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

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Basic information

Entry
Database: PDB / ID: 3nvk
TitleStructural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle
Components
  • 50S ribosomal protein L7AeRibosome
  • Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
  • NOP5/NOP56 related protein
  • RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
  • RNA (5'-R(*GP*CP*CP*GP*UP*UP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3')
KeywordsTRANSFERASE/RNA / Nop domain kink turn methyl transferase / ribosome biogenesis spliceosome biogenesis / 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 / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / rRNA processing / methylation ...box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / snoRNA binding / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / rRNA processing / methylation / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / 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 / 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-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: 3.209 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NOP5/NOP56 related protein
F: NOP5/NOP56 related protein
E: 50S ribosomal protein L7Ae
H: 50S ribosomal protein L7Ae
I: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
J: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
K: RNA (5'-R(*GP*CP*CP*GP*UP*UP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3')
G: RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3')
L: RNA (5'-R(*GP*CP*CP*GP*UP*UP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3')
S: 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)200,07812
Polymers199,28110
Non-polymers7972
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18250 Å2
ΔGint-103 kcal/mol
Surface area67330 Å2
Unit cell
Length a, b, c (Å)330.039, 94.548, 97.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 8:290 or resseq 313:369 )
211chain F and (resseq 8:290 or resseq 313:369 )
112chain E and (resseq 4:124 )
212chain H and (resseq 4:124 )
113chain I and (resseq 1:227 )
213chain J and (resseq 1:227 )
114chain K and (resseq 6:24 )
214chain L and (resseq 6:24 )

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 3 types, 6 molecules AFEHIJ

#1: Protein NOP5/NOP56 related protein


Mass: 43470.082 Da / Num. of mol.: 2
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 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) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: rpl7ae, PF1367 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U160
#3: 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) / 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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RNA chain , 2 types, 4 molecules KLGS

#4: RNA chain RNA (5'-R(*GP*CP*CP*GP*UP*UP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3')


Mass: 11009.606 Da / Num. of mol.: 2 / Source method: obtained synthetically
#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

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Non-polymers , 1 types, 2 molecules

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


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: 3.83 Å3/Da / Density % sol: 67.85 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 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, 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 23-BM-B2
Detector
TypeIDDetector
MAR scanner 300 mm plate1IMAGE PLATE
MARMOSAIC 225 mm CCD2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
11SINGLE WAVELENGTHMx-ray1
21SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 45020 / Num. obs: 42641 / % possible obs: 83.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 80.34 Å2
Reflection shellResolution: 3.2→50 Å / % possible all: 83.3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.209→39.69 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 31.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 4099 10.09 %
Rwork0.2304 --
obs0.2361 40618 79.56 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.429 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-42.6477 Å2-0 Å2-0 Å2
2---27.5423 Å2-0 Å2
3----15.1054 Å2
Refinement stepCycle: LAST / Resolution: 3.209→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11392 1162 52 0 12606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112956
X-RAY DIFFRACTIONf_angle_d1.62217750
X-RAY DIFFRACTIONf_dihedral_angle_d20.225160
X-RAY DIFFRACTIONf_chiral_restr0.1182018
X-RAY DIFFRACTIONf_plane_restr0.0072076
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2771X-RAY DIFFRACTIONPOSITIONAL
12F2771X-RAY DIFFRACTIONPOSITIONAL0.06
21E926X-RAY DIFFRACTIONPOSITIONAL
22H926X-RAY DIFFRACTIONPOSITIONAL0.024
31I1822X-RAY DIFFRACTIONPOSITIONAL
32J1822X-RAY DIFFRACTIONPOSITIONAL0.052
41K413X-RAY DIFFRACTIONPOSITIONAL
42L413X-RAY DIFFRACTIONPOSITIONAL0.029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2088-3.24650.425950.3388791X-RAY DIFFRACTION50
3.2465-3.28610.4283910.3307834X-RAY DIFFRACTION54
3.2861-3.32770.40061010.3194901X-RAY DIFFRACTION58
3.3277-3.37150.37791140.3102969X-RAY DIFFRACTION62
3.3715-3.41760.39091150.31621037X-RAY DIFFRACTION69
3.4176-3.46640.34721100.2991123X-RAY DIFFRACTION70
3.4664-3.51810.33411290.27991152X-RAY DIFFRACTION74
3.5181-3.57310.37991350.29691196X-RAY DIFFRACTION77
3.5731-3.63160.35061460.28711241X-RAY DIFFRACTION78
3.6316-3.69420.35511560.28531278X-RAY DIFFRACTION84
3.6942-3.76130.35551650.27171301X-RAY DIFFRACTION82
3.7613-3.83360.36691520.25471249X-RAY DIFFRACTION83
3.8336-3.91180.29331430.26021302X-RAY DIFFRACTION81
3.9118-3.99680.3061290.24291310X-RAY DIFFRACTION83
3.9968-4.08960.33331630.24061277X-RAY DIFFRACTION81
4.0896-4.19180.27061430.23041292X-RAY DIFFRACTION84
4.1918-4.3050.28831700.21611293X-RAY DIFFRACTION82
4.305-4.43150.26491540.20021314X-RAY DIFFRACTION84
4.4315-4.57440.27441550.19911295X-RAY DIFFRACTION83
4.5744-4.73760.23271640.20521301X-RAY DIFFRACTION82
4.7376-4.9270.30241500.21771311X-RAY DIFFRACTION83
4.927-5.15070.25611310.21321329X-RAY DIFFRACTION83
5.1507-5.42170.28421370.23071330X-RAY DIFFRACTION83
5.4217-5.76040.26381200.26481359X-RAY DIFFRACTION83
5.7604-6.20360.32721460.23981405X-RAY DIFFRACTION87
6.2036-6.82510.27171710.20571449X-RAY DIFFRACTION90
6.8251-7.80620.23061800.17781495X-RAY DIFFRACTION93
7.8062-9.81030.19351380.15481661X-RAY DIFFRACTION97
9.8103-39.69340.26351960.24341724X-RAY DIFFRACTION100

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