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- PDB-4nut: Crystal structure of the complex between Snu13p and the PEP domai... -

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Basic information

Entry
Database: PDB / ID: 4nut
TitleCrystal structure of the complex between Snu13p and the PEP domain of Rsa1
Components
  • 13 kDa ribonucleoprotein-associated protein
  • Ribosome assembly 1 protein
KeywordsRNA BINDING PROTEIN / SnoRNP assembly
Function / homology
Function and homology information


snoRNA guided rRNA 2'-O-methylation / box C/D sno(s)RNA 3'-end processing / box C/D methylation guide snoRNP complex / U4/U6 snRNP / U4 snRNA binding / U3 snoRNA binding / box C/D snoRNP assembly / U4 snRNP / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol ...snoRNA guided rRNA 2'-O-methylation / box C/D sno(s)RNA 3'-end processing / box C/D methylation guide snoRNP complex / U4/U6 snRNP / U4 snRNA binding / U3 snoRNA binding / box C/D snoRNP assembly / U4 snRNP / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / U4/U6 x U5 tri-snRNP complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / spliceosomal complex / mRNA splicing, via spliceosome / ribosomal large subunit assembly / nucleolus / RNA binding / nucleoplasm / nucleus
Similarity search - Function
FMR1-interacting protein 1, conserved domain / FMR1-interacting protein 1 (NUFIP1) / H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 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 ...FMR1-interacting protein 1, conserved domain / FMR1-interacting protein 1 (NUFIP1) / H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
13 kDa ribonucleoprotein-associated protein / Ribosome assembly 1 protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsCharron, C. / Chagot, M.E. / Manival, X. / Branlant, C. / Charpentier, B.
CitationJournal: J.Cell Biol. / Year: 2014
Title: Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control
Authors: Bizarro, J. / Charron, C. / Boulon, S. / Westman, B. / Pradet-Balade, B. / Vandermoere, F. / Chagot, M.E. / Hallais, M. / Ahmad, Y. / Leonhardt, H. / Lamond, A. / Manival, X. / Branlant, C. ...Authors: Bizarro, J. / Charron, C. / Boulon, S. / Westman, B. / Pradet-Balade, B. / Vandermoere, F. / Chagot, M.E. / Hallais, M. / Ahmad, Y. / Leonhardt, H. / Lamond, A. / Manival, X. / Branlant, C. / Charpentier, B. / Verheggen, C. / Bertrand, E.
History
DepositionDec 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: 13 kDa ribonucleoprotein-associated protein
B: Ribosome assembly 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9863
Polymers20,8902
Non-polymers961
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-19 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.732, 59.732, 92.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-367-

HOH

21A-368-

HOH

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Components

#1: Protein 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein 1


Mass: 13875.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SNU13, YEL026W / Production host: Escherichia coli (E. coli) / References: UniProt: P39990
#2: Protein Ribosome assembly 1 protein


Mass: 7015.143 Da / Num. of mol.: 1 / Fragment: PEP domain, UNP residues 238-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RSA1, YPL193W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08932
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.3M ammonium sulfate, 70mM sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2013
RadiationMonochromator: a channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→55 Å / Num. all: 24971 / Num. obs: 24971 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.55→1.63 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.55→36.58 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.356 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23507 1254 5.1 %RANDOM
Rwork0.19648 ---
all0.19831 23363 --
obs0.19831 23363 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.495 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.55→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 5 95 1267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191190
X-RAY DIFFRACTIONr_bond_other_d0.0010.021215
X-RAY DIFFRACTIONr_angle_refined_deg2.2061.9871609
X-RAY DIFFRACTIONr_angle_other_deg0.94232799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8575147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.11925.20848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64815229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.854157
X-RAY DIFFRACTIONr_chiral_restr0.1380.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
X-RAY DIFFRACTIONr_mcbond_it1.971.656594
X-RAY DIFFRACTIONr_mcbond_other1.9671.651593
X-RAY DIFFRACTIONr_mcangle_it2.7512.467739
X-RAY DIFFRACTIONr_mcangle_other2.7512.471740
X-RAY DIFFRACTIONr_scbond_it3.3322.144595
X-RAY DIFFRACTIONr_scbond_other3.3312.145591
X-RAY DIFFRACTIONr_scangle_other5.1953.026864
X-RAY DIFFRACTIONr_long_range_B_refined7.20214.9861444
X-RAY DIFFRACTIONr_long_range_B_other7.18514.4541396
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 98 -
Rwork0.291 1698 -
obs--98.9 %
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)
10.49290.3030.51420.68240.71111.3597-0.04920.0175-0.016-0.0708-0.05090.0209-0.09130.01750.10010.0675-0.0108-0.02080.0228-0.00350.0458-8.5441-9.8966-14.6792
23.57080.64230.06460.69390.26120.1272-0.09870.0751-0.3729-0.04980.1054-0.136-0.03180.0837-0.00660.03-0.0346-0.02460.11540.04930.11597.3013-14.0984-9.5539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 125
2X-RAY DIFFRACTION2B239 - 265

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