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- PDB-6zdt: Crystal structure of eukaryotic Fibrillarin with Nop56 N-terminal... -

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Basic information

Entry
Database: PDB / ID: 6zdt
TitleCrystal structure of eukaryotic Fibrillarin with Nop56 N-terminal domain
Components
  • Nucleolar protein 56
  • rRNA 2'-O-methyltransferase fibrillarin
KeywordsRIBOSOMAL PROTEIN / 2'-O-Methylation / Methyltransferase / Box C/D snoRNP enzyme / Ribosome biogenesis
Function / homology
Function and homology information


rRNA 2'-O-methylation / snoRNA guided rRNA 2'-O-methylation / rRNA modification / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / regulation of transcription by RNA polymerase I / box C/D methylation guide snoRNP complex / O-methyltransferase activity / rRNA methylation / histone H2AQ104 methyltransferase activity ...rRNA 2'-O-methylation / snoRNA guided rRNA 2'-O-methylation / rRNA modification / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / regulation of transcription by RNA polymerase I / box C/D methylation guide snoRNP complex / O-methyltransferase activity / rRNA methylation / histone H2AQ104 methyltransferase activity / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of SSU-rRNA / small-subunit processome / rRNA processing / mRNA binding / nucleolus / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Nucleolar protein 58/56, N-terminal / NOP5NT (NUC127) domain / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / NOSIC / NOSIC (NUC001) domain ...Nucleolar protein 58/56, N-terminal / NOP5NT (NUC127) domain / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
rRNA 2'-O-methyltransferase fibrillarin / Nucleolar protein 56
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
AuthorsHoefler, S. / Lukat, P. / Carlomagno, T. / Blankenfeldt, W.
CitationJournal: Rna / Year: 2021
Title: High-resolution structure of eukaryotic Fibrillarin interacting with Nop56 amino-terminal domain.
Authors: Hofler, S. / Lukat, P. / Blankenfeldt, W. / Carlomagno, T.
History
DepositionJun 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Nucleolar protein 56


Theoretical massNumber of molelcules
Total (without water)45,9122
Polymers45,9122
Non-polymers00
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Clear assembly formation of both proteins determined via gel filtration using S200 Increase 10/300 (Cytiva). Verified also by SDS-gelelectrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-8 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.004, 118.286, 48.828
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

21A-480-

HOH

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Components

#1: Protein rRNA 2'-O-methyltransferase fibrillarin / Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA- ...Histone-glutamine methyltransferase / U3 small nucleolar RNA-associated protein NOP1 / U3 snoRNA-associated protein NOP1


Mass: 27460.850 Da / Num. of mol.: 1 / Fragment: Nop1short
Source method: isolated from a genetically manipulated source
Details: Cysteine 314 was found to be oxidized.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NOP1, LOT3, YDL014W, D2870 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P15646, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Nucleolar protein 56 / Ribosome biosynthesis protein SIK1 / Suppressor of I kappa b protein 1


Mass: 18451.061 Da / Num. of mol.: 1 / Fragment: 56NTD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NOP56, SIK1, YLR197W, L8167.9 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12460
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M LiCl, 0.1 M HEPES, 19 % PEG 400, Cryo: 10% 2,3-butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033198 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033198 Å / Relative weight: 1
ReflectionResolution: 1.71→48.83 Å / Num. obs: 44280 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 22.56 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.021 / Rrim(I) all: 0.078 / Net I/σ(I): 22.1 / Num. measured all: 582147
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.71-1.813.11.0168360163680.8960.291.0572.6100
5.4-48.8312.30.02119171155810.0060.0228099.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.6 Å48.83 Å
Translation3.6 Å48.83 Å

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Processing

Software
NameVersionClassification
PHENIX1.18rc4_3812refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IPX

2ipx


Resolution: 1.71→48.83 Å / SU ML: 0.1569 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2049 2184 4.94 %
Rwork0.1628 42027 -
obs0.165 44211 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.73 Å2
Refinement stepCycle: LAST / Resolution: 1.71→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 0 367 3420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533198
X-RAY DIFFRACTIONf_angle_d0.68634337
X-RAY DIFFRACTIONf_chiral_restr0.0515490
X-RAY DIFFRACTIONf_plane_restr0.0044567
X-RAY DIFFRACTIONf_dihedral_angle_d19.39951232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.740.22771320.21312587X-RAY DIFFRACTION99.93
1.74-1.790.24111090.20152588X-RAY DIFFRACTION99.89
1.79-1.830.23351290.19112608X-RAY DIFFRACTION99.96
1.83-1.880.22921370.18462617X-RAY DIFFRACTION99.93
1.88-1.930.23531190.17462588X-RAY DIFFRACTION99.89
1.93-20.20251290.1732576X-RAY DIFFRACTION100
2-2.070.21761490.16812611X-RAY DIFFRACTION99.96
2.07-2.150.21111390.16192581X-RAY DIFFRACTION99.96
2.15-2.250.21091310.15072614X-RAY DIFFRACTION99.96
2.25-2.370.2011300.15012626X-RAY DIFFRACTION99.96
2.37-2.520.1931220.15552638X-RAY DIFFRACTION100
2.52-2.710.19591510.15862625X-RAY DIFFRACTION100
2.71-2.980.19651500.16752620X-RAY DIFFRACTION99.96
2.98-3.410.20561670.16522625X-RAY DIFFRACTION100
3.41-4.30.18681520.14442688X-RAY DIFFRACTION100
4.3-48.830.21561380.16812835X-RAY DIFFRACTION99.83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.366666464320.6047776181621.136353364841.50160257121-0.1891569009111.400891134170.0909492760843-0.0155125918374-0.12226294332-0.1097213717910.0521248982813-0.06887894776050.2033965399550.02950192876540.01452344019960.1768936801730.02276944543410.01397964501390.186778531878-0.004895635690760.2053057279817.6584544178-15.170110208911.9827311097
20.2084952264360.00651558336047-0.3661579394520.5576680141470.4209012497950.9552012724130.0463755958155-0.2912611001630.1854489183560.283159924408-0.0696293356388-0.0648382870524-0.04658923004940.05950391839170.0001090886360180.186892614715-0.00873418753120.005346299717240.227753473274-0.004953794827730.22428005683420.82667275623.4863061536123.5291557365
30.54246588777-0.2459213546030.1006153428670.3088292505380.2707748881220.496377402467-0.078904862015-0.1030882275650.484251340388-0.190053280918-0.04992225041630.502152177258-0.324477974903-0.444514843957-0.02040727785780.3308214913280.0637904786971-0.05899368081160.2464558381810.02652407734310.3865066457116.7941786031127.79951084096.377823715
40.8640064485730.1477619511040.2619380126571.03996572242-0.6028608945530.673313493981-0.0805593135409-0.09148113478980.2075026825590.01851139008990.08322633486690.0443676618832-0.251803204274-0.103432896326-3.37839312459E-50.2604102152650.0087202357041-0.004102848680930.206544314282-0.02053248187790.22742912181411.739911006523.240573790210.9103199722
50.762465654986-0.0826257133287-0.02350115272781.34170366250.01030713663060.535554764879-0.0440683877181-0.04164831801860.11537105084-0.006566242837890.0512070528594-0.127184381755-0.01560605342130.01616126768095.71708036775E-60.144927170829-0.003614334269660.007980449332720.193273231557-0.00666017552330.16661675859320.98585362129.2499045321415.10972138
60.204536956885-0.05260743351740.3013366738390.451338594610.06581392354530.6475008386190.000804398979366-0.02341538163850.13795950453-0.2463388470990.00341718535528-0.219946159292-0.01235934525550.2133230159266.029541433E-60.22894153102-0.02014603383880.05798654446190.237152357907-0.0007075066355010.23094785534822.06883938563.185694212363.90751984074
70.0674592814991-0.092653096229-0.02780546251710.4096781209040.4220906818530.488273952852-0.3017408256240.396865015698-0.144465089141-0.5689282235620.278396651662-0.356880689408-0.06578400061290.0135618511427-0.004155965567020.319175209362-0.06627115701030.05976725904350.261956491562-0.004443129239710.25045244112921.50343022278.50063718111-2.20734155659
80.0635377518753-0.06188741640710.01118875560860.254235714080.1154466529710.0891913077104-0.4698571877560.03155164946980.000377058217817-0.7454207815440.305649326597-0.498979708814-0.01665323072530.130419530579-0.09528510184530.51283826983-0.09344101011030.1431603791170.397887680763-0.01926455186990.29248250322725.65010648216.13792803677-10.2856397523
90.46805678235-0.522601467431-0.5573500101921.070061687730.1566935305571.07159940841-0.1382843066810.203817068019-0.0292042112321-1.146407656010.00889274428578-0.2934502646340.07210167318560.201144027610.02729233788780.409836257267-0.08015356639070.02301426265990.2763544001090.02369786302950.20535145570217.762980017410.3373374261-5.98041311207
100.403135086119-0.2980647250140.1733044880510.468236421441-0.2984967175340.3727115377540.04752249906030.0482811998529-0.165327085422-0.08313787583450.006423312739410.03046351999640.1238565510440.1317568109189.89154573446E-50.2214267756430.0148910825036-0.001155323853350.177416246544-0.01825696308260.20100879314513.8371700836-19.222164876710.0355242528
110.129964137589-0.0597454996014-0.07394745255680.8447936142760.00392899707350.222378308555-0.03487900414940.399679966071-0.19792283843-0.8238268259160.167297884260.411733149060.266200273352-0.08576483436940.04437259193590.356750431436-0.01501690691830.0007628347520150.330401224503-0.05612627657770.2731129294655.79192889964-14.10025036780.638537937597
120.9477419164940.0536824228810.4610157094890.2194715892720.06051920497550.6616276668720.4348736203590.0185388341277-0.3331241544740.230614252924-0.0184150681047-0.007703633798380.399866052718-0.3372681527590.07242240946440.257535473793-0.03397007309410.04822636697630.2301621686550.002146922763890.19659479945811.1487930448-14.906513131622.3477988809
130.752531784573-0.429905423590.08709345495190.682548551204-0.5475294475861.269765934030.07416002508070.0166717366422-0.2075754138070.2412569640730.0778386474958-0.1174748577550.339162281240.09666415094820.0002297413814440.2592269021290.00972625495392-0.01865179967270.1964495281630.002038705775260.22611600272321.9607926129-19.250335771121.0490068997
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 96 through 145 )BB96 - 145102 - 152
22chain 'B' and (resid 146 through 165 )BB146 - 165153 - 175
33chain 'A' and (resid 86 through 109 )AA86 - 1091 - 24
44chain 'A' and (resid 110 through 168 )AA110 - 16825 - 83
55chain 'A' and (resid 169 through 233 )AA169 - 23384 - 158
66chain 'A' and (resid 234 through 260 )AA234 - 260159 - 185
77chain 'A' and (resid 261 through 281 )AA261 - 281186 - 204
88chain 'A' and (resid 282 through 296 )AA282 - 296205 - 219
99chain 'A' and (resid 297 through 326 )AA297 - 326220 - 253
1010chain 'B' and (resid -1 through 26 )BB-1 - 261 - 28
1111chain 'B' and (resid 27 through 47 )BB27 - 4729 - 49
1212chain 'B' and (resid 48 through 58 )BB48 - 5850 - 60
1313chain 'B' and (resid 59 through 95 )BB59 - 9561 - 101

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