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- PDB-3id5: Crystal structure of Sulfolobus solfataricus C/D RNP assembled wi... -

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Basic information

Entry
Database: PDB / ID: 3id5
TitleCrystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA
Components
  • 50S ribosomal protein L7Ae
  • Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
  • Pre mRNA splicing protein
  • half C/D RNA
KeywordsTRANSFERASE/RIBOSOMAL PROTEIN/RNA / C/D guide RNA / 2'-O-methylation / coiled-coil / Methyltransferase / RNA-binding / rRNA processing / Transferase / tRNA processing / Ribonucleoprotein / Ribosomal protein / SPLICING-TRANSFERASE-RIBOSOMAL PROTEIN-RNA COMPLEX / TRANSFERASE-RIBOSOMAL PROTEIN-RNA complex
Function / homology
Function and homology information


box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / rRNA methylation / histone H2A Q104 methyltransferase activity / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases ...box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / rRNA methylation / histone H2A Q104 methyltransferase activity / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function
: / Archaeal Nop5/56-rel, N-terminal domain / : / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / NOSIC ...: / Archaeal Nop5/56-rel, N-terminal 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. / Ribosomal protein L7Ae, archaea / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / RNA / RNA (> 10) / Large ribosomal subunit protein eL8 / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / Pre mRNA splicing protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 4.01 Å
AuthorsYe, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural organization of box C/D RNA-guided RNA methyltransferase.
Authors: Ye, K. / Jia, R. / Lin, J. / Ju, M. / Peng, J. / Xu, A. / Zhang, L.
History
DepositionJul 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre mRNA splicing protein
B: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
C: 50S ribosomal protein L7Ae
D: half C/D RNA
E: Pre mRNA splicing protein
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: 50S ribosomal protein L7Ae
H: half C/D RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,68710
Polymers191,8908
Non-polymers7972
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19350 Å2
ΔGint-109 kcal/mol
Surface area72140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.485, 265.485, 129.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H
15D
25H
16A
26E

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALALAALAAA2 - 1322 - 132
21VALVALALAALAEE2 - 1322 - 132
12ILEILESAMSAMBB - I5 - 3015
22ILEILESAMSAMFF - J5 - 3015
13ALAALAGLYGLYCC7 - 1267 - 126
23ALAALAGLYGLYGG7 - 1267 - 126
14CCUUDD11 - 3411 - 34
24CCUUHH11 - 3411 - 34
15GGCCDD1 - 91 - 9
25GGCCHH1 - 91 - 9
16ALAALAPHEPHEAA133 - 378133 - 378
26ALAALAPHEPHEEE133 - 378133 - 378

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Pre mRNA splicing protein / Nop5


Mass: 44168.531 Da / Num. of mol.: 2 / Fragment: Residues 1-380 / Mutation: M2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO0939 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/RIL+ / References: UniProt: Q97ZH3
#2: Protein Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / fibrillarin / FIB


Mass: 26439.375 Da / Num. of mol.: 2 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: flpA, SSO0940, C33_014 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/RIL+
References: UniProt: P58032, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Protein 50S ribosomal protein L7Ae


Mass: 14075.301 Da / Num. of mol.: 2 / Mutation: N2D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: rpl7ae, SSO0091, C04_031 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/RIL+ / References: UniProt: P55858
#4: RNA chain half C/D RNA


Mass: 11261.667 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: prepared by in vitro transcription
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S

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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: 5.94 Å3/Da / Density % sol: 79.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.7M (NH4)2SO4, 50mM Na cacodylate, pH 5.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.00821 Å
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00821 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 39544 / % possible obs: 98.5 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 17.5
Reflection shellResolution: 4→4.07 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.6 / % possible all: 85.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 4.01→20 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 109.392 / SU ML: 0.659 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.747 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1888 5 %RANDOM
Rwork0.285 ---
obs0.286 37665 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 282.71 Å2 / Biso mean: 166.712 Å2 / Biso min: 44.41 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å20 Å20 Å2
2---2.34 Å20 Å2
3---4.68 Å2
Refinement stepCycle: LAST / Resolution: 4.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11276 1400 54 0 12730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02213070
X-RAY DIFFRACTIONr_angle_refined_deg1.1352.12217980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.68551418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7424.559522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.923152116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3821578
X-RAY DIFFRACTIONr_chiral_restr0.0970.22116
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029186
X-RAY DIFFRACTIONr_nbd_refined0.1730.25254
X-RAY DIFFRACTIONr_nbtor_refined0.2920.28677
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.211
X-RAY DIFFRACTIONr_mcbond_it0.6951.57384
X-RAY DIFFRACTIONr_mcangle_it1.281211480
X-RAY DIFFRACTIONr_scbond_it0.8636910
X-RAY DIFFRACTIONr_scangle_it1.2124.56500
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1066TIGHT POSITIONAL0.010.05
1A1066TIGHT THERMAL0.020.5
2B1823TIGHT POSITIONAL0.010.05
2B1823TIGHT THERMAL0.010.5
3C911TIGHT POSITIONAL0.05
3C911TIGHT THERMAL0.5
4D485TIGHT POSITIONAL0.070.05
4D485TIGHT THERMAL0.010.5
5D195TIGHT POSITIONAL0.10.05
5D195TIGHT THERMAL0.010.5
6A1865TIGHT POSITIONAL0.010.05
6A1865TIGHT THERMAL0.010.5
LS refinement shellResolution: 4.007→4.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 101 -
Rwork0.334 2003 -
all-2104 -
obs--76.37 %
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)
114.18120.56846.6492.21770.89295.89470.4216-0.7304-1.60840.3975-0.13590.27781.0236-0.6269-0.2857-0.95480.0874-0.0856-1.3127-0.075-1.039224.26770.67227.364
213.453-3.62292.67253.2119-1.12374.4660.32442.22640.7044-0.6450.0236-0.28710.50851.616-0.348-1.03150.3328-0.1496-0.4896-0.2492-1.261853.97680.72220.099
313.4801-0.45041.68584.5591-1.86456.664-0.0727-0.06440.63240.29850.35950.21560.1647-0.6895-0.2868-0.254-0.1311-0.0404-0.29010.1027-0.0988-10.76394.19827.33
410.2619-1.4773-0.14943.9782-1.09483.22950.10611.0170.6489-0.292-0.4117-0.5982-0.59640.5350.30560.06530.1211-0.01360.14620.2064-0.212784.73688.28147.715
56.95740.4992.33416.29770.9924.4112-0.2907-0.15620.73150.28390.2229-0.2824-0.13320.22540.0678-0.23330.0259-0.1379-0.2957-0.0017-0.016913.099103.20439.808
65.5779-2.22030.6264.26690.94335.09070.0410.37370.3041-0.1068-0.44560.1197-0.2805-0.15220.4045-0.06860.1812-0.0668-0.23610.1208-0.159558.35398.39550.938
78.0764-5.4303-4.884316.51313.53329.23650.77021.921-0.3731-3.2025-0.50371.3546-0.1834-0.2629-0.26650.0567-0.3415-0.81490.6739-0.4017-0.6323-0.37873.094-9.138
86.90634.4732-1.65446.25595.295212.46520.32280.7223-1.85960.4730.1312-0.60912.22241.7301-0.45410.14781.6866-0.21920.2521-0.66560.517482.80748.33530.043
98.90152.50692.398413.5468-3.11076.96940.48361.3746-2.11670.49370.51122.61711.2848-1.1245-0.9947-0.3385-0.3363-0.1872-0.5235-0.6521.0481-1.62555.6087.683
1019.91133.08636.682114.8493-1.744918.2643-1.01443.1169-2.1625-2.08950.6204-1.1396-1.83552.82460.3940.32231.3650.13711.6019-1.2007-0.715583.71563.44311.342
1142.752614.3776-13.12536.89780.23614.51212.27370.69616.0995-1.6894-0.85941.558-0.1827-0.4958-1.41440.24870.42571.00220.13150.016-0.037131.47366.211-11.695
124.3995-10.2033-7.540859.600856.129454.4728-0.9814-2.72610.3144-0.4698-1.57814.5249-0.4149-1.87992.55950.03030.0601-0.2802-0.2988-0.31220.292761.24234.53610.224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A133 - 378
2X-RAY DIFFRACTION2E133 - 378
3X-RAY DIFFRACTION3A2 - 132
4X-RAY DIFFRACTION4E2 - 132
5X-RAY DIFFRACTION5B5 - 231
6X-RAY DIFFRACTION6F5 - 231
7X-RAY DIFFRACTION7C7 - 126
8X-RAY DIFFRACTION8G7 - 126
9X-RAY DIFFRACTION9D10 - 34
10X-RAY DIFFRACTION10H10 - 34
11X-RAY DIFFRACTION11D1 - 9
12X-RAY DIFFRACTION12H1 - 9

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