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- PDB-9jgd: Crystal structure of Nep1 in complex with 5'-methylthioadenosine ... -

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Basic information

Entry
Database: PDB / ID: 9jgd
TitleCrystal structure of Nep1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii OT3
ComponentsRibosomal RNA small subunit methyltransferase Nep1
KeywordsTRANSFERASE / Conserved arginine residues / Globular loop extension / Inter-subunit interactions / Nep1 / N1-pseudouridine methyltransferase / Trefoil knot
Function / homology
Function and homology information


rRNA (pseudouridine) methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA binding
Similarity search - Function
Ribosome biogenesis methyltransferase NEP1, archaea / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
ACETATE ION / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Ribosomal RNA small subunit methyltransferase Nep1
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSaha, S. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR51982/NER/95/2011/2023 India
CitationJournal: Febs J. / Year: 2025
Title: Structural analysis of the ribosome assembly factor Nep1, an N1-specific pseudouridine methyltransferase, reveals mechanistic insights.
Authors: Saha, S. / Kanaujia, S.P.
History
DepositionSep 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase Nep1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5657
Polymers26,9261
Non-polymers6386
Water1,62190
1
A: Ribosomal RNA small subunit methyltransferase Nep1
hetero molecules

A: Ribosomal RNA small subunit methyltransferase Nep1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,12914
Polymers53,8532
Non-polymers1,27612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_454y-1/3,x+1/3,-z-2/31
Buried area6560 Å2
ΔGint-27 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.240, 113.240, 102.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-468-

HOH

21A-474-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribosomal RNA small subunit methyltransferase Nep1 / 16S rRNA (pseudouridine-N1-)-methyltransferase Nep1


Mass: 26926.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: nep1, PH1379 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: O50087, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 6 types, 96 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: Trigonal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dihydrate pH 5.6, 2.0 ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 22, 2023 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→70.97 Å / Num. obs: 13053 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.04 / Rrim(I) all: 0.141 / Χ2: 1.06 / Net I/σ(I): 13.3 / Num. measured all: 160893
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.552 / Num. measured all: 13625 / Num. unique obs: 1127 / CC1/2: 0.952 / Rpim(I) all: 0.164 / Rrim(I) all: 0.576 / Χ2: 1.45 / Net I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.4.0data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
Coot0.9.4.1model building
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→70.97 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.044 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24986 669 5.2 %RANDOM
Rwork0.18537 ---
obs0.1886 12283 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.882 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å2-0.66 Å20 Å2
2---1.32 Å20 Å2
3---4.29 Å2
Refinement stepCycle: 1 / Resolution: 2.2→70.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 41 90 2002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121949
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161932
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6682626
X-RAY DIFFRACTIONr_angle_other_deg0.5241.5824459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.915225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.936516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25310371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02419
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_it2.5962.609904
X-RAY DIFFRACTIONr_mcbond_other2.592.604903
X-RAY DIFFRACTIONr_mcangle_it4.0164.6631127
X-RAY DIFFRACTIONr_mcangle_other4.0164.6671128
X-RAY DIFFRACTIONr_scbond_it3.7683.2131045
X-RAY DIFFRACTIONr_scbond_other3.7673.2171046
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0295.6131500
X-RAY DIFFRACTIONr_long_range_B_refined9.01626.62207
X-RAY DIFFRACTIONr_long_range_B_other9.02126.552193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.57 65 -
Rwork0.538 866 -
obs--95.1 %
Refinement TLS params.Method: refined / Origin x: -16.4452 Å / Origin y: 12.2807 Å / Origin z: -32.5755 Å
111213212223313233
T0.0215 Å20.0187 Å20.0076 Å2-0.03 Å2-0.018 Å2--0.061 Å2
L2.4904 °2-0.5618 °2-0.1161 °2-2.0369 °20.2051 °2--0.5863 °2
S-0.0642 Å °-0.0157 Å °0.0728 Å °0.0734 Å °0.0822 Å °-0.0807 Å °0.0255 Å °0.0359 Å °-0.018 Å °

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