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- PDB-7seb: Crystal structure of human Fibrillarin in complex with compound 2... -

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Basic information

Entry
Database: PDB / ID: 7seb
TitleCrystal structure of human Fibrillarin in complex with compound 2 from single soak
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 / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA methylation / histone H2AQ104 methyltransferase activity / rRNA modification in the nucleus and cytosol / TFIID-class transcription factor complex binding ...U6 snRNA 2'-O-ribose methyltransferase activity / snoRNA localization / granular component / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA methylation / histone H2AQ104 methyltransferase activity / 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 / Vaccinia Virus protein VP39 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / Vaccinia Virus protein VP39 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-(trifluoromethyl)pyrimidin-4-amine / FORMIC ACID / rRNA 2'-O-methyltransferase fibrillarin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,9835
Polymers26,6821
Non-polymers3014
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.210, 138.905, 66.483
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-8XF / 6-(trifluoromethyl)pyrimidin-4-amine


Mass: 163.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4F3N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
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: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→48.03 Å / Num. obs: 29246 / % possible obs: 97.5 % / Redundancy: 13.1 % / Biso Wilson estimate: 29.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.023 / Rrim(I) all: 0.081 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.658 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1359 / CC1/2: 0.745 / Rpim(I) all: 0.495 / Rrim(I) all: 1.733

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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: 1.81→48.03 Å / SU ML: 0.2244 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2328 1462 5.01 %
Rwork0.1942 27738 -
obs0.1961 29200 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.71 Å2
Refinement stepCycle: LAST / Resolution: 1.81→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 20 136 1933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071840
X-RAY DIFFRACTIONf_angle_d1.09132492
X-RAY DIFFRACTIONf_chiral_restr0.0694281
X-RAY DIFFRACTIONf_plane_restr0.0087331
X-RAY DIFFRACTIONf_dihedral_angle_d11.9055685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.870.32261410.27512666X-RAY DIFFRACTION96.46
1.87-1.950.28161430.24772726X-RAY DIFFRACTION97.55
1.95-2.040.25651440.23432739X-RAY DIFFRACTION98.03
2.04-2.140.24361440.21152723X-RAY DIFFRACTION97.65
2.14-2.280.24491450.2032755X-RAY DIFFRACTION98.44
2.28-2.450.23221450.20172750X-RAY DIFFRACTION98.44
2.45-2.70.2631460.21772771X-RAY DIFFRACTION98.88
2.7-3.090.2491490.21332818X-RAY DIFFRACTION99.03
3.09-3.90.24921490.18562834X-RAY DIFFRACTION99.4
3.9-48.030.18671560.16132956X-RAY DIFFRACTION99.36

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