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

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Basic information

Entry
Database: PDB / ID: 3oij
TitleCrystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 2 molecules of cognate RNA
Components
  • 5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3'
  • Essential 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 / nuclear microtubule / rRNA (pseudouridine) methyltransferase activity / 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 / 90S preribosome / 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) ...rRNA small subunit pseudouridine methyltransferase Nep1 / nuclear microtubule / rRNA (pseudouridine) methyltransferase activity / 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 / 90S preribosome / 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 / 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 / RNA / RNA (> 10) / Ribosomal RNA small subunit methyltransferase NEP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsThomas, S.R. / 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 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
C: 5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3'
D: 5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6567
Polymers64,8624
Non-polymers7933
Water1,09961
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-24 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.377, 91.860, 96.931
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: RNA chain 5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3'


Mass: 4437.699 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Cognate RNA fragment synthesized to mimic natural RNA substrate
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05M MES, 15mM MgS04, 7% PEG 4000, 20% glycerol, pH 6.0, 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: 2.9→30 Å / Num. all: 17064 / Num. obs: 16553 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Χ2: 0.824 / Net I/σ(I): 21.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-32.90.36112650.49276.5
3-3.124.10.29315940.52294.6
3.12-3.275.70.26316560.56898.7
3.27-3.446.90.18916820.64199.9
3.44-3.657.20.13316900.743100
3.65-3.937.30.09716800.91100
3.93-4.337.20.0816940.961100
4.33-4.957.20.07217251.03899.9
4.95-6.2370.06117310.856100
6.23-306.70.04918361.0199.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V3J

2v3j


Resolution: 3→29.886 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7812 / SU ML: 0.35 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 761 4.97 %
Rwork0.1864 --
all0.1901 15321 -
obs0.1901 15321 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.289 Å2 / ksol: 0.274 e/Å3
Displacement parametersBiso max: 169.32 Å2 / Biso mean: 70.9897 Å2 / Biso min: 20.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.487 Å20 Å20 Å2
2--1.0985 Å2-0 Å2
3---0.3885 Å2
Refinement stepCycle: LAST / Resolution: 3→29.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 586 51 61 4062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084125
X-RAY DIFFRACTIONf_angle_d1.295707
X-RAY DIFFRACTIONf_chiral_restr0.078702
X-RAY DIFFRACTIONf_plane_restr0.004609
X-RAY DIFFRACTIONf_dihedral_angle_d18.5171647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0001-3.23140.37491420.24352780292296
3.2314-3.55620.29811750.204628663041100
3.5562-4.06960.22561320.160929183050100
4.0696-5.12310.19941440.13629523096100
5.1231-29.88710.26951680.204230443212100
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)
12.034-0.02351.40971.45330.16943.8348-0.048-0.01880.21140.1150.1047-0.176-0.3019-0.5095-0.02720.15770.19450.00770.21050.07240.127218.03494.43178.2072
22.0831-0.37480.74812.66140.53611.87520.0591-0.0959-0.02920.1959-0.0912-0.23740.09810.0794-0.00370.23780.0466-0.06760.21060.01620.205438.9785-5.065821.4929
32.47830.9614-0.83020.3807-0.27110.20740.2827-0.4377-0.91680.203-0.57370.30280.6596-1.0623-0.05250.6923-0.2432-0.11250.5293-0.14930.663715.0497-21.396815.0301
41.96340.4051-0.48042.05570.49930.6260.26510.6805-0.3863-0.2381-0.2082-0.31590.60860.017-0.09310.63720.28980.12110.7231-0.18880.569342.585-7.7645-4.6446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:252)A27 - 252
2X-RAY DIFFRACTION2(chain B and resid 28:252)B28 - 252
3X-RAY DIFFRACTION3(chain C and resid 1:14)C1 - 14
4X-RAY DIFFRACTION4(chain D and resid 1:14)D1 - 14

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