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- PDB-5ewr: C merolae U4 snRNP protein Snu13 -

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Basic information

Entry
Database: PDB / ID: 5ewr
TitleC merolae U4 snRNP protein Snu13
ComponentsBox C/D snoRNP and U4 snRNP component Snu13p
KeywordsRNA BINDING PROTEIN / splicing
Function / homology
Function and homology information


ribosome biogenesis / ribonucleoprotein complex / nucleolus / RNA binding
Similarity search - Function
H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsGarside, E.L. / Black, C. / Rader, S. / MacMillan, A.M.
CitationJournal: Protein Sci. / Year: 2016
Title: Conserved structure of Snu13 from the highly reduced spliceosome of Cyanidioschyzon merolae.
Authors: Black, C.S. / Garside, E.L. / MacMillan, A.M. / Rader, S.D.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Box C/D snoRNP and U4 snRNP component Snu13p


Theoretical massNumber of molelcules
Total (without water)15,7901
Polymers15,7901
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.330, 57.582, 65.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Box C/D snoRNP and U4 snRNP component Snu13p


Mass: 15790.304 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (eukaryote) / Gene: CYME_CMP335C / Production host: Escherichia coli (E. coli) / References: UniProt: M1VFX0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.81 Å3/Da / Density % sol: 31.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 31% PEG 3350, 100 mM sodium acetate pH 4.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12171 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12171 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 5143 / % possible obs: 99.8 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.031 / Rrim(I) all: 0.114 / Χ2: 0.96 / Net I/av σ(I): 23.136 / Net I/σ(I): 10.5 / Num. measured all: 70926
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.3914.30.2512470.990.0680.260.964100
2.39-2.4314.10.2432460.9840.0660.2521.008100
2.43-2.4814.40.2242480.990.0610.2320.949100
2.48-2.53140.2012620.9930.0550.2081.024100
2.53-2.5914.30.1952370.9890.0530.2020.976100
2.59-2.6514.10.1642530.9950.0450.171.006100
2.65-2.7114.20.1662590.9960.0450.1720.844100
2.71-2.7914.10.1362460.9960.0370.1410.98100
2.79-2.8714.20.132540.9940.0360.1350.983100
2.87-2.9614.20.1162460.9960.0320.120.937100
2.96-3.07140.0982610.9980.0270.1020.926100
3.07-3.19140.092480.9970.0250.0930.936100
3.19-3.33140.0762580.9990.0210.0790.916100
3.33-3.5113.80.0722540.9980.020.0750.869100
3.51-3.7313.70.0632610.9980.0180.0650.871100
3.73-4.0213.70.0632570.9990.0180.0661.025100
4.02-4.4213.40.0752660.9980.0210.0781.00798.2
4.42-5.0613.20.0912660.9970.0260.0950.94999.3
5.06-6.3712.90.1062660.9960.030.1111.07899.3
6.37-5011.80.163080.9940.0470.1670.951100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ALE

2ale


Resolution: 2.35→43.212 Å / FOM work R set: 0.8309 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 262 5.12 %
Rwork0.1662 4851 -
obs0.169 5113 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.14 Å2 / Biso mean: 40.51 Å2 / Biso min: 19.51 Å2
Refinement stepCycle: final / Resolution: 2.35→43.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 0 42 975
Biso mean---40.04 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016947
X-RAY DIFFRACTIONf_angle_d1.5211287
X-RAY DIFFRACTIONf_chiral_restr0.055158
X-RAY DIFFRACTIONf_plane_restr0.008165
X-RAY DIFFRACTIONf_dihedral_angle_d14.14360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3496-2.96010.25111390.196123522491
2.9601-43.21930.20761230.15524992622
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)
14.0757-4.26761.26694.5916-1.59451.2497-1.2726-1.38331.16250.85290.61-0.5005-1.2722-0.8160.72740.56540.132-0.06730.406-0.06920.41324.121913.965885.7241
27.4146-3.2723-4.50894.99935.30086.0389-0.16620.028-0.0372-0.3897-0.11840.58590.0964-0.22330.36470.3848-0.0766-0.03960.40310.06470.3297-3.81732.667772.4342
39.0239-2.73545.24697.8108-5.00894.9803-0.01880.5265-0.21350.1527-0.813-0.64920.20990.49680.40190.33980.05610.02470.3028-0.05030.33967.2714-3.003670.3841
47.3372.8724-2.63212.5256-0.14943.0903-0.0830.4738-0.3933-0.09780.1554-0.1590.0830.43560.04590.29870.02040.00460.4435-0.00580.318312.79224.279673.028
53.901-1.0583-0.94960.89980.86044.10890.0247-0.2960.25190.44410.1065-0.2398-0.35190.4371-0.09680.3062-0.0082-0.04290.2792-0.04050.339612.65518.258984.2201
64.84162.2599-3.70975.3132-1.76314.7255-0.3964-0.22890.7692-0.24950.25340.06580.50990.18120.07180.2520.0106-0.02230.26570.00660.29826.804210.372277.8082
78.74511.2415.49849.02265.51035.92420.4969-0.9713-0.07220.3292-0.6611.02561.0254-1.51910.35970.3674-0.1329-0.04550.42140.11810.3442-0.4227-2.102981.7741
89.21667.58096.12288.66996.51235.82380.1153-0.8171-0.49580.0302-0.45810.23340.84040.92370.1010.44490.01160.03040.29520.04520.31263.8111-5.367980.8501
97.98082.51890.36925.28114.84089.1216-0.37110.2336-0.1394-0.7730.0984-0.4939-0.38490.40670.40520.3728-0.02270.01580.3140.05870.34485.70283.328464.4695
105.4779-0.52450.9188.55214.7948.9024-0.2357-0.04650.2314-0.5290.0909-0.1462-1.1289-0.6420.22850.44050.0606-0.02740.36940.06070.3180.89412.256467.5387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 32 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 49 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 55 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 74 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 92 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 93 through 102 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 103 through 109 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 110 through 117 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 118 through 127 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 128 through 145 )A0

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