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- PDB-6f4g: 'Crystal structure of the Drosophila melanogaster SNF/U2A'/U2-SL4... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6f4g
Title'Crystal structure of the Drosophila melanogaster SNF/U2A'/U2-SL4 complex
Components
  • Probable U2 small nuclear ribonucleoprotein A'
  • U1 small nuclear ribonucleoprotein A
  • U2-SL4
KeywordsSPLICING / SNF / 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 / poly(U) RNA binding / U1 snRNP / precatalytic spliceosome ...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 / poly(U) RNA binding / U1 snRNP / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / oogenesis / U2 snRNA binding / U1 snRNA binding / catalytic step 2 spliceosome / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mitotic cell cycle / chromatin organization / 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
RNA / RNA (> 10) / 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: 1.9 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

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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: U1 small nuclear ribonucleoprotein A
C: U2-SL4
D: Probable U2 small nuclear ribonucleoprotein A'
E: U1 small nuclear ribonucleoprotein A
F: U2-SL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,41610
Polymers79,1536
Non-polymers2634
Water15,763875
1
A: Probable U2 small nuclear ribonucleoprotein A'
B: U1 small nuclear ribonucleoprotein A
C: U2-SL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6124
Polymers39,5763
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-43 kcal/mol
Surface area16940 Å2
MethodPISA
2
D: Probable U2 small nuclear ribonucleoprotein A'
E: U1 small nuclear ribonucleoprotein A
F: U2-SL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8046
Polymers39,5763
Non-polymers2283
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-47 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.045, 103.914, 116.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ADBE

#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

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RNA chain , 1 types, 2 molecules CF

#3: RNA chain U2-SL4


Mass: 8020.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)

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Non-polymers , 3 types, 879 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 277 K / Method: batch mode
Details: 20 % (w/v) PEG 3350, 0.2 M Li2SO4 and 15 mM sarcosine 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 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 62952 / % possible obs: 99.7 % / Redundancy: 5.78 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.64
Reflection shellResolution: 1.9→2.01 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.442 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.97
RfactorNum. reflection% reflection
Rfree0.2177 2097 3.33 %
Rwork0.167 --
obs0.1687 62935 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 1066 12 875 6295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155803
X-RAY DIFFRACTIONf_angle_d1.3988099
X-RAY DIFFRACTIONf_dihedral_angle_d14.5312463
X-RAY DIFFRACTIONf_chiral_restr0.073955
X-RAY DIFFRACTIONf_plane_restr0.008867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8972-1.94130.29171370.273847X-RAY DIFFRACTION96
1.9413-1.98980.29391380.25084017X-RAY DIFFRACTION100
1.9898-2.04360.27191370.22464036X-RAY DIFFRACTION100
2.0436-2.10380.24811380.20924018X-RAY DIFFRACTION100
2.1038-2.17170.29831400.19884011X-RAY DIFFRACTION100
2.1717-2.24930.21951410.18774042X-RAY DIFFRACTION100
2.2493-2.33940.23961360.18344022X-RAY DIFFRACTION100
2.3394-2.44580.25641400.17274044X-RAY DIFFRACTION100
2.4458-2.57480.20761370.17184046X-RAY DIFFRACTION100
2.5748-2.73610.24931400.16924072X-RAY DIFFRACTION100
2.7361-2.94730.24371430.17614056X-RAY DIFFRACTION100
2.9473-3.24380.20731410.16724090X-RAY DIFFRACTION100
3.2438-3.7130.1781390.14824099X-RAY DIFFRACTION100
3.713-4.67740.18961450.13014143X-RAY DIFFRACTION100
4.6774-47.45640.18421450.14184295X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.0381-0.84783.76268.1313-1.22643.18570.26590.0104-0.2716-0.37310.0430.22640.6532-0.5105-0.30350.43190.04450.01470.323-0.10930.2544-19.6523-24.9778-12.6377
20.9967-1.2351-1.47568.54160.96742.99150.0790.03790.1238-1.0658-0.14880.04850.00580.1710.02970.26120.05180.03250.2235-0.01780.1481-14.4913-7.9324-11.6412
35.5457-0.7676-0.84565.97430.16235.25450.26650.1012-0.6804-0.5184-0.04520.23690.43830.1679-0.21780.26710.0001-0.04130.117-0.06180.2261-22.1861-22.3327-6.2663
42.8702-0.5449-0.27641.82430.22763.0295-0.0001-0.1079-0.27110.02340.0411-0.06330.28590.1893-0.02470.12530.0315-0.01270.1152-0.00250.1547-16.924-15.67074.8001
55.10111.98921.60836.5475-3.0817.6146-0.2551-0.20730.15580.46360.0224-0.3527-0.38270.21620.20540.16350.0425-0.02190.2011-0.04240.1104-16.6238-3.589115.074
66.53811.1545-2.11446.4563-4.5743.50930.0407-0.48940.62431.0429-0.2412-0.7296-0.910.80130.22160.4473-0.0196-0.12350.3566-0.05320.286-14.12310.454124.4069
76.3549-0.41552.21789.2242-1.6137.00180.0921-0.7921-0.18390.6606-0.01790.37651.3343-0.7345-0.10110.4389-0.0356-0.0570.51050.08150.2009-19.2393-12.782231.3792
88.9182-5.008-0.2335.03222.85853.40240.74680.24580.5486-0.3901-1.01-0.4025-1.0225-0.92120.30140.59090.1438-0.08540.45030.0390.3482-40.26077.7061-11.3116
97.18113.49753.70626.80776.43586.9855-0.21730.02920.3766-0.28830.05470.3462-0.2121-0.14690.13830.18030.0001-0.02270.13470.01310.1502-29.99158.5187-5.2093
106.5681-2.338-3.37776.69121.05864.9732-0.1263-0.31351.00880.09670.214-0.5378-0.30730.2436-0.06480.1718-0.0138-0.01670.1152-0.02850.1577-19.739711.76653.3968
113.96092.48410.77283.6788-0.95732.48020.0718-0.0849-0.24710.046-0.0868-0.1252-0.1107-0.02970.00620.12470.02860.01220.1308-0.01240.1196-19.68340.5639-1.6515
128.12594.2197-2.92794.9172-1.96085.1193-0.32490.2212-0.6832-0.75460.0703-0.03120.4421-0.08330.22050.18960.0186-0.03680.1283-0.02440.1761-24.7902-1.8396-9.4994
135.9650.6878-2.35028.27820.29412.82210.03170.07720.3896-0.1589-0.02960.2461-0.65770.299-0.00870.2303-0.0325-0.04290.1356-0.00950.146-20.846915.8023-5.3214
146.43123.42011.59997.27230.23787.9409-0.24780.7697-0.4449-0.75910.2276-0.03220.156-0.15660.04870.1527-0.0263-0.00020.2042-0.03190.1678-28.30170.2918-10.7889
152.84050.3669-1.86094.94362.93633.3312-0.18870.1058-0.27410.11280.01170.74270.149-0.63820.16820.12170.0229-0.03680.23080.02570.2811-35.4001-2.1034-3.7219
165.0578-0.78751.18071.6162-0.23762.3869-0.1008-0.40660.19950.21940.0885-0.0745-0.1236-0.03150.00450.19930.02880.01590.1905-0.0180.1668-27.3495.57866.2532
174.70781.1302-3.1941.2739-0.5076.6219-0.00710.49470.0562-0.37130.30820.2646-0.4178-0.5294-0.26430.14970.0093-0.05140.17010.03690.2036-33.47587.8903-9.5441
188.3816-2.58020.78060.7945-0.24170.07340.34060.9671-0.6576-1.35960.20670.67860.6393-0.3041-0.39650.732-0.2009-0.12080.61270.01580.2163-27.17712.4879-21.9412
197.1522-6.08290.80265.5655-1.59932.293-0.32080.2325-1.58940.42620.2111-0.76870.37280.81230.08180.34070.06310.01720.5504-0.14611.0259-8.907315.359911.8947
202.47520.6526-0.09723.21391.88062.6414-0.0432-0.10240.1545-0.14160.1893-0.2552-0.25610.3028-0.12880.213-0.00620.00570.18980.00330.1737-16.85118.7301-0.4246
212.68950.68330.10837.6134-3.21646.5906-0.1195-0.36040.02050.7330.0151-0.2198-0.26960.03480.02360.17540.00380.04090.23790.00010.141117.596-10.500741.204
224.78690.85080.00623.8999-0.86483.01070.0387-0.1641-0.12520.14220.06770.09940.142-0.1556-0.09570.1828-0.01140.03420.16190.03170.090617.3248-16.056134.2871
233.60130.3432-0.84021.92460.25994.1304-0.07270.165-0.1743-0.10970.05110.05950.1728-0.11580.01370.119-0.026-0.00090.10140.00910.120619.9009-12.579720.7247
247.0905-0.03622.45028.3730.83554.2451-0.17680.2390.1842-0.42110.0440.2022-0.2293-0.09670.12120.1706-0.0274-0.00360.16490.03080.123719.1923-3.435112.1477
257.0207-0.5936-0.7245.81535.67135.5442-0.04740.48650.3877-1.3543-0.20080.7186-0.6553-1.17070.25570.4354-0.0621-0.10140.39290.07040.25316.7573-2.04681.3861
269.6486-1.5879-0.73646.571-0.23824.14560.10750.5295-0.4459-1.332-0.29710.34710.6926-0.37220.16930.4377-0.07010.0080.2681-0.09010.233221.2467-15.005-2.0635
279.20561.67464.36768.66626.70526.2536-0.00210.14790.6215-0.1878-0.2462-0.6148-0.88330.62780.13390.4336-0.1927-0.13740.3740.10540.47139.32938.835739.2647
284.82381.58310.01365.6364-0.58532.6316-0.02740.0180.22040.1094-0.07170.0832-0.4444-0.03790.11850.2585-0.0251-0.0090.1343-0.00210.154924.01557.078527.6528
295.5619-5.1617-5.5445.19346.28478.669-0.227-0.5836-0.48241.0608-0.01310.60960.3961-0.18770.24990.3302-0.083-0.04980.22660.02130.251324.43163.133237.8392
305.16320.2883-2.36014.3341-0.98851.2424-0.0786-0.25480.74640.17090.03030.2769-0.7639-0.1949-0.01320.51410.0376-0.09090.1841-0.04040.377323.305919.101329.8828
312.6255-1.9918-0.05032.20570.98991.3573-0.1232-0.3045-0.35611.01050.0811-0.0019-0.42030.5946-0.08360.50750.0081-0.09820.3130.020.266229.22584.275838.0249
326.8673-1.30143.6533.3351-1.64025.8946-0.04710.106-0.12370.1565-0.0578-0.416-0.17680.42410.10040.2129-0.0706-0.0530.15890.02590.261233.23573.624226.1563
336.71490.1434-0.67014.77182.36591.27220.24-0.82030.46390.4949-0.1655-0.3214-0.36080.5084-0.06120.53-0.182-0.13890.30920.00870.347232.886110.708238.4528
342.87453.6653-0.06445.17341.04323.6203-0.4505-1.629-0.8078-0.2384-0.11051.3967-0.1298-0.18630.43570.47950.1451-0.02880.76720.21061.130512.384615.514612.2621
351.84740.04541.062.3241-1.12754.3793-0.22920.1070.52570.36560.030.3692-0.9807-0.22580.15150.56740.0544-0.04560.2719-0.00310.506119.662821.108724.5653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 36 )
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 130 )
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 151 )
6X-RAY DIFFRACTION6chain 'A' and (resid 152 through 162 )
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 175 )
8X-RAY DIFFRACTION8chain 'B' and (resid -1 through 7 )
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 12 )
10X-RAY DIFFRACTION10chain 'B' and (resid 13 through 19 )
11X-RAY DIFFRACTION11chain 'B' and (resid 20 through 33 )
12X-RAY DIFFRACTION12chain 'B' and (resid 34 through 41 )
13X-RAY DIFFRACTION13chain 'B' and (resid 42 through 51 )
14X-RAY DIFFRACTION14chain 'B' and (resid 52 through 58 )
15X-RAY DIFFRACTION15chain 'B' and (resid 59 through 69 )
16X-RAY DIFFRACTION16chain 'B' and (resid 70 through 79 )
17X-RAY DIFFRACTION17chain 'B' and (resid 80 through 88 )
18X-RAY DIFFRACTION18chain 'B' and (resid 89 through 93 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 8 )
20X-RAY DIFFRACTION20chain 'C' and (resid 9 through 25 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 25 )
22X-RAY DIFFRACTION22chain 'D' and (resid 26 through 64 )
23X-RAY DIFFRACTION23chain 'D' and (resid 66 through 130 )
24X-RAY DIFFRACTION24chain 'D' and (resid 131 through 151 )
25X-RAY DIFFRACTION25chain 'D' and (resid 152 through 164 )
26X-RAY DIFFRACTION26chain 'D' and (resid 165 through 175 )
27X-RAY DIFFRACTION27chain 'E' and (resid 3 through 7 )
28X-RAY DIFFRACTION28chain 'E' and (resid 8 through 34 )
29X-RAY DIFFRACTION29chain 'E' and (resid 35 through 41 )
30X-RAY DIFFRACTION30chain 'E' and (resid 42 through 51 )
31X-RAY DIFFRACTION31chain 'E' and (resid 52 through 58 )
32X-RAY DIFFRACTION32chain 'E' and (resid 59 through 79 )
33X-RAY DIFFRACTION33chain 'E' and (resid 80 through 92 )
34X-RAY DIFFRACTION34chain 'F' and (resid 1 through 8 )
35X-RAY DIFFRACTION35chain 'F' and (resid 9 through 25 )

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