY DIFFRACTIONf_plane_restr0.0033065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.94750.38431370.36742639X-RAY DIFFRACTION94
2.9475-2.99830.39141380.33952645X-RAY DIFFRACTION96
2.9983-3.05290.36121590.3362654X-RAY DIFFRACTION96
3.0529-3.11160.35851360.32332674X-RAY DIFFRACTION96
3.1116-3.1750.35421620.30932575X-RAY DIFFRACTION96
3.175-3.24410.37741440.30122715X-RAY DIFFRACTION96
3.2441-3.31950.32871500.30492620X-RAY DIFFRACTION97
3.3195-3.40250.32611420.29852662X-RAY DIFFRACTION95
3.4025-3.49440.35361230.30672511X-RAY DIFFRACTION92
3.4944-3.59720.30331440.29362707X-RAY DIFFRACTION96
3.5972-3.71320.35291150.28862530X-RAY DIFFRACTION93
3.7132-3.84590.27651380.27022680X-RAY DIFFRACTION95
3.8459-3.99970.30561220.25452549X-RAY DIFFRACTION93
3.9997-4.18160.27481280.23852609X-RAY DIFFRACTION95
4.1816-4.40180.2661350.21872657X-RAY DIFFRACTION95
4.4018-4.67730.27061490.20252603X-RAY DIFFRACTION95
4.6773-5.03790.21951760.19282587X-RAY DIFFRACTION95
5.0379-5.54380.23471290.21142669X-RAY DIFFRACTION95
5.5438-6.34360.24571340.21962597X-RAY DIFFRACTION95
6.3436-7.98320.27291450.22262605X-RAY DIFFRACTION94
7.9832-41.81760.25641140.2032519X-RAY DIFFRACTION91
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)
11.6548-0.6114-0.18331.39720.25231.65640.0589-0.25230.08890.1390.0165-0.24520.0870.1954-0.08310.957-0.2203-0.09380.5738-0.00260.354515.61632.534957.4987
21.59680.46120.38314.0038-0.26693.25710.1683-0.17520.07630.6311-0.21830.2823-0.0067-0.37060.08060.3333-0.05330.02180.1851-0.04570.23563.61538.956317.4961
30.91310.67280.16272.8104-0.27791.8029-0.0444-0.36230.29330.7196-0.0358-0.0308-0.3661-0.214-0.04050.30170.0251-0.02440.1665-0.10880.369421.184534.50418.1566
42.1156-0.0351-0.1391.4075-0.88153.37480.01860.2198-0.1845-0.23810.2555-0.19250.3368-0.7076-0.08780.17250.0581-0.01860.16720.00770.355712.432820.4471-4.1438
52.8251.11081.89934.60850.38145.46580.32421.13390.34140.0972-0.1448-1.0449-0.3440.77970.01460.3488-0.0551-0.08390.34770.02670.705334.059737.2052-6.8178
64.2912-1.23221.09313.0711-1.02595.4887-0.1460.6495-1.0762-0.40060.4454-0.05331.45280.1273-0.32090.6473-0.02010.02070.4343-0.2180.504615.018117.5481-13.7492
72.1607-0.15761.02431.2498-0.45982.8421-0.06890.176-0.29710.24090.1373-0.84580.02620.6440.06710.21270.0302-0.09860.2796-0.02620.559431.409725.75233.2473
82.6916-0.20941.00411.992-0.8021.82650.2323-0.21930.3178-0.12160.06440.08860.1711-0.88940.11320.21150.0913-0.08680.3903-0.02830.27996.955831.1912-4.1686
91.9725-1.00680.34522.4688-0.53291.94840.0039-0.2442-0.1514-0.07870.10740.24790.1866-0.3358-0.03180.1437-0.03190.01580.43460.04060.345636.615611.0458-36.5235
102.5537-0.18680.2822.3867-0.43112.6638-0.20590.20630.2411-0.22090.0952-0.1383-0.27030.29580.01960.2452-0.0680.03010.4311-0.02080.255551.796621.7364-42.0344
111.94740.2127-0.04964.16080.50223.2736-0.0954-0.0674-0.0844-0.04210.0487-0.17770.04390.36540.05580.3614-0.08070.03030.30890.01040.208847.008510.4469-80.0424
122.25360.32340.26794.38280.15631.67950.1177-0.4487-0.42170.51510.0723-0.09080.56190.09880.00440.8184-0.02440.07280.13830.03090.443628.0214-15.2536-88.4248
133.480.5215-0.91142.1449-0.02123.6785-0.19660.3511-0.0181-0.58610.28780.4540.1256-0.3805-0.04280.6546-0.162-0.06350.32750.02850.438326.5188-7.476-101.967
143.2132-0.9205-1.87782.9325-1.78443.2328-0.33540.91171.2209-0.66390.54840.3982-1.27980.5453-0.13521.0828-0.1872-0.19660.49320.19890.585332.65544.6644-109.6964
152.30760.5573-1.66141.49120.26484.077-0.13390.4597-0.10430.21390.11850.99720.4541-0.89310.08060.3454-0.07580.04630.36630.04010.592419.6316-9.2012-92.9879
162.7046-0.2029-1.39192.30390.65943.5691-0.1646-0.1012-0.02030.06010.10011.0292-0.0211-0.2677-0.04830.23390.03260.18770.2718-0.00480.660422.5045-5.7984-90.4624
176.45781.7429-1.53885.62850.14895.2552-0.40920.5966-0.856-0.84760.5366-0.94930.73791.08690.11720.54690.01780.09890.6361-0.21480.621645.0118-13.3537-114.2013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 563 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 564 THROUGH 844 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 1 THROUGH 26 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 27 THROUGH 68 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 69 THROUGH 102 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 103 THROUGH 125 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 126 THROUGH 238 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 239 THROUGH 287 )
9X-RAY DIFFRACTION9CHAIN D AND (RESID 1 THROUGH 384 )
10X-RAY DIFFRACTION10CHAIN D AND (RESID 385 THROUGH 527 )
11X-RAY DIFFRACTION11CHAIN D AND (RESID 528 THROUGH 844 )
12X-RAY DIFFRACTION12CHAIN E AND (RESID 1 THROUGH 26 )
13X-RAY DIFFRACTION13CHAIN E AND (RESID 27 THROUGH 107 )
14X-RAY DIFFRACTION14CHAIN E AND (RESID 108 THROUGH 130 )
15X-RAY DIFFRACTION15CHAIN E AND (RESID 131 THROUGH 193 )
16X-RAY DIFFRACTION16CHAIN E AND (RESID 194 THROUGH 268 )
17X-RAY DIFFRACTION17CHAIN E AND (RESID 269 THROUGH 287 )

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