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- PDB-9jgc: Crystal structure of Nep1 in complex with adenosine from Pyrococc... -

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Basic information

Entry
Database: PDB / ID: 9jgc
TitleCrystal structure of Nep1 in complex with adenosine 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
ADENOSINE / DI(HYDROXYETHYL)ETHER / SULFITE ION / Ribosomal RNA small subunit methyltransferase Nep1
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 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)27,96413
Polymers26,9261
Non-polymers1,03712
Water2,540141
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)55,92826
Polymers53,8532
Non-polymers2,07524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area8880 Å2
ΔGint-24 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.410, 113.410, 102.180
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-501-

HOH

21A-512-

HOH

31A-529-

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 , 7 types, 153 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: microbatch / pH: 7.5
Details: 0.1M sodium chloride, 0.1M HEPES pH 7.5, 1.6M 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 20, 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: 2.01→70.81 Å / Num. obs: 17065 / % possible obs: 100 % / Redundancy: 14.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.026 / Rrim(I) all: 0.1 / Χ2: 1.02 / Net I/σ(I): 20.2 / Num. measured all: 246585
Reflection shellResolution: 2.01→2.06 Å / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.484 / Num. measured all: 16745 / Num. unique obs: 1245 / CC1/2: 0.965 / Rpim(I) all: 0.137 / Rrim(I) all: 0.504 / Χ2: 0.92 / Net I/σ(I) obs: 6

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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: 2.01→70.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.72 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20933 848 5 %RANDOM
Rwork0.15792 ---
obs0.16042 16216 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.296 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å2-0.5 Å20 Å2
2---1 Å20 Å2
3---3.24 Å2
Refinement stepCycle: 1 / Resolution: 2.01→70.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 64 141 2076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121973
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161953
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.6722650
X-RAY DIFFRACTIONr_angle_other_deg0.5151.5824509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5535227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.899516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19210373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
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_it1.7791.701905
X-RAY DIFFRACTIONr_mcbond_other1.7651.701905
X-RAY DIFFRACTIONr_mcangle_it2.8573.0411130
X-RAY DIFFRACTIONr_mcangle_other2.8563.0431131
X-RAY DIFFRACTIONr_scbond_it3.0022.2561068
X-RAY DIFFRACTIONr_scbond_other3.0012.261069
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7323.8661520
X-RAY DIFFRACTIONr_long_range_B_refined7.8919.662289
X-RAY DIFFRACTIONr_long_range_B_other7.8719.182262
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.058 Å
RfactorNum. reflection% reflection
Rfree0.233 49 -
Rwork0.181 1195 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 18.842 Å / Origin y: 8.3209 Å / Origin z: 18.9153 Å
111213212223313233
T0.0669 Å2-0.0188 Å2-0.0221 Å2-0.1177 Å20.0013 Å2--0.0155 Å2
L1.8002 °20.2277 °2-0.1134 °2-1.4032 °2-0.1403 °2--0.3401 °2
S-0.0127 Å °-0.1337 Å °-0.043 Å °-0.0058 Å °0.0338 Å °-0.057 Å °-0.0061 Å °-0.0614 Å °-0.0211 Å °

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