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- PDB-3nmu: Crystal Structure of substrate-bound halfmer box C/D RNP -

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Basic information

Entry
Database: PDB / ID: 3nmu
TitleCrystal Structure of substrate-bound halfmer box C/D RNP
Components
  • 50S ribosomal protein L7AeRibosome
  • Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
  • NOP5/NOP56 related protein
  • RNA (34-MER)
  • RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
KeywordsTransferase/RNA / Kink-turn motif / RNA assembly motif / Transferase-RNA complex
Function / homology
Function and homology information


box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / methyltransferase activity / rRNA processing / methylation ...box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / methyltransferase activity / rRNA processing / 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 / Helix hairpin bin domain superfamily / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site ...Nucleotidyltransferase; domain 5 - #220 / Helix Hairpins - #4070 / Nop domain / : / : / Archaeal Nop5/56-rel, N-terminal domain / Helix hairpin bin domain superfamily / 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-ADENOSYLMETHIONINE / RNA / RNA (> 10) / Large ribosomal subunit protein eL8 / NOP5/NOP56 related protein / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.729 Å
AuthorsLi, H. / Xue, S. / Wang, R.
CitationJournal: Mol.Cell / Year: 2010
Title: Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle.
Authors: Xue, S. / Wang, R. / Yang, F. / Terns, R.M. / Terns, M.P. / Zhang, X. / Maxwell, E.S. / Li, H.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NOP5/NOP56 related protein
B: NOP5/NOP56 related protein
C: 50S ribosomal protein L7Ae
D: RNA (34-MER)
E: RNA (34-MER)
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: 50S ribosomal protein L7Ae
J: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
I: RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
K: RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,01312
Polymers200,21610
Non-polymers7972
Water48627
1
A: NOP5/NOP56 related protein
D: RNA (34-MER)
F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
G: 50S ribosomal protein L7Ae
I: RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5076
Polymers100,1085
Non-polymers3981
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-60 kcal/mol
Surface area37820 Å2
MethodPISA
2
B: NOP5/NOP56 related protein
C: 50S ribosomal protein L7Ae
E: RNA (34-MER)
J: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
K: RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5076
Polymers100,1085
Non-polymers3981
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-65 kcal/mol
Surface area37440 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24320 Å2
ΔGint-152 kcal/mol
Surface area71560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)293.506, 94.054, 96.810
Angle α, β, γ (deg.)90.00, 101.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 6 molecules ABCGFJ

#1: Protein NOP5/NOP56 related protein


Mass: 43937.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0060 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U4M1
#2: Protein 50S ribosomal protein L7Ae / Ribosome


Mass: 14243.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rpl7ae, PF1367 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U160
#4: Protein Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Mass: 26760.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: flpA, PF0059 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8U4M2, Transferases; Transferring one-carbon groups; Methyltransferases

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RNA chain , 2 types, 4 molecules DEIK

#3: RNA chain RNA (34-MER)


Mass: 11009.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: box C/D RNA / Source: (gene. exp.) Pyrococcus furiosus (archaea)
#5: RNA chain RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')


Mass: 4156.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The RNA was chemically synthesized

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Non-polymers , 2 types, 29 molecules

#6: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The complex was equilibrated with reservoir solutions containing 0-400 mM potassium chloride, 200 mM-1.5 M sodium chloride, 150-250 mM magnesium acetate, 200 mM ammonium acetate, 50 mM HEPES- ...Details: The complex was equilibrated with reservoir solutions containing 0-400 mM potassium chloride, 200 mM-1.5 M sodium chloride, 150-250 mM magnesium acetate, 200 mM ammonium acetate, 50 mM HEPES-NaOH (pH 7.0), and 0 5% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 63177 / Num. obs: 61445 / % possible obs: 89.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Biso Wilson estimate: 56.33 Å2 / Rsym value: 0.074
Reflection shellResolution: 2.7→2.8 Å / % possible all: 58.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.729→33.572 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 34.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2845 1789 3.26 %
Rwork0.2218 --
obs0.2238 54883 79.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.602 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-50.8446 Å20 Å217.4718 Å2
2---26.8336 Å2-0 Å2
3----24.011 Å2
Refinement stepCycle: LAST / Resolution: 2.729→33.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11458 1994 52 27 13531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113955
X-RAY DIFFRACTIONf_angle_d1.49119289
X-RAY DIFFRACTIONf_dihedral_angle_d19.1025661
X-RAY DIFFRACTIONf_chiral_restr0.12214
X-RAY DIFFRACTIONf_plane_restr0.0082127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.729-2.80310.4137760.32682307X-RAY DIFFRACTION45
2.8031-2.88560.3698900.3262642X-RAY DIFFRACTION52
2.8856-2.97870.3908950.30592998X-RAY DIFFRACTION59
2.9787-3.0850.35821160.30023481X-RAY DIFFRACTION68
3.085-3.20850.40071300.29523845X-RAY DIFFRACTION76
3.2085-3.35440.32421420.28394220X-RAY DIFFRACTION83
3.3544-3.5310.35581520.25724454X-RAY DIFFRACTION87
3.531-3.7520.29181580.23384559X-RAY DIFFRACTION89
3.752-4.04120.31351580.20984650X-RAY DIFFRACTION91
4.0412-4.44710.23311620.18664793X-RAY DIFFRACTION94
4.4471-5.08870.23921670.19084902X-RAY DIFFRACTION95
5.0887-6.40390.27221700.23175056X-RAY DIFFRACTION98
6.4039-33.57420.2371730.17975187X-RAY DIFFRACTION99

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