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- PDB-5gin: Crystal structure of box C/D RNP with 12 nt guide regions and 9 n... -

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Basic information

Entry
Database: PDB / ID: 5gin
TitleCrystal structure of box C/D RNP with 12 nt guide regions and 9 nt substrates
Components
  • 50S ribosomal protein L7AeRibosome
  • 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 / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / 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 / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / rRNA methylation / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / methyltransferase activity / rRNA processing / ribosome biogenesis / methylation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / cytoplasm
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 / 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 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 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Vaccinia Virus protein VP39 / 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: 3.308 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
C: 50S ribosomal protein L7Ae
E: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
B: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
D: 50S ribosomal protein L7Ae
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: C/D RNA
H: C/D RNA
I: substrate
J: substrate
N: C/D RNA
O: substrate
K: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
L: 50S ribosomal protein L7Ae
M: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,37618
Polymers301,22315
Non-polymers1,1533
Water0
1
A: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
C: 50S ribosomal protein L7Ae
E: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
B: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
D: 50S ribosomal protein L7Ae
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)201,58412
Polymers200,81510
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33010 Å2
ΔGint-203 kcal/mol
Surface area64440 Å2
MethodPISA
2
N: C/D RNA
O: substrate
K: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
L: 50S ribosomal protein L7Ae
M: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
hetero molecules

N: C/D RNA
O: substrate
K: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit
L: 50S ribosomal protein L7Ae
M: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,58412
Polymers200,81510
Non-polymers7692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area32940 Å2
ΔGint-199 kcal/mol
Surface area64180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.676, 242.676, 146.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 3 types, 9 molecules ABKCDLEFM

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


Mass: 44168.531 Da / Num. of mol.: 3
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 / Ribosome / Ribosomal protein L8e


Mass: 14075.301 Da / Num. of mol.: 3
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.: 3
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, 6 molecules GHNIJO

#4: RNA chain C/D RNA


Mass: 12852.657 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Sulfolobus solfataricus (archaea)
#5: RNA chain substrate


Mass: 2871.767 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Sulfolobus solfataricus (archaea)

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Non-polymers , 1 types, 3 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / 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: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.0 M ammonium sulfate, 2% v/v PEG 400, 10 mM magnesium chloride, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 63174 / % possible obs: 96.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 12
Reflection shellResolution: 3.3→3.36 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PLA

3pla


Resolution: 3.308→19.999 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 32.82
RfactorNum. reflection% reflection
Rfree0.3031 3202 5.1 %
Rwork0.2504 --
obs0.2531 62833 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.308→19.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17325 2661 0 0 19986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01320583
X-RAY DIFFRACTIONf_angle_d1.71128403
X-RAY DIFFRACTIONf_dihedral_angle_d17.0128238
X-RAY DIFFRACTIONf_chiral_restr0.0753337
X-RAY DIFFRACTIONf_plane_restr0.0093182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3082-3.35730.35391180.30522012X-RAY DIFFRACTION77
3.3573-3.40950.37431110.31672229X-RAY DIFFRACTION83
3.4095-3.46510.33751240.31672335X-RAY DIFFRACTION88
3.4651-3.52460.37021220.31832454X-RAY DIFFRACTION92
3.5246-3.58830.37411300.32582546X-RAY DIFFRACTION95
3.5883-3.65690.33721430.31062539X-RAY DIFFRACTION96
3.6569-3.73110.36831400.30062588X-RAY DIFFRACTION96
3.7311-3.81170.38581590.31462570X-RAY DIFFRACTION97
3.8117-3.89970.34261480.29672601X-RAY DIFFRACTION98
3.8997-3.99650.41361500.29932627X-RAY DIFFRACTION98
3.9965-4.10360.34871490.29292615X-RAY DIFFRACTION99
4.1036-4.22330.31061170.27292649X-RAY DIFFRACTION98
4.2233-4.35830.28141480.27922656X-RAY DIFFRACTION99
4.3583-4.51230.36721310.26442683X-RAY DIFFRACTION99
4.5123-4.69080.29281310.25712667X-RAY DIFFRACTION99
4.6908-4.90120.26321480.26062689X-RAY DIFFRACTION99
4.9012-5.15550.31591310.24532699X-RAY DIFFRACTION100
5.1555-5.47230.33481270.24842708X-RAY DIFFRACTION99
5.4723-5.88480.32821580.24012692X-RAY DIFFRACTION99
5.8848-6.45880.29251520.2362719X-RAY DIFFRACTION100
6.4588-7.35240.28091530.22022733X-RAY DIFFRACTION100
7.3524-9.1150.23841620.17422756X-RAY DIFFRACTION100
9.115-19.99910.20941500.17582864X-RAY DIFFRACTION99

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