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- PDB-7sed: Crystal structure of human Fibrillarin in complex with compound 2a -

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Basic information

Entry
Database: PDB / ID: 7sed
TitleCrystal structure of human Fibrillarin in complex with compound 2a
ComponentsrRNA 2'-O-methyltransferase fibrillarin
KeywordsTRANSFERASE / Methyltransferase / S-adenosyl methionine
Function / homology
Function and homology information


U6 snRNA 2'-O-ribose methyltransferase activity / snoRNA localization / granular component / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA methylation / rRNA modification in the nucleus and cytosol / TFIID-class transcription factor complex binding ...U6 snRNA 2'-O-ribose methyltransferase activity / snoRNA localization / granular component / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA methylation / rRNA modification in the nucleus and cytosol / TFIID-class transcription factor complex binding / Major pathway of rRNA processing in the nucleolus and cytosol / Cajal body / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / fibrillar center / rRNA processing / osteoblast differentiation / ATPase binding / ribosomal small subunit biogenesis / nucleolus / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane
Similarity search - Function
rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-8VD / FORMIC ACID / rRNA 2'-O-methyltransferase fibrillarin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShi, Y. / El-Deeb, I.M. / Masic, V. / Hartley-Tassell, L. / Maggioni, A. / von Itzstein, M. / Ve, T.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Australian Research Council (ARC) Australia
CitationJournal: Pharmaceuticals / Year: 2021
Title: Discovery of Cofactor Competitive Inhibitors against the Human Methyltransferase Fibrillarin.
Authors: Shi, Y. / El-Deeb, I.M. / Masic, V. / Hartley-Tassell, L. / Maggioni, A. / Itzstein, M.V. / Ve, T.
History
DepositionSep 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rRNA 2'-O-methyltransferase fibrillarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9743
Polymers26,6821
Non-polymers2922
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.291, 139.581, 66.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein rRNA 2'-O-methyltransferase fibrillarin / 34 kDa nucleolar scleroderma antigen / Histone-glutamine methyltransferase / U6 snRNA 2'-O- ...34 kDa nucleolar scleroderma antigen / Histone-glutamine methyltransferase / U6 snRNA 2'-O-methyltransferase fibrillarin


Mass: 26681.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBL, FIB1, FLRN / Production host: Escherichia coli (E. coli)
References: UniProt: P22087, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-8VD / N-(piperidin-4-yl)-6-(trifluoromethyl)pyrimidin-4-amine


Mass: 246.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13F3N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.75-3.3 M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→48.05 Å / Num. obs: 25684 / % possible obs: 99.5 % / Redundancy: 12.8 % / Biso Wilson estimate: 31.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.014 / Rrim(I) all: 0.05 / Net I/σ(I): 22.6
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 4 / Num. unique obs: 1570 / CC1/2: 0.95 / Rpim(I) all: 0.136 / Rrim(I) all: 0.474

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IPX

2ipx


Resolution: 1.9→38.63 Å / SU ML: 0.2194 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.1369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 2000 7.8 %
Rwork0.1886 23657 -
obs0.1914 25657 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.56 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 20 89 1870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111827
X-RAY DIFFRACTIONf_angle_d1.10542477
X-RAY DIFFRACTIONf_chiral_restr0.0714280
X-RAY DIFFRACTIONf_plane_restr0.0084328
X-RAY DIFFRACTIONf_dihedral_angle_d13.196687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.3041360.29141612X-RAY DIFFRACTION96.1
1.95-20.27551400.23071665X-RAY DIFFRACTION99.18
2-2.060.21891410.20091658X-RAY DIFFRACTION99.17
2.06-2.120.21961400.18591660X-RAY DIFFRACTION99.45
2.12-2.20.23871410.19091667X-RAY DIFFRACTION99.4
2.2-2.290.21661430.20131696X-RAY DIFFRACTION99.51
2.29-2.390.24341400.19921652X-RAY DIFFRACTION99.22
2.39-2.520.27091430.20911690X-RAY DIFFRACTION99.73
2.52-2.670.23961440.20931691X-RAY DIFFRACTION99.78
2.67-2.880.21881430.20991705X-RAY DIFFRACTION99.95
2.88-3.170.25871440.22371692X-RAY DIFFRACTION99.84
3.17-3.630.23641440.18621715X-RAY DIFFRACTION100
3.63-4.570.18481470.15261744X-RAY DIFFRACTION100
4.57-38.630.20821540.1691810X-RAY DIFFRACTION99.54

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