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- PDB-7bb3: Structure of S. pombe YG-box oligomer -

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Basic information

Entry
Database: PDB / ID: 7bb3
TitleStructure of S. pombe YG-box oligomer
ComponentsSurvival motor neuron-like protein 1,Survival motor neuron-like protein 1
KeywordsSPLICING / UsnRNP / Biogenesis / SMN / Oligomerization
Function / homology: / SMN complex / mRNA cis splicing, via spliceosome / spliceosomal snRNP assembly / RNA binding / nucleus / SMN complex subunit smn1
Function and homology information
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.158 Å
AuthorsVeepaschit, J. / Grimm, C. / Fischer, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Fi573/7-2, 8-2 Germany
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Identification and structural analysis of the Schizosaccharomyces pombe SMN complex.
Authors: Veepaschit, J. / Viswanathan, A. / Bordonne, R. / Grimm, C. / Fischer, U.
History
DepositionDec 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Mar 31, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Survival motor neuron-like protein 1,Survival motor neuron-like protein 1
B: Survival motor neuron-like protein 1,Survival motor neuron-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7976
Polymers16,3242
Non-polymers4734
Water543
1
A: Survival motor neuron-like protein 1,Survival motor neuron-like protein 1
B: Survival motor neuron-like protein 1,Survival motor neuron-like protein 1
hetero molecules

A: Survival motor neuron-like protein 1,Survival motor neuron-like protein 1
B: Survival motor neuron-like protein 1,Survival motor neuron-like protein 1
hetero molecules


  • defined by author
  • Evidence: SAXS, Mutating the serine and the alanine residues within the serine-motif (KxxxSWxxAxxxT) results in perfect YG-box-dimeric-units in solution (SAXS data), showing that the serine-motif is ...Evidence: SAXS, Mutating the serine and the alanine residues within the serine-motif (KxxxSWxxAxxxT) results in perfect YG-box-dimeric-units in solution (SAXS data), showing that the serine-motif is exclusively involved in multimerization of dimers and is located in an interface distinct from the YG-motif.
  • 33.6 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)33,59312
Polymers32,6484
Non-polymers9458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-47 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.190, 83.710, 160.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Survival motor neuron-like protein 1,Survival motor neuron-like protein 1


Mass: 8162.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: smn1, yab8, SPAC2G11.08c / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q09808
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.61 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 65 % 2-methylpentanediol, 80 mM KCl, 40 mM HEPES / PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.158→40.493 Å / Num. obs: 10282 / % possible obs: 99.38 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.47 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1046 / Rpim(I) all: 0.04472 / Rrim(I) all: 0.1142 / Net I/σ(I): 10.85
Reflection shellResolution: 2.158→2.235 Å / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 1010 / CC1/2: 0.708 / CC star: 0.911 / Rpim(I) all: 0.3344 / Rrim(I) all: 0.8907 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RG5
Resolution: 2.158→40.493 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 37.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2919 531 5.17 %
Rwork0.2567 9732 -
obs0.2586 10263 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.82 Å2 / Biso min: 33.29 Å2
Refinement stepCycle: final / Resolution: 2.158→40.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 88 3 983
Biso mean--81.08 54.93 -
Num. residues----108
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1582-2.37530.35071230.3412375100
2.3753-2.7190.3011400.2877240799
2.719-3.42530.33831210.27222432100
3.4253-40.4930.27021470.2336251899

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