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- PDB-1n9r: Crystal structure of a heptameric ring complex of yeast SmF in sp... -

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Basic information

Entry
Database: PDB / ID: 1n9r
TitleCrystal structure of a heptameric ring complex of yeast SmF in spacegroup P4122
ComponentsSmall nuclear ribonucleoprotein F
KeywordsTRANSLATION / snrnp / Sm protein / heptamer
Function / homology
Function and homology information


splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / U2-type prespliceosome assembly / commitment complex / U4 snRNP / U2 snRNP / poly(U) RNA binding / U1 snRNP ...splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / U2-type prespliceosome assembly / commitment complex / U4 snRNP / U2 snRNP / poly(U) RNA binding / U1 snRNP / spliceosomal complex assembly / mRNA 5'-splice site recognition / U5 snRNP / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / RNA binding / nucleus / cytoplasm
Similarity search - Function
Small nuclear ribonucleoprotein F / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. ...Small nuclear ribonucleoprotein F / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Small nuclear ribonucleoprotein F
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCollins, B.M. / Cubeddu, L. / Naidoo, N. / Harrop, S.J. / Kornfeld, G.D. / Dawes, I.W. / Curmi, P.M.G. / Mabbutt, B.C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA: Crystal structure of an oligomeric complex of yeast SmF
Authors: Collins, B.M. / Cubeddu, L. / Naidoo, N. / Harrop, S.J. / Kornfeld, G.D. / Dawes, I.W. / Curmi, P.M.G. / Mabbutt, B.C.
History
DepositionNov 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 2023Group: 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 / 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: Small nuclear ribonucleoprotein F
B: Small nuclear ribonucleoprotein F
C: Small nuclear ribonucleoprotein F
D: Small nuclear ribonucleoprotein F
E: Small nuclear ribonucleoprotein F
F: Small nuclear ribonucleoprotein F
G: Small nuclear ribonucleoprotein F


Theoretical massNumber of molelcules
Total (without water)74,4107
Polymers74,4107
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-48 kcal/mol
Surface area21710 Å2
MethodPISA
2
A: Small nuclear ribonucleoprotein F
B: Small nuclear ribonucleoprotein F
C: Small nuclear ribonucleoprotein F
D: Small nuclear ribonucleoprotein F
E: Small nuclear ribonucleoprotein F
F: Small nuclear ribonucleoprotein F
G: Small nuclear ribonucleoprotein F

A: Small nuclear ribonucleoprotein F
B: Small nuclear ribonucleoprotein F
C: Small nuclear ribonucleoprotein F
D: Small nuclear ribonucleoprotein F
E: Small nuclear ribonucleoprotein F
F: Small nuclear ribonucleoprotein F
G: Small nuclear ribonucleoprotein F


Theoretical massNumber of molelcules
Total (without water)148,82014
Polymers148,82014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area18540 Å2
ΔGint-114 kcal/mol
Surface area41260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.891, 79.891, 251.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Cell settingtetragonal
Space group name H-MP4122

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Components

#1: Protein
Small nuclear ribonucleoprotein F / SmF / Sm-like snRNP protein / snRNP-F / Sm protein F / Sm-F


Mass: 10630.022 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P54999

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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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
210 mMdithiothreitol1drop
320 mg/mlprotein1drop
424 %PEG33501reservoir
50.1 MTris1reservoirpH8.5
60.1 Msodium acetate1reservoir
1Tris-NaCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.8→79 Å / Num. all: 19819 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 84.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.6
Reflection
*PLUS
Highest resolution: 2.8 Å
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I81 truncated to poly-serine

1i81


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.911 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement used / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26783 1075 5.1 %RANDOM
Rwork0.25357 ---
all0.25431 19819 --
obs0.25431 19819 99.96 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.316 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 0 0 3837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0213902
X-RAY DIFFRACTIONr_bond_other_d0.0010.023525
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.9495268
X-RAY DIFFRACTIONr_angle_other_deg0.93238160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6183471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5115682
X-RAY DIFFRACTIONr_chiral_restr0.1130.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024382
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02838
X-RAY DIFFRACTIONr_nbd_refined0.2820.3859
X-RAY DIFFRACTIONr_nbd_other0.2720.33826
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.5326
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0470.513
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5160.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.321
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5580.52
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2391.52355
X-RAY DIFFRACTIONr_mcangle_it2.30723789
X-RAY DIFFRACTIONr_scbond_it2.64131547
X-RAY DIFFRACTIONr_scangle_it4.5324.51479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.381 68
Rwork0.322 1416
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)
12.76421.28250.85175.57250.64042.4033-0.06440.135-0.1269-0.20310.2398-0.0093-0.04710.1758-0.17530.2294-0.02380.0110.1114-0.06740.123770.951728.51253.7655
25.99341.57371.93234.2002-0.66016.4702-0.1840.11550.1069-0.1911-0.0681-0.0604-0.52780.12560.25210.33430.017-0.01170.0784-0.03280.101363.21973940.3467
33.50561.6885-0.80194.46870.25014.1164-0.0299-0.0563-0.2082-0.10740.0174-0.0938-0.33760.14610.01250.3305-0.03-0.0340.0213-0.00970.153966.739538.954822.2039
45.5281-0.54770.56973.76470.89324.480.0722-0.02450.07030.0842-0.0069-0.1427-0.31270.3167-0.06530.1879-0.09020.00970.2080.00780.085178.768928.562912.6916
53.45351.42651.47845.1779-0.47353.50870.07410.0302-0.06360.121-0.1471-0.1648-0.16740.33760.07310.0746-0.0324-0.00180.3562-0.02770.167190.466915.583318.7988
63.65151.48541.24164.5781-0.36315.3079-0.0581-0.10070.2166-0.039-0.07540.1733-0.12270.22220.13360.0011-0.00870.0140.2648-0.03550.219492.864610.052736.631
75.03980.89220.01896.45711.11263.5978-0.0011-0.16450.17760.15990.0436-0.1291-0.08930.3425-0.04250.12140.0025-0.05190.1907-0.08010.164184.263715.576351.9372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 8626 - 93
2X-RAY DIFFRACTION2BB18 - 8625 - 93
3X-RAY DIFFRACTION3CC19 - 8626 - 93
4X-RAY DIFFRACTION4DD19 - 8626 - 93
5X-RAY DIFFRACTION5EE19 - 8626 - 93
6X-RAY DIFFRACTION6FF18 - 8625 - 93
7X-RAY DIFFRACTION7GG19 - 8626 - 93
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.023
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.1

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