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- PDB-6f4i: Crystal structure of Drosophila melanogaster SNF -

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Basic information

Entry
Database: PDB / ID: 6f4i
TitleCrystal structure of Drosophila melanogaster SNF
ComponentsU1 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 / female germ-line sex determination / mRNA Splicing - Major Pathway / small nuclear ribonucleoprotein complex / U2 snRNP / U1 snRNP / poly(U) RNA binding / oogenesis ...primary sex determination, soma / snRNA stem-loop binding / pre-mRNA intronic pyrimidine-rich binding / female germ-line sex determination / mRNA Splicing - Major Pathway / small nuclear ribonucleoprotein complex / U2 snRNP / U1 snRNP / poly(U) RNA binding / 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
U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 1.1Jan 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: U1 small nuclear ribonucleoprotein A
B: U1 small nuclear ribonucleoprotein A
C: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein A
E: U1 small nuclear ribonucleoprotein A
F: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)66,4926
Polymers66,4926
Non-polymers00
Water11,349630
1
A: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)11,0821
Polymers11,0821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)11,0821
Polymers11,0821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)11,0821
Polymers11,0821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)11,0821
Polymers11,0821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)11,0821
Polymers11,0821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)11,0821
Polymers11,0821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.309, 119.653, 122.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 11082.006 Da / Num. of mol.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 0.1 M Tris-HCl, pH 7.5, 0.2 M sodium chloride, 1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918417 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918417 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 125117 / % possible obs: 98.6 % / Redundancy: 4.5 % / Rrim(I) all: 0.034 / Rsym value: 0.03 / Net I/σ(I): 22.15
Reflection shellResolution: 1.49→1.58 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URN

1urn


Resolution: 1.49→24.329 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.68
RfactorNum. reflection% reflection
Rfree0.1882 6254 5 %
Rwork0.1464 --
obs0.1485 125046 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.49→24.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4235 0 0 630 4865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164430
X-RAY DIFFRACTIONf_angle_d1.5215954
X-RAY DIFFRACTIONf_dihedral_angle_d16.4451742
X-RAY DIFFRACTIONf_chiral_restr0.11661
X-RAY DIFFRACTIONf_plane_restr0.008750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4886-1.50550.29611950.29143718X-RAY DIFFRACTION94
1.5055-1.52320.31672070.26513920X-RAY DIFFRACTION100
1.5232-1.54170.29172100.24664001X-RAY DIFFRACTION100
1.5417-1.56130.27952060.22123895X-RAY DIFFRACTION99
1.5613-1.58180.24012110.20694015X-RAY DIFFRACTION100
1.5818-1.60350.24262060.20163922X-RAY DIFFRACTION99
1.6035-1.62640.28512090.20083952X-RAY DIFFRACTION100
1.6264-1.65060.27662070.18373949X-RAY DIFFRACTION99
1.6506-1.67640.22842090.17253964X-RAY DIFFRACTION99
1.6764-1.70390.21052050.16413891X-RAY DIFFRACTION98
1.7039-1.73330.21972100.15363994X-RAY DIFFRACTION100
1.7333-1.76480.21272080.14813941X-RAY DIFFRACTION100
1.7648-1.79870.19472100.14183985X-RAY DIFFRACTION100
1.7987-1.83540.18512070.13213932X-RAY DIFFRACTION99
1.8354-1.87530.18892110.1334019X-RAY DIFFRACTION100
1.8753-1.91890.18872080.13363954X-RAY DIFFRACTION99
1.9189-1.96690.19312090.14163955X-RAY DIFFRACTION99
1.9669-2.020.19192100.14554008X-RAY DIFFRACTION100
2.02-2.07950.21642080.14213947X-RAY DIFFRACTION99
2.0795-2.14650.19222080.13943940X-RAY DIFFRACTION98
2.1465-2.22320.16032080.1373963X-RAY DIFFRACTION99
2.2232-2.31220.18812100.14333989X-RAY DIFFRACTION99
2.3122-2.41730.20142110.14964004X-RAY DIFFRACTION99
2.4173-2.54460.19482090.14463961X-RAY DIFFRACTION99
2.5446-2.70380.18452090.14733983X-RAY DIFFRACTION98
2.7038-2.91230.21232090.15563973X-RAY DIFFRACTION97
2.9123-3.20480.17632070.15223919X-RAY DIFFRACTION97
3.2048-3.66720.20122100.13734005X-RAY DIFFRACTION98
3.6672-4.61510.1412110.11664010X-RAY DIFFRACTION97
4.6151-24.33250.17052160.15154083X-RAY DIFFRACTION95

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