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- PDB-6f4j: Crystal structure of Drosophila melanogaster SNF/U2A' complex -

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Basic information

Entry
Database: PDB / ID: 6f4j
TitleCrystal structure of Drosophila melanogaster SNF/U2A' complex
Components
  • Probable U2 small nuclear ribonucleoprotein A'
  • U1 small nuclear ribonucleoprotein A
KeywordsSPLICING / SNF / U2A' / RRM / Evolution
Function / homology
Function and homology information


primary sex determination, soma / snRNA stem-loop binding / pre-mRNA intronic pyrimidine-rich binding / mRNA Splicing - Major Pathway / female germ-line sex determination / small nuclear ribonucleoprotein complex / poly(U) RNA binding / U2 snRNP / U1 snRNP / oogenesis ...primary sex determination, soma / snRNA stem-loop binding / pre-mRNA intronic pyrimidine-rich binding / mRNA Splicing - Major Pathway / female germ-line sex determination / small nuclear ribonucleoprotein complex / poly(U) RNA binding / U2 snRNP / U1 snRNP / oogenesis / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / U2 snRNA binding / U1 snRNA binding / catalytic step 2 spliceosome / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / chromatin organization / mitotic cell cycle / spermatogenesis / ribonucleoprotein complex / mRNA binding / protein-containing complex / identical protein binding / nucleus
Similarity search - Function
U2 small nuclear ribonucleoprotein A' / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / RRM (RNA recognition motif) domain / Leucine-rich repeat profile. / Leucine-rich repeat / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...U2 small nuclear ribonucleoprotein A' / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / RRM (RNA recognition motif) domain / Leucine-rich repeat profile. / Leucine-rich repeat / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Leucine-rich repeat domain superfamily / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
U1 small nuclear ribonucleoprotein A / Probable U2 small nuclear ribonucleoprotein A'
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsWeber, G. / DeKoster, G. / Holton, N. / Hall, K.B. / Wahl, M.C.
CitationJournal: Nat Commun / Year: 2018
Title: Molecular principles underlying dual RNA specificity in the Drosophila SNF protein.
Authors: Weber, G. / DeKoster, G.T. / Holton, N. / Hall, K.B. / Wahl, M.C.
History
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Probable U2 small nuclear ribonucleoprotein A'
B: Probable U2 small nuclear ribonucleoprotein A'
C: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,61512
Polymers63,1114
Non-polymers6,5048
Water11,908661
1
A: Probable U2 small nuclear ribonucleoprotein A'
C: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3746
Polymers31,5562
Non-polymers1,8184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-28 kcal/mol
Surface area13370 Å2
MethodPISA
2
B: Probable U2 small nuclear ribonucleoprotein A'
D: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2416
Polymers31,5562
Non-polymers4,6864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-31 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.978, 53.763, 75.839
Angle α, β, γ (deg.)90.00, 103.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable U2 small nuclear ribonucleoprotein A' / U2 snRNP A'


Mass: 20473.631 Da / Num. of mol.: 2 / Mutation: C19V, C68T, C119S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: U2A, CG1406 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V4Q8
#2: Protein U1 small nuclear ribonucleoprotein A / U1A / Sex determination protein snf


Mass: 11082.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: snf, D25, fs(1)1621, liz, CG4528 / Production host: Escherichia coli (E. coli) / References: UniProt: P43332
#3: Chemical
ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 277 K / Method: batch mode
Details: 0.2 M Li2SO4, 0.1 M sodium cacodylate, pH 6.5, 30 % (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 97210 / % possible obs: 99 % / Redundancy: 3.6 % / Rsym value: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 1.42→1.5 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→19.905 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.18
RfactorNum. reflection% reflection
Rfree0.1932 4859 5 %
Rwork0.1458 --
obs0.1482 97179 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.42→19.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 77 661 5063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074674
X-RAY DIFFRACTIONf_angle_d1.1836317
X-RAY DIFFRACTIONf_dihedral_angle_d14.1351910
X-RAY DIFFRACTIONf_chiral_restr0.084716
X-RAY DIFFRACTIONf_plane_restr0.007807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.418-1.43410.33281380.28912622X-RAY DIFFRACTION85
1.4341-1.4510.31741580.26372991X-RAY DIFFRACTION97
1.451-1.46870.29181620.22673087X-RAY DIFFRACTION100
1.4687-1.48720.26111600.20823043X-RAY DIFFRACTION100
1.4872-1.50680.23751610.19473060X-RAY DIFFRACTION100
1.5068-1.52740.25431650.18643130X-RAY DIFFRACTION100
1.5274-1.54920.23781640.18323105X-RAY DIFFRACTION100
1.5492-1.57240.22051610.16853089X-RAY DIFFRACTION100
1.5724-1.59690.22971610.16563053X-RAY DIFFRACTION100
1.5969-1.62310.21291650.15423125X-RAY DIFFRACTION100
1.6231-1.65110.23491610.14653061X-RAY DIFFRACTION100
1.6511-1.68110.21271630.14123103X-RAY DIFFRACTION100
1.6811-1.71340.20951610.14493064X-RAY DIFFRACTION100
1.7134-1.74830.19931640.13523103X-RAY DIFFRACTION100
1.7483-1.78630.21191640.13443123X-RAY DIFFRACTION100
1.7863-1.82790.17911620.13393076X-RAY DIFFRACTION100
1.8279-1.87350.1851620.12893088X-RAY DIFFRACTION100
1.8735-1.92420.1841640.12563113X-RAY DIFFRACTION100
1.9242-1.98070.17741650.12653121X-RAY DIFFRACTION100
1.9807-2.04460.18351600.1243057X-RAY DIFFRACTION100
2.0446-2.11760.17991640.13183108X-RAY DIFFRACTION100
2.1176-2.20230.18921640.12833121X-RAY DIFFRACTION100
2.2023-2.30240.17571630.13313100X-RAY DIFFRACTION100
2.3024-2.42360.19051630.13953081X-RAY DIFFRACTION100
2.4236-2.57510.20471650.14253140X-RAY DIFFRACTION100
2.5751-2.77340.18311620.15223075X-RAY DIFFRACTION100
2.7734-3.05170.16771640.14983129X-RAY DIFFRACTION100
3.0517-3.49120.19711650.15023134X-RAY DIFFRACTION100
3.4912-4.39070.16391650.12853132X-RAY DIFFRACTION99
4.3907-19.90690.18581630.1523086X-RAY DIFFRACTION96

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