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

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Basic information

Entry
Database: PDB / ID: 5lsb
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 / Prp19 complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome ...U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / Prp19 complex / 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 ...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: 2.7 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
DepositionAug 24, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,9796
Polymers101,9796
Non-polymers00
Water1086
1
A: Protein HSH49
B: Cold sensitive U2 snRNA suppressor 1


Theoretical massNumber of molelcules
Total (without water)33,9932
Polymers33,9932
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-10 kcal/mol
Surface area12950 Å2
MethodPISA
2
C: Protein HSH49
D: Cold sensitive U2 snRNA suppressor 1


Theoretical massNumber of molelcules
Total (without water)33,9932
Polymers33,9932
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-11 kcal/mol
Surface area12850 Å2
MethodPISA
3
F: Protein HSH49
H: Cold sensitive U2 snRNA suppressor 1


Theoretical massNumber of molelcules
Total (without water)33,9932
Polymers33,9932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-11 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.083, 142.083, 40.355
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Protein HSH49


Mass: 24604.141 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: GGS sequence at the N-terminus is non-natural and left over from TEV-protease cleavage site
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HSH49, YOR319W, O6142 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99181
#2: Protein Cold sensitive U2 snRNA suppressor 1


Mass: 9388.993 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Hsh49p binding domain of Cus1p between residues 290-368
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CUS1, YMR240C, YM9408.02C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q02554
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.31 Å3/Da / Density % sol: 46.66 % / Description: Thin needles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Equal volumes of 10-15 mg/ml protein solution were mixed with an equal volume of reservoir solution containing 2.45-2.65 M NaCl in 0.1M sodium acetate pH 4.8-4.9
PH range: 4.8-4.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L \10.638
11-K, -H, -L \20.362
ReflectionResolution: 2.7→35.52 Å / Num. obs: 25001 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.984 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.083 / Rrim(I) all: 0.171 / Net I/σ(I): 13 / Num. measured all: 104708 / Scaling rejects: 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.7-2.834.20.6250.6771100
8.96-35.523.90.0470.996198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.5 Å28.77 Å
Translation4.5 Å28.77 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDS2012-09-26data reduction
Aimless0.1.29data scaling
PHASER2.5.2phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LSL, 1CVJ

5lsl

1cvj


Resolution: 2.7→35.52 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.847 / SU B: 20.317 / SU ML: 0.204 / SU R Cruickshank DPI: 0.3657 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1300 5.2 %random
Rwork0.1836 ---
obs0.1862 23691 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.82 Å2 / Biso mean: 30.827 Å2 / Biso min: 9.01 Å2
Baniso -1Baniso -2Baniso -3
1-10.08 Å20 Å20 Å2
2--10.08 Å20 Å2
3----20.16 Å2
Refinement stepCycle: final / Resolution: 2.7→35.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5793 0 0 6 5799
Biso mean---22.86 -
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025901
X-RAY DIFFRACTIONr_bond_other_d0.0020.025874
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.987946
X-RAY DIFFRACTIONr_angle_other_deg0.943313501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1295697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86324.769281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.939151103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2751533
X-RAY DIFFRACTIONr_chiral_restr0.0850.2869
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021334
X-RAY DIFFRACTIONr_mcbond_it1.9781.4852833
X-RAY DIFFRACTIONr_mcbond_other1.9771.4852832
X-RAY DIFFRACTIONr_mcangle_it3.0772.223515
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 99 -
Rwork0.202 1734 -
all-1833 -
obs--99.95 %
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)
10.64680.68120.1881.8410.34170.63570.02820.1384-0.0816-0.0427-0.002-0.0467-0.005-0.0036-0.02610.04750.00090.0170.10160.00570.081646.557124.461-6.825
24.04151.51550.9160.57020.3112.9962-0.0353-0.00990.0994-0.0071-0.00380.03150.2358-0.35620.03910.0867-0.00420.00240.06560.01910.049358.85140.43314.121
31.8339-0.32950.08540.8488-0.04940.6151-0.1109-0.2929-0.05510.06190.06410.1140.0483-0.03830.04670.1515-0.04060.01340.1042-0.02360.122262.263182.18726.884
41.82012.1442-0.21215.6675-0.51952.5722-0.16070.19670.1977-0.20740.2690.20650.0116-0.0793-0.10830.1090.0140.03830.05420.01150.098981.794186.4635.771
51.48251.55310.82462.47590.40380.73650.0807-0.041-0.02860.0459-0.0846-0.15830.0367-0.0060.00390.14830.0327-0.00120.1446-0.02530.1385130.793185.72139.412
60.1676-0.30210.1495.19991.53622.1681-0.0675-0.0420.2177-0.2489-0.0429-0.2999-0.4690.22030.11040.2204-0.0353-0.07160.1927-0.04220.3104120.802168.27318.433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 205
2X-RAY DIFFRACTION2B289 - 350
3X-RAY DIFFRACTION3C8 - 205
4X-RAY DIFFRACTION4D289 - 350
5X-RAY DIFFRACTION5F8 - 205
6X-RAY DIFFRACTION6H289 - 350

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