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- PDB-5lsl: Crystal structure of yeast Hsh49p in complex with Cus1p binding d... -

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Basic information

Entry
Database: PDB / ID: 5lsl
TitleCrystal structure of yeast Hsh49p in complex with Cus1p binding domain.
Components
  • Cold sensitive U2 snRNA suppressor 1
  • Protein HSH49
KeywordsRNA binding domain / Splicing / U2 snRNP / SF3b complex
Function / homology
Function and homology information


U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / RNA binding / nucleus
Similarity search - Function
SF3B4, RNA recognition motif 1 / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...SF3B4, RNA recognition motif 1 / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cold sensitive U2 snRNA suppressor 1 / Protein HSH49
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
Authorsvan Roon, A.M. / Obayashi, E. / Sposito, B. / Oubridge, C. / Nagai, K.
CitationJournal: RNA / Year: 2017
Title: Crystal structure of U2 snRNP SF3b components: Hsh49p in complex with Cus1p-binding domain.
Authors: van Roon, A.M. / Oubridge, C. / Obayashi, E. / Sposito, B. / Newman, A.J. / Seraphin, B. / Nagai, K.
History
DepositionSep 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Protein HSH49
E: Cold sensitive U2 snRNA suppressor 1
B: Protein HSH49
F: Cold sensitive U2 snRNA suppressor 1
C: Protein HSH49
H: Cold sensitive U2 snRNA suppressor 1
D: Protein HSH49
G: Cold sensitive U2 snRNA suppressor 1


Theoretical massNumber of molelcules
Total (without water)84,0048
Polymers84,0048
Non-polymers00
Water7,242402
1
A: Protein HSH49
E: Cold sensitive U2 snRNA suppressor 1


Theoretical massNumber of molelcules
Total (without water)21,0012
Polymers21,0012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-12 kcal/mol
Surface area7250 Å2
MethodPISA
2
B: Protein HSH49
F: Cold sensitive U2 snRNA suppressor 1


Theoretical massNumber of molelcules
Total (without water)21,0012
Polymers21,0012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-12 kcal/mol
Surface area7410 Å2
MethodPISA
3
C: Protein HSH49
G: Cold sensitive U2 snRNA suppressor 1


Theoretical massNumber of molelcules
Total (without water)21,0012
Polymers21,0012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-12 kcal/mol
Surface area7380 Å2
MethodPISA
4
H: Cold sensitive U2 snRNA suppressor 1
D: Protein HSH49


Theoretical massNumber of molelcules
Total (without water)21,0012
Polymers21,0012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-11 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.888, 47.776, 88.019
Angle α, β, γ (deg.)89.890, 83.610, 85.570
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein HSH49


Mass: 11612.056 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HSH49, YOR319W, O6142 / Plasmid: pRK-172 / Details (production host): His-tag with a TEV cleavage site / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q99181
#2: Protein
Cold sensitive U2 snRNA suppressor 1


Mass: 9388.993 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CUS1, YMR240C, YM9408.02C / Plasmid: pRK-172
Details (production host): His-tagged protein with TEV cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q02554
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.23 Å3/Da / Density % sol: 44.75 % / Description: thin plate with dimensions 0.25x0.1 mm
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 18% PEG4000, 0.1M Tris HCl pH 8.5, 45 mM LiSO4 / PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→44.47 Å / Num. obs: 84322 / % possible obs: 96.7 % / Redundancy: 2.3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.65-1.681.90.3380.801195
9.04-44.473.90.0390.998198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MDF

3mdf


Resolution: 1.65→44.47 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.978 / SU ML: 0.068 / SU R Cruickshank DPI: 0.0955 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.092 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 4234 5 %random
Rwork0.1952 ---
obs0.1963 80084 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 79.41 Å2 / Biso mean: 18.689 Å2 / Biso min: 6.32 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.3 Å2-0.05 Å2
2---0.26 Å2-0.38 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 1.65→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4583 0 0 402 4985
Biso mean---23.47 -
Num. residues----564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024689
X-RAY DIFFRACTIONr_bond_other_d0.0020.024681
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9846344
X-RAY DIFFRACTIONr_angle_other_deg0.976310753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54224.233215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9915858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9681532
X-RAY DIFFRACTIONr_chiral_restr0.110.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021056
X-RAY DIFFRACTIONr_mcbond_it1.410.6652249
X-RAY DIFFRACTIONr_mcbond_other1.410.6652248
X-RAY DIFFRACTIONr_mcangle_it2.0720.9832796
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 274 -
Rwork0.257 5859 -
all-6133 -
obs--95.16 %
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)
10.53530.34080.12072.704-0.51090.71580.00920.0006-0.0652-0.0251-0.0112-0.02920.07920.0290.0020.04870.0051-0.00740.0097-0.00150.023348.09121.48971.692
21.53540.0483-0.511.9193-0.42910.6969-0.01140.0176-0.0098-0.00780.0430.20160.0051-0.1053-0.03170.058-0-0.00920.04850.00030.081639.08137.29972.756
30.46320.4687-0.14212.81510.77291.5550.0233-0.01650.04520.1047-0.0264-0.0322-0.0971-0.00240.00310.1746-0.0043-0.01070.020.00610.024250.18115.93527.102
41.946-0.11830.83592.86490.34421.64070.0079-0.02460.01280.14480.0463-0.44360.14590.3456-0.05410.23970.0134-0.02380.1127-0.00110.119859.1340.18725.754
50.74570.10280.45051.81060.57371.55450.01480.0071-0.06410.1065-0.0090.02060.059-0.0643-0.00580.0465-0.0008-0.00860.00540.00240.024355.389-3.0587.112
61.5397-0.06730.18462.5411-0.46072.1005-0.02560.0290.0079-0.11730.0490.4880.0966-0.3769-0.02340.2192-0.0241-0.02980.0927-0.01160.145935.08826.03445.352
70.4368-0.2254-0.27682.8597-0.71511.61370.0015-0.00050.0511-0.1253-0.00140.0325-0.1113-0.0016-0.00020.156-0.0073-0.00530.0183-0.00530.01946.45140.21644.131
81.5731-0.3104-0.6411.30770.40241.5633-0.03990.02110.09210.12480.0061-0.2663-0.25130.19950.03380.1975-0.0445-0.0640.05730.0250.1266.90210.99286.085
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 86
2X-RAY DIFFRACTION2E289 - 350
3X-RAY DIFFRACTION3B8 - 86
4X-RAY DIFFRACTION4F288 - 350
5X-RAY DIFFRACTION5C8 - 86
6X-RAY DIFFRACTION6H289 - 350
7X-RAY DIFFRACTION7D8 - 86
8X-RAY DIFFRACTION8G289 - 350

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