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- PDB-5aff: Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis... -

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Basic information

Entry
Database: PDB / ID: 5aff
TitleSymportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site
Components
  • RIBOSOMAL PROTEIN L11
  • RIBOSOMAL PROTEIN L5
  • SYMPORTIN 1
KeywordsCHAPERONE / RIBOSOME BIOGENESIS / ALPHA SOLENOID.
Function / homology
Function and homology information


ribosomal large subunit biogenesis / protein import into nucleus / unfolded protein binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex
Similarity search - Function
: / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Armadillo-like helical / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. ...: / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Armadillo-like helical / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Symportin 1 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5
Similarity search - Component
Biological speciesCHAETOMIUM THERMOPHILUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.398 Å
AuthorsCalvino, F.R. / Kharde, S. / Wild, K. / Bange, G. / Sinning, I.
CitationJournal: Nat.Commun. / Year: 2015
Title: Symportin 1 Chaperones 5S Rnp Assembly During Ribosome Biogenesis by Occupying an Essential Rrna-Binding Site.
Authors: Calvino, F.R. / Kharde, S. / Ori, A. / Hendricks, A. / Wild, K. / Kressler, D. / Bange, G. / Hurt, E. / Beck, M. / Sinning, I.
History
DepositionJan 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SYMPORTIN 1
B: RIBOSOMAL PROTEIN L5
C: RIBOSOMAL PROTEIN L11


Theoretical massNumber of molelcules
Total (without water)98,3413
Polymers98,3413
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-11.6 kcal/mol
Surface area34270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.087, 105.959, 147.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SYMPORTIN 1


Mass: 72162.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G0S5S6
#2: Protein/peptide RIBOSOMAL PROTEIN L5


Mass: 6060.083 Da / Num. of mol.: 1 / Fragment: N-TERMINUS LINEAR MOTIF, UNP RESIDUES 1-41
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G0SEG2
#3: Protein RIBOSOMAL PROTEIN L11


Mass: 20119.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHAETOMIUM THERMOPHILUM (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G0SHQ2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM ACETATE, 8% (V/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2012 / Details: PT COATED MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.4→49.29 Å / Num. obs: 13505 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Biso Wilson estimate: 112.54 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.8
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.19 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4GMO AND 3U5E, CHAIN J

4gmo

3u5e
PDB Unreleased entry


Resolution: 3.398→49.256 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 33.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2998 665 4.9 %
Rwork0.2361 --
obs0.2391 13499 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.398→49.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 0 0 5606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075700
X-RAY DIFFRACTIONf_angle_d1.3327720
X-RAY DIFFRACTIONf_dihedral_angle_d18.1872112
X-RAY DIFFRACTIONf_chiral_restr0.053911
X-RAY DIFFRACTIONf_plane_restr0.007980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3976-3.65990.35251370.30612483X-RAY DIFFRACTION99
3.6599-4.02810.31661360.25482524X-RAY DIFFRACTION100
4.0281-4.61060.27871380.22282541X-RAY DIFFRACTION100
4.6106-5.80730.30261260.25622579X-RAY DIFFRACTION100
5.8073-49.26130.28981280.21372707X-RAY DIFFRACTION100

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