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- PDB-3nvm: Structural basis for substrate placement by an archaeal box C/D r... -

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Basic information

Entry
Database: PDB / ID: 3nvm
TitleStructural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle
Components
  • Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
  • NOP5/NOP56 related protein
KeywordsTRANSFERASE / Nop domain / methyltransferase / ribosome biogenesis / spliceosome biogenesis
Function / homology
Function and homology information


box C/D methylation guide snoRNP complex / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / methyltransferase activity / rRNA processing / methylation / RNA binding
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. / Serum Albumin; Chain A, Domain 1 / 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
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: 3.408 Å
AuthorsXue, S. / Wang, R. / Li, H.
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
DepositionJul 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)69,7072
Polymers69,7072
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-18 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.623, 100.623, 265.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein NOP5/NOP56 related protein


Mass: 42946.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0060 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U4M1
#2: Protein Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Mass: 26760.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: flpA, PF0059 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8U4M2, Transferases; Transferring one-carbon groups; Methyltransferases

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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: 5.56 Å3/Da / Density % sol: 77.89 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1 M imidazole pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 22-ID1
SYNCHROTRONAPS 22-BM2
Detector
TypeIDDetector
MAR scanner 300 mm plate1IMAGE PLATE
MARMOSAIC 225 mm CCD2CCD
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 35269 / Num. obs: 32901 / % possible obs: 80 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.4→50 Å / % possible all: 26

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.408→49.431 Å / SU ML: 0.51 / σ(F): 1.91 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.316 1606 5.09 %
Rwork0.2418 --
obs0.2455 31528 76.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 191.675 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-31.0898 Å2-0 Å2-0 Å2
2--31.0898 Å20 Å2
3----62.1797 Å2
Refinement stepCycle: LAST / Resolution: 3.408→49.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 0 0 4597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084687
X-RAY DIFFRACTIONf_angle_d1.2646321
X-RAY DIFFRACTIONf_dihedral_angle_d18.8981810
X-RAY DIFFRACTIONf_chiral_restr0.079691
X-RAY DIFFRACTIONf_plane_restr0.006817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4077-3.51760.3688550.3017864X-RAY DIFFRACTION25
3.5176-3.64330.3235790.28781328X-RAY DIFFRACTION38
3.6433-3.78920.30741250.28631825X-RAY DIFFRACTION52
3.7892-3.96150.3211440.2622496X-RAY DIFFRACTION71
3.9615-4.17030.31461450.23933179X-RAY DIFFRACTION88
4.1703-4.43140.24832010.19823369X-RAY DIFFRACTION96
4.4314-4.77330.22191690.19333419X-RAY DIFFRACTION97
4.7733-5.25320.22541950.18283390X-RAY DIFFRACTION96
5.2532-6.01220.29621740.22113404X-RAY DIFFRACTION96
6.0122-7.57040.28311640.21633387X-RAY DIFFRACTION95
7.5704-49.4360.3511550.23793261X-RAY DIFFRACTION92
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)
1-2.232-0.261.47710.9170.24321.4450.2111-0.5942-0.54140.18790.0191-0.2699-0.0143-0.7952-0.26870.4248-0.35830.07372.54610.13181.222825.311923.871718.9248
20.328-0.09382.2932.5898-0.58822.1604-0.6046-0.23211.17170.38270.1839-0.4895-0.1295-1.11860.3530.1904-0.07490.19282.7397-0.04181.351731.616312.232349.7715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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