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- PDB-5gip: Crystal structure of box C/D RNP with 13 nt guide regions and 11 ... -

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Basic information

Entry
Database: PDB / ID: 5gip
TitleCrystal structure of box C/D RNP with 13 nt guide regions and 11 nt substrates
Components
  • 50S ribosomal protein L7Ae
  • C/D RNA
  • C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
  • Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
  • substrate
KeywordsTRANSFERASE/RNA / 2'-O-methylation / guide RNA / RNP / TRANSFERASE-RNA complex
Function / homology
Function and homology information


histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / rRNA methylation / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases ...histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / rRNA methylation / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / ribosome biogenesis / cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / RNA binding
Similarity search - Function
Nucleotidyltransferase; domain 5 - #220 / Helix Hairpins - #4070 / Nop domain / : / : / Archaeal Nop5/56-rel, N-terminal domain / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin ...Nucleotidyltransferase; domain 5 - #220 / Helix Hairpins - #4070 / Nop domain / : / : / Archaeal Nop5/56-rel, N-terminal domain / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / Ribosomal protein L7Ae, archaea / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Ribosomal protein L30/S12 / Serum Albumin; Chain A, Domain 1 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Vaccinia Virus protein VP39 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Helix Hairpins / Nucleotidyltransferase; domain 5 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / Large ribosomal subunit protein eL8 / C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / 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 / MOLECULAR REPLACEMENT / Resolution: 3.129 Å
AuthorsYang, Z. / Lin, J. / Ye, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Box C/D guide RNAs recognize a maximum of 10 nt of substrates
Authors: Yang, Z. / Lin, J. / Ye, K.
History
DepositionJun 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
B: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
C: 50S ribosomal protein L7Ae
D: 50S ribosomal protein L7Ae
E: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: C/D RNA
H: C/D RNA
I: substrate
J: substrate
K: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
L: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
M: 50S ribosomal protein L7Ae
N: 50S ribosomal protein L7Ae
O: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
P: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Q: C/D RNA
R: C/D RNA
S: substrate
T: substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,99824
Polymers405,46120
Non-polymers1,5384
Water00
1
A: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
B: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
C: 50S ribosomal protein L7Ae
D: 50S ribosomal protein L7Ae
E: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: C/D RNA
H: C/D RNA
I: substrate
J: substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,49912
Polymers202,73010
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33550 Å2
ΔGint-203 kcal/mol
Surface area62380 Å2
MethodPISA
2
K: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
L: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
M: 50S ribosomal protein L7Ae
N: 50S ribosomal protein L7Ae
O: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
P: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Q: C/D RNA
R: C/D RNA
S: substrate
T: substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,49912
Polymers202,73010
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33820 Å2
ΔGint-195 kcal/mol
Surface area62210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.916, 97.718, 128.793
Angle α, β, γ (deg.)108.98, 104.42, 89.86
Int Tables number1
Space group name H-MP1

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Components

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Protein , 3 types, 12 molecules ABKLCDMNEFOP

#1: Protein
C/D box methylation guide ribonucleoprotein complex aNOP56 subunit


Mass: 44168.531 Da / Num. of mol.: 4 / Fragment: UNP residues 3-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SULA_1947, SULB_1948, SULC_1946 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3MJI1, UniProt: Q97ZH3*PLUS
#2: Protein
50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 14075.301 Da / Num. of mol.: 4 / Fragment: UNP residues 3-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: rpl7ae, SULA_1106, SULB_1107, SULC_1105 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3JZF7, UniProt: P55858*PLUS
#3: Protein
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Mass: 26439.375 Da / Num. of mol.: 4 / Fragment: UNP residues 3-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: flpA, SSOP1_0970, SULA_1948, SULB_1949, SULC_1947 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E3JUC9, UniProt: P58032*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases

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RNA chain , 2 types, 8 molecules GHQRIJST

#4: RNA chain
C/D RNA


Mass: 13197.862 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Sulfolobus solfataricus (archaea)
#5: RNA chain
substrate


Mass: 3484.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Sulfolobus solfataricus (archaea)

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Non-polymers , 1 types, 4 molecules

#6: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.7M DL-malic acid, 0.1M potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.12→25 Å / Num. obs: 74336 / % possible obs: 97.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 22.5
Reflection shellResolution: 3.13→3.21 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PLA

3pla


Resolution: 3.129→24.859 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 2002 2.7 %
Rwork0.178 --
obs0.1796 74281 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.129→24.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23100 3508 0 0 26608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01327398
X-RAY DIFFRACTIONf_angle_d1.47937798
X-RAY DIFFRACTIONf_dihedral_angle_d18.83216452
X-RAY DIFFRACTIONf_chiral_restr0.1734441
X-RAY DIFFRACTIONf_plane_restr0.0064241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1292-3.20730.31851310.24534930X-RAY DIFFRACTION93
3.2073-3.29380.29561520.2355201X-RAY DIFFRACTION98
3.2938-3.39050.31471440.22775220X-RAY DIFFRACTION98
3.3905-3.49970.27531510.21685235X-RAY DIFFRACTION98
3.4997-3.62440.26991290.20025224X-RAY DIFFRACTION98
3.6244-3.7690.291610.19975198X-RAY DIFFRACTION98
3.769-3.93990.23491380.18565200X-RAY DIFFRACTION97
3.9399-4.14680.25921430.17515147X-RAY DIFFRACTION97
4.1468-4.40520.18251460.15955209X-RAY DIFFRACTION97
4.4052-4.74320.19961360.15425180X-RAY DIFFRACTION97
4.7432-5.21650.20391410.16045176X-RAY DIFFRACTION97
5.2165-5.96230.25141470.17185169X-RAY DIFFRACTION97
5.9623-7.47780.20871430.17265145X-RAY DIFFRACTION96
7.4778-24.85930.19411400.14925045X-RAY DIFFRACTION95

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