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- PDB-6f4h: Crystal structure of the Drosophila melanogaster SNF/U1-SL2 complex -

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Basic information

Entry
Database: PDB / ID: 6f4h
TitleCrystal structure of the Drosophila melanogaster SNF/U1-SL2 complex
Components
  • U1 small nuclear ribonucleoprotein A
  • U1-SL2
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 / ribonucleoprotein complex / mRNA binding / protein-containing complex / identical protein binding / nucleus
Similarity search - Function
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
CITRATE ANION / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWeber, G. / Holton, N. / Hall, K.B. / DeKoster, G. / 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: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: U1 small nuclear ribonucleoprotein A
B: U1-SL2
C: U1 small nuclear ribonucleoprotein A
D: U1-SL2
E: U1 small nuclear ribonucleoprotein A
F: U1-SL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4367
Polymers54,2476
Non-polymers1891
Water6,810378
1
A: U1 small nuclear ribonucleoprotein A
B: U1-SL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2713
Polymers18,0822
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-8 kcal/mol
Surface area8570 Å2
MethodPISA
2
C: U1 small nuclear ribonucleoprotein A
D: U1-SL2


Theoretical massNumber of molelcules
Total (without water)18,0822
Polymers18,0822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-6 kcal/mol
Surface area8820 Å2
MethodPISA
3
E: U1 small nuclear ribonucleoprotein A
F: U1-SL2


Theoretical massNumber of molelcules
Total (without water)18,0822
Polymers18,0822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-6 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.705, 150.028, 133.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-157-

HOH

21E-185-

HOH

31F-103-

HOH

41F-121-

HOH

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Components

#1: Protein U1 small nuclear ribonucleoprotein A / U1A / Sex determination protein snf


Mass: 11082.006 Da / Num. of mol.: 3
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
#2: RNA chain U1-SL2


Mass: 7000.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 277 K / Method: batch mode
Details: 0.2 M tri-lithium citrate, 20 % (w/v) PEG 3350 and 15 mM NiCl2 as an additive

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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: Jul 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 39021 / % possible obs: 99.7 % / Redundancy: 10.9 % / Rsym value: 0.11 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.12 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.302 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.68
RfactorNum. reflection% reflection
Rfree0.2116 1951 5 %
Rwork0.1695 --
obs0.1716 39017 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→38.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 1395 13 378 4002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123851
X-RAY DIFFRACTIONf_angle_d1.2595500
X-RAY DIFFRACTIONf_dihedral_angle_d15.4771676
X-RAY DIFFRACTIONf_chiral_restr0.059672
X-RAY DIFFRACTIONf_plane_restr0.007456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9973-2.04730.38041340.30052556X-RAY DIFFRACTION98
2.0473-2.10260.32611380.24122616X-RAY DIFFRACTION100
2.1026-2.16450.26991380.22972631X-RAY DIFFRACTION100
2.1645-2.23430.28421370.21482598X-RAY DIFFRACTION100
2.2343-2.31420.23291380.20572628X-RAY DIFFRACTION100
2.3142-2.40680.23541380.1912608X-RAY DIFFRACTION100
2.4068-2.51630.24131390.1822657X-RAY DIFFRACTION100
2.5163-2.6490.26341380.17822622X-RAY DIFFRACTION100
2.649-2.81490.24131390.18242639X-RAY DIFFRACTION100
2.8149-3.03210.2371400.19622652X-RAY DIFFRACTION100
3.0321-3.33710.19711410.16662679X-RAY DIFFRACTION100
3.3371-3.81960.18461410.15292684X-RAY DIFFRACTION100
3.8196-4.81080.1691420.13192691X-RAY DIFFRACTION100
4.8108-38.30890.18031480.14842805X-RAY DIFFRACTION99

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