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- PDB-7se8: Crystal structure of human Fibrillarin in complex with fragment 1... -

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Basic information

Entry
Database: PDB / ID: 7se8
TitleCrystal structure of human Fibrillarin in complex with fragment 1 from cocktail soak
ComponentsrRNA 2'-O-methyltransferase fibrillarin
KeywordsTRANSFERASE / Methyltransferase / S-adenosyl methionine
Function / homology
Function and homology information


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 ...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 / osteoblast differentiation / rRNA processing / ribosomal small subunit biogenesis / ATPase binding / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus
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-8W1 / FORMIC ACID / rRNA 2'-O-methyltransferase fibrillarin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,32014
Polymers53,3632
Non-polymers95712
Water5,675315
1
A: rRNA 2'-O-methyltransferase fibrillarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2068
Polymers26,6821
Non-polymers5247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: rRNA 2'-O-methyltransferase fibrillarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1146
Polymers26,6821
Non-polymers4325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.038, 68.874, 138.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,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.: 2
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-8W1 / (5S)-3-methyl-7-(trifluoromethyl)pyrrolo[1,2-a]pyrazin-1(2H)-one


Mass: 216.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7F3N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.04 Å3/Da / Density % sol: 59.59 %
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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→48.4 Å / Num. obs: 65541 / % possible obs: 98.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 21.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.025 / Rrim(I) all: 0.07 / Net I/σ(I): 19.8
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.762 / Num. unique obs: 3509 / CC1/2: 0.822 / Rpim(I) all: 0.295 / Rrim(I) all: 0.818

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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: 1.75→48.4 Å / SU ML: 0.188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7682
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2136 3158 4.82 %
Rwork0.1877 62297 -
obs0.1889 65455 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.44 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3538 0 62 315 3915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00953754
X-RAY DIFFRACTIONf_angle_d1.04865092
X-RAY DIFFRACTIONf_chiral_restr0.065566
X-RAY DIFFRACTIONf_plane_restr0.0078663
X-RAY DIFFRACTIONf_dihedral_angle_d13.72481399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.26391390.24192628X-RAY DIFFRACTION97.33
1.78-1.80.28161240.23412658X-RAY DIFFRACTION97.27
1.8-1.830.26771300.24062654X-RAY DIFFRACTION97.89
1.83-1.870.25781310.24632659X-RAY DIFFRACTION97.21
1.87-1.90.24671450.22982645X-RAY DIFFRACTION97.86
1.9-1.940.25341350.21862670X-RAY DIFFRACTION98.21
1.94-1.980.24641220.21592652X-RAY DIFFRACTION97.4
1.98-2.020.26141360.20722675X-RAY DIFFRACTION98.05
2.02-2.060.24971400.19922695X-RAY DIFFRACTION98.57
2.06-2.120.22131640.19832633X-RAY DIFFRACTION98.42
2.12-2.170.20481260.18622679X-RAY DIFFRACTION98.15
2.17-2.240.22561230.18492699X-RAY DIFFRACTION98.12
2.24-2.310.20811620.17892679X-RAY DIFFRACTION98.44
2.31-2.390.20541310.17172688X-RAY DIFFRACTION98.77
2.39-2.490.20381520.1812714X-RAY DIFFRACTION98.93
2.49-2.60.22121470.18672706X-RAY DIFFRACTION99.03
2.6-2.740.20961260.18752739X-RAY DIFFRACTION99.1
2.74-2.910.2291170.18992758X-RAY DIFFRACTION98.93
2.91-3.130.22121440.19052753X-RAY DIFFRACTION99.21
3.14-3.450.22791360.18392774X-RAY DIFFRACTION99.35
3.45-3.950.18811250.17322786X-RAY DIFFRACTION99.66
3.95-4.970.15261620.15272818X-RAY DIFFRACTION99.6
4.98-48.40.23291410.19812935X-RAY DIFFRACTION98.59

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