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- PDB-3kyh: Saccharomyces cerevisiae Cet1-Ceg1 capping apparatus -

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Basic information

Entry
Database: PDB / ID: 3kyh
TitleSaccharomyces cerevisiae Cet1-Ceg1 capping apparatus
Components
  • mRNA-capping enzyme subunit alpha
  • mRNA-capping enzyme subunit beta
KeywordsPROTEIN BINDING / Capping / RNA / 5' modification / triphosphatase / guanylyltransferase / complex / Hydrolase / mRNA capping / mRNA processing / Nucleus / Phosphoprotein / GTP-binding / Nucleotide-binding / Nucleotidyltransferase / Transferase
Function / homology
Function and homology information


polynucleotide 5' dephosphorylation / mRNA capping enzyme complex / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / tRNA processing / 7-methylguanosine mRNA capping / positive regulation of transcription elongation by RNA polymerase II / positive regulation of protein localization to nucleus / mRNA guanylyltransferase activity ...polynucleotide 5' dephosphorylation / mRNA capping enzyme complex / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / tRNA processing / 7-methylguanosine mRNA capping / positive regulation of transcription elongation by RNA polymerase II / positive regulation of protein localization to nucleus / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
mRNA capping enzyme, alpha subunit / mRNA triphosphatase Cet1-like / RNA 5'-triphosphatase Cet1/Ctl1 / mRNA capping enzyme, beta chain / mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like superfamily / mRNA Triphosphatase Cet1; Chain A / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain ...mRNA capping enzyme, alpha subunit / mRNA triphosphatase Cet1-like / RNA 5'-triphosphatase Cet1/Ctl1 / mRNA capping enzyme, beta chain / mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like superfamily / mRNA Triphosphatase Cet1; Chain A / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / CYTH-like domain superfamily / DNA ligase/mRNA capping enzyme / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Alpha-Beta Barrel / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
mRNA-capping enzyme subunit beta / mRNA-capping enzyme subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3 Å
AuthorsLima, C.D.
CitationJournal: Structure / Year: 2010
Title: Structure of the Saccharomyces cerevisiae Cet1-Ceg1 mRNA Capping Apparatus.
Authors: Gu, M. / Rajashankar, K.R. / Lima, C.D.
History
DepositionDec 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA-capping enzyme subunit beta
B: mRNA-capping enzyme subunit beta
C: mRNA-capping enzyme subunit alpha
D: mRNA-capping enzyme subunit alpha


Theoretical massNumber of molelcules
Total (without water)177,1114
Polymers177,1114
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-63 kcal/mol
Surface area66950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.993, 165.993, 172.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C D
12C D
13A B
14A B

NCS domain segments:

Dom-ID: 1 / Refine code: 3

Component-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPROCC11 - 25013 - 252
21PROPROPROPRODD11 - 25013 - 252
31VALVALMETMETCC392 - 415394 - 417
41VALVALMETMETDD392 - 415394 - 417
12GLUGLUSERSERCC251 - 391253 - 393
22GLUGLUSERSERDD251 - 391253 - 393
13ILEILEPROPROAA268 - 43529 - 196
23ILEILEPROPROBB268 - 43529 - 196
33ILEILETYRTYRAA451 - 539212 - 300
43ILEILETYRTYRBB451 - 539212 - 300
14PROPROILEILEAA245 - 2616 - 22
24PROPROILEILEBB245 - 2616 - 22

NCS ensembles :
ID
1
2
3
4
DetailsAuthors state that the biological unit is a HETEROTETRAMER. Chains A and B form a HOMODIMER. Chain A interacts extensively with Chain D and Chain B interacts extensively with Chain C. The protein was purified as a HETEROTETRAMER by gel filtration.

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Components

#1: Protein mRNA-capping enzyme subunit beta / Polynucleotide 5'-triphosphatase / mRNA 5'-triphosphatase / TPase


Mass: 35525.305 Da / Num. of mol.: 2 / Fragment: Triphosphatase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: W303-1A / Gene: CET1, P1433, YPL228W / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 CP RIL / References: UniProt: O13297, polynucleotide 5'-phosphatase
#2: Protein mRNA-capping enzyme subunit alpha / mRNA guanylyltransferase / GTP--RNA guanylyltransferase / GTase


Mass: 53030.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: W303-1A / Gene: CEG1, G2853, YGL130W / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 CP RIL / References: UniProt: Q01159, mRNA guanylyltransferase

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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: 3.87 Å3/Da / Density % sol: 68.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.0 M ammonium citrate, 0.1 M sodium citrate, 1.0% PEG (polyethylene glycerol) 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.514
11h+k,-k,-l20.486
ReflectionResolution: 3→25 Å / Num. obs: 52300 / % possible obs: 97.7 % / Observed criterion σ(I): -0.5 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.7
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.9 / % possible all: 93.9

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Phasing

PhasingMethod: MIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MIRAS / Resolution: 3→19.98 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.839 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.904 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29801 2465 4.8 %RANDOM
Rwork0.24925 ---
obs0.2516 48524 95.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 79.011 Å2
Baniso -1Baniso -2Baniso -3
1-35.39 Å20 Å20 Å2
2--35.39 Å20 Å2
3----70.78 Å2
Refinement stepCycle: LAST / Resolution: 3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10696 0 0 0 10696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210932
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3691.97314796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.27651314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.17924.549510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.125151986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1081566
X-RAY DIFFRACTIONr_chiral_restr0.1780.21654
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0218188
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.7371.56648
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.984210842
X-RAY DIFFRACTIONr_scbond_it14.41434284
X-RAY DIFFRACTIONr_scangle_it19.3624.53954
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
1C1056TIGHT POSITIONAL0.310.05
1D1066LOOSE POSITIONAL0.445
1C1056TIGHT THERMAL7.980.5
1D1066LOOSE THERMAL12.210
2C492TIGHT POSITIONAL0.30.05
2D523LOOSE POSITIONAL0.435
2C492TIGHT THERMAL3.40.5
2D523LOOSE THERMAL5.5210
3A976TIGHT POSITIONAL0.250.05
3B982LOOSE POSITIONAL0.45
3A976TIGHT THERMAL8.130.5
3B982LOOSE THERMAL12.210
4A68TIGHT POSITIONAL0.370.05
4B75LOOSE POSITIONAL0.55
4A68TIGHT THERMAL11.390.5
4B75LOOSE THERMAL12.5910
LS refinement shellResolution: 3→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 160 -
Rwork0.238 3024 -
obs--81.87 %

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