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- PDB-3nvi: Structure of N-terminal truncated Nop56/58 bound with L7Ae and bo... -

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Basic information

Entry
Database: PDB / ID: 3nvi
TitleStructure of N-terminal truncated Nop56/58 bound with L7Ae and box C/D RNA
Components
  • 50S ribosomal protein L7Ae
  • NOP5/NOP56 related protein
  • RNA (5'-R(*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 / Kink turn / ribosome biogenesis / Transferase-RNA complex
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / snoRNA binding / small-subunit processome / rRNA processing / cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Helix Hairpins - #4070 / Nop domain / : / : / Archaeal Nop5/56-rel, N-terminal domain / Helix hairpin bin domain superfamily / Nucleolar protein Nop56/Nop58 / Ribosomal protein L7Ae, archaea / NOSIC / NOSIC (NUC001) domain ...Helix Hairpins - #4070 / Nop domain / : / : / Archaeal Nop5/56-rel, N-terminal domain / Helix hairpin bin domain superfamily / Nucleolar protein Nop56/Nop58 / 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 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein eL8 / NOP5/NOP56 related protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.709 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
DepositionJul 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Derived calculations
Revision 1.2Feb 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: 50S ribosomal protein L7Ae
C: NOP5/NOP56 related protein
D: 50S ribosomal protein L7Ae
E: RNA (5'-R(*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')
F: RNA (5'-R(*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')


Theoretical massNumber of molelcules
Total (without water)131,8586
Polymers131,8586
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13070 Å2
ΔGint-99 kcal/mol
Surface area36680 Å2
MethodPISA
2
A: NOP5/NOP56 related protein
B: 50S ribosomal protein L7Ae
E: RNA (5'-R(*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')


Theoretical massNumber of molelcules
Total (without water)65,9293
Polymers65,9293
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-41 kcal/mol
Surface area19890 Å2
MethodPISA
3
C: NOP5/NOP56 related protein
D: 50S ribosomal protein L7Ae
F: RNA (5'-R(*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')


Theoretical massNumber of molelcules
Total (without water)65,9293
Polymers65,9293
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-37 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.216, 91.841, 155.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 127:372 )
211chain C and (resseq 127:372 )
112chain E and (resseq 2:25 )
212chain F and (resseq 2:25 )
113chain B and (resseq 4:124 )
213chain D and (resseq 4:124 )

NCS ensembles :
ID
1
2
3

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Components

#1: Protein NOP5/NOP56 related protein


Mass: 43937.555 Da / Num. of mol.: 2 / Fragment: Sequence database residues 1-369
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


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: PF1367, rpl7ae / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U160
#3: RNA chain RNA (5'-R(*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: 7747.679 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: box C/D RNA / Source: (gene. exp.) Pyrococcus furiosus (archaea)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM potassium chloride, 5 mM magnesium chloride, 50 mM TrisHCl (pH 7.5), and 4%- 8% PEG4000 or PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 22-BM21
Detector
TypeIDDetector
MAR scanner 300 mm plate1IMAGE PLATE
MARMOSAIC 225 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 2.7→50 Å / Num. all: 34629 / Num. obs: 29910 / % possible obs: 86.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.129
Reflection shellResolution: 2.7→50 Å / % possible all: 86.4

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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: 2.709→31.621 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 30.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 1372 4.9 %
Rwork0.2079 --
obs0.21 27997 80.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.819 Å2 / ksol: 0.287 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4837 Å2-0 Å20 Å2
2---16.7855 Å20 Å2
3---18.2691 Å2
Refinement stepCycle: LAST / Resolution: 2.709→31.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5832 1026 0 12 6870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017072
X-RAY DIFFRACTIONf_angle_d1.3419772
X-RAY DIFFRACTIONf_dihedral_angle_d18.1032890
X-RAY DIFFRACTIONf_chiral_restr0.0931142
X-RAY DIFFRACTIONf_plane_restr0.0071072
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1981X-RAY DIFFRACTIONPOSITIONAL
12C1981X-RAY DIFFRACTIONPOSITIONAL0.064
21E513X-RAY DIFFRACTIONPOSITIONAL
22F513X-RAY DIFFRACTIONPOSITIONAL0.034
31B914X-RAY DIFFRACTIONPOSITIONAL
32D914X-RAY DIFFRACTIONPOSITIONAL0.029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7085-2.80530.3455840.32591596X-RAY DIFFRACTION49
2.8053-2.91750.4431220.32942341X-RAY DIFFRACTION72
2.9175-3.05020.38481520.29152801X-RAY DIFFRACTION86
3.0502-3.21090.31241620.25613012X-RAY DIFFRACTION93
3.2109-3.41180.31561530.24233106X-RAY DIFFRACTION94
3.4118-3.67490.2687890.25121978X-RAY DIFFRACTION84
3.6749-4.0440.2511940.2211852X-RAY DIFFRACTION64
4.044-4.62760.231680.16853268X-RAY DIFFRACTION99
4.6276-5.82440.22911640.19133324X-RAY DIFFRACTION99
5.8244-31.62360.20821840.1873347X-RAY DIFFRACTION96

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