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- PDB-7sec: Crystal structure of human Fibrillarin in complex with compound 1a -

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Basic information

Entry
Database: PDB / ID: 7sec
TitleCrystal structure of human Fibrillarin in complex with compound 1a
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-8WP / 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
B: rRNA 2'-O-methyltransferase fibrillarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,40814
Polymers53,3632
Non-polymers1,04512
Water2,072115
1
A: rRNA 2'-O-methyltransferase fibrillarin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2047
Polymers26,6821
Non-polymers5226
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)27,2047
Polymers26,6821
Non-polymers5226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.384, 68.874, 136.436
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-8WP / 2-[(8S)-4-oxo-2-(trifluoromethyl)-4,5-dihydropyrazolo[1,5-a]pyrazin-6-yl]acetamide


Mass: 260.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7F3N4O2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 115 / 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: 3.01 Å3/Da / Density % sol: 59.14 %
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: 1.9→48.53 Å / Num. obs: 51310 / % possible obs: 99.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 28.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Net I/σ(I): 7
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 1.078 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3233 / CC1/2: 0.894 / Rpim(I) all: 0.54 / Rrim(I) all: 1.21

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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→48.3 Å / SU ML: 0.2861 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.0438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2663 2502 4.9 %
Rwork0.2225 48555 -
obs0.2246 51057 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.98 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 68 115 3690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213671
X-RAY DIFFRACTIONf_angle_d1.13064971
X-RAY DIFFRACTIONf_chiral_restr0.0652556
X-RAY DIFFRACTIONf_plane_restr0.0076669
X-RAY DIFFRACTIONf_dihedral_angle_d13.55161371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.4311390.35162623X-RAY DIFFRACTION98.85
1.94-1.980.35721340.3162660X-RAY DIFFRACTION98.76
1.98-2.020.30781300.29162657X-RAY DIFFRACTION98.59
2.02-2.070.31771530.27932639X-RAY DIFFRACTION98.55
2.07-2.120.32171460.25992619X-RAY DIFFRACTION98.22
2.12-2.170.33191490.25752644X-RAY DIFFRACTION98.76
2.17-2.240.27841390.24542647X-RAY DIFFRACTION98.58
2.24-2.310.29191490.23132686X-RAY DIFFRACTION98.99
2.31-2.390.28361330.22632654X-RAY DIFFRACTION98.17
2.39-2.490.28911370.2232682X-RAY DIFFRACTION99.61
2.49-2.60.30151370.22512712X-RAY DIFFRACTION99.72
2.6-2.740.24371350.22372723X-RAY DIFFRACTION99.86
2.74-2.910.28761520.24342678X-RAY DIFFRACTION99.86
2.91-3.140.28961500.22432756X-RAY DIFFRACTION99.9
3.14-3.450.27521390.2242726X-RAY DIFFRACTION99.58
3.45-3.950.24991040.20892765X-RAY DIFFRACTION99
3.95-4.980.19371270.16982813X-RAY DIFFRACTION99.69
4.98-48.30.23571490.21162871X-RAY DIFFRACTION97.86

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