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- PDB-6g70: Structure of murine Prpf39 -

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Basic information

Entry
Database: PDB / ID: 6g70
TitleStructure of murine Prpf39
ComponentsPre-mRNA-processing factor 39
KeywordsSPLICING / U1snRNP / HAT repeat protein
Function / homology
Function and homology information


commitment complex / U1 snRNP / U2-type prespliceosome / mRNA 5'-splice site recognition / RNA processing
Similarity search - Function
HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Pre-mRNA-processing factor 39 / Pre-mRNA-processing factor 39
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDe Bortoli, F.D. / Loll, B. / Wahl, M. / Heyd, F.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Increased versatility despite reduced molecular complexity: evolution, structure and function of metazoan splicing factor PRPF39.
Authors: De Bortoli, F. / Neumann, A. / Kotte, A. / Timmermann, B. / Schuler, T. / Wahl, M.C. / Loll, B. / Heyd, F.
History
DepositionApr 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_data_processing_status / pdbx_database_proc / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-processing factor 39
B: Pre-mRNA-processing factor 39


Theoretical massNumber of molelcules
Total (without water)156,8752
Polymers156,8752
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-5 kcal/mol
Surface area55220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.490, 72.760, 207.100
Angle α, β, γ (deg.)90.00, 112.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pre-mRNA-processing factor 39


Mass: 78437.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prpf39 / Plasmid: pGEX 6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLys / References: UniProt: E9QJV4, UniProt: Q8K2Z2*PLUS

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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: 4.21 Å3/Da / Density % sol: 70.75 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M bis-tris-propane pH 6.5, 1.8 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2016
RadiationMonochromator: SI111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 39170 / % possible obs: 98.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 102 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.149 / Net I/σ(I): 9.4
Reflection shellResolution: 3.3→3.45 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4809 / CC1/2: 0.637 / Rrim(I) all: 2.6 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→47.848 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.52
RfactorNum. reflection% reflection
Rfree0.2953 3032 7.8 %
Rwork0.2468 --
obs0.2507 38895 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→47.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8592 0 0 0 8592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048802
X-RAY DIFFRACTIONf_angle_d0.80211873
X-RAY DIFFRACTIONf_dihedral_angle_d7.0415289
X-RAY DIFFRACTIONf_chiral_restr0.0471242
X-RAY DIFFRACTIONf_plane_restr0.0061535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2999-3.35150.47151340.45351559X-RAY DIFFRACTION97
3.3515-3.40640.43551470.43111582X-RAY DIFFRACTION96
3.4064-3.46520.40511310.41811610X-RAY DIFFRACTION97
3.4652-3.52810.45331250.44431606X-RAY DIFFRACTION96
3.5281-3.5960.45331390.39251593X-RAY DIFFRACTION97
3.596-3.66940.41981360.35551633X-RAY DIFFRACTION97
3.6694-3.74910.42661320.34731572X-RAY DIFFRACTION97
3.7491-3.83630.38031490.32271628X-RAY DIFFRACTION98
3.8363-3.93220.3391350.30621583X-RAY DIFFRACTION97
3.9322-4.03840.35441350.28961653X-RAY DIFFRACTION98
4.0384-4.15720.33191330.27331594X-RAY DIFFRACTION98
4.1572-4.29130.32331440.25751655X-RAY DIFFRACTION99
4.2913-4.44460.26261260.23891646X-RAY DIFFRACTION99
4.4446-4.62240.261560.22811654X-RAY DIFFRACTION99
4.6224-4.83260.27711340.21481661X-RAY DIFFRACTION99
4.8326-5.08710.2621440.21621633X-RAY DIFFRACTION99
5.0871-5.40540.28581530.21921654X-RAY DIFFRACTION99
5.4054-5.82210.27581260.23581653X-RAY DIFFRACTION99
5.8221-6.40680.33561320.23961682X-RAY DIFFRACTION99
6.4068-7.3310.28421410.24641687X-RAY DIFFRACTION99
7.331-9.22550.22861380.19421670X-RAY DIFFRACTION99
9.2255-47.8530.23191420.19111655X-RAY DIFFRACTION94
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)
11.85510.40461.17786.41832.90095.5736-0.2954-0.17990.07040.39110.14950.0211-0.05320.3058-0.03760.9138-0.06080.03480.67910.03380.47964.164136.500260.9202
20.4076-0.20520.04081.50651.01493.24190.10150.19090.27780.092-0.1126-0.1135-1.2045-0.3728-0.15921.6769-0.2267-0.00111.11560.04550.814263.760555.31954.1948
31.8671-0.7035-0.88650.27-0.04594.96440.06950.2702-0.4158-0.2802-0.1170.310.98460.13290.14071.3341-0.26120.16411.5453-0.04010.918880.006333.968318.1765
46.1786-0.27410.87983.285-1.8571.1299-1.17820.15120.2848-0.76530.51451.16260.2405-1.56450.40481.4338-0.0526-0.19441.82030.07321.178374.68437.6256-17.3994
51.65230.2932-0.54016.80693.24735.9832-0.22250.03250.134-0.44960.24420.1019-0.01830.4265-0.05980.73320.0818-0.08040.72830.08930.544554.264659.0416-58.8541
60.9037-0.12260.46061.0577-0.00382.7559-0.0510.0411-0.2983-0.29190.1265-0.04980.86830.5797-0.10441.32290.2257-0.02740.86870.01260.659557.303834.9157-59.1712
71.3017-0.17582.1570.58710.31555.7306-0.0560.31150.5575-0.1755-0.1308-0.0662-1.10450.48130.24381.32690.0773-0.17031.50050.03341.192779.582956.2145-14.4803
86.4781-1.9591-0.45191.24160.23960.04760.1235-0.61950.85621.05970.10510.3823-0.6333-1.71350.24111.37960.09730.35311.93130.08831.319473.607750.667115.2086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 74:273)
2X-RAY DIFFRACTION2(chain A and resid 274:387)
3X-RAY DIFFRACTION3(chain A and resid 388:535)
4X-RAY DIFFRACTION4(chain A and resid 536:602)
5X-RAY DIFFRACTION5(chain B and resid 74:227)
6X-RAY DIFFRACTION6(chain B and resid 228:417)
7X-RAY DIFFRACTION7(chain B and resid 418:555)
8X-RAY DIFFRACTION8(chain B and resid 556:602)

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