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- PDB-3oii: Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to ... -

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Basic information

Entry
Database: PDB / ID: 3oii
TitleCrystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine
ComponentsEssential for mitotic growth 1
KeywordsRIBOSOMAL PROTEIN / EMG1 / scNEP1 / SPOUT / ribosome biogenesis / methyltransferase / rRNA processing
Function / homology
Function and homology information


rRNA small subunit pseudouridine methyltransferase Nep1 / rRNA (pseudouridine) methyltransferase activity / nuclear microtubule / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA base methylation / rRNA methylation / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery ...rRNA small subunit pseudouridine methyltransferase Nep1 / rRNA (pseudouridine) methyltransferase activity / nuclear microtubule / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA base methylation / rRNA methylation / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / 90S preribosome / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / rRNA binding / nucleolus / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Ribosomal RNA small subunit methyltransferase NEP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsThomas, S.R. / Szyk, A. / LaRonde-LeBlanc, N.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
Authors: Thomas, S.R. / Keller, C.A. / Szyk, A. / Cannon, J.R. / Laronde-Leblanc, N.A.
History
DepositionAug 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Essential for mitotic growth 1
B: Essential for mitotic growth 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8485
Polymers55,9872
Non-polymers8613
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-7 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.988, 84.662, 112.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Essential for mitotic growth 1 / Nucleolar essential protein 1


Mass: 27993.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EMG1, NEP1, YLR186W, L9470.5 / Plasmid: pdest527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q06287
#2: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M Ammonium Sulfate, 0.05M Bis-Tris, 30% Pentaerythritol ethoxylate, 20% glycerol, pH 6.5, Vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.00931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2007
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00931 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 42237 / Num. obs: 39930 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Χ2: 0.585 / Net I/σ(I): 22.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.863.20.40326320.44163.1
1.86-1.944.30.3535380.5384.9
1.94-2.035.60.27940650.52397.7
2.03-2.136.90.21841210.51999.1
2.13-2.277.60.1741680.58199.3
2.27-2.447.90.12142110.57799.5
2.44-2.6980.08841820.54999.9
2.69-3.0880.06942570.57999.9
3.08-3.887.90.05242900.657100
3.88-307.60.0444660.70999.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.4.0057refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V3J

2v3j


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.066 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 1891 5.1 %RANDOM
Rwork0.1715 ---
all0.1736 37397 --
obs0.1736 37397 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.7 Å2 / Biso mean: 37.649 Å2 / Biso min: 14.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2--0.21 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 58 224 3614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223525
X-RAY DIFFRACTIONr_angle_refined_deg1.8812.0044775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1735437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91824.13138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59115681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1151523
X-RAY DIFFRACTIONr_chiral_restr0.1350.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212509
X-RAY DIFFRACTIONr_mcbond_it1.2121.52166
X-RAY DIFFRACTIONr_mcangle_it2.10423548
X-RAY DIFFRACTIONr_scbond_it3.21231359
X-RAY DIFFRACTIONr_scangle_it5.1454.51219
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 113 -
Rwork0.183 2114 -
all-2227 -
obs--81.01 %
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)
11.2866-0.00790.16711.02560.12431.5494-0.0354-0.0404-0.11050.0201-0.01350.01410.13530.01150.0489-0.0705-0.01180.0289-0.0463-0.0057-0.0306-6.80374.93-3.6461
21.8595-0.68370.80321.4480.19752.13470.19120.2278-0.2119-0.1393-0.13080.09150.33770.0966-0.0604-0.01750.0287-0.0218-0.0551-0.0519-0.0978-11.2828-6.4736-26.9515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 251
2X-RAY DIFFRACTION2B1 - 251

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