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- PDB-5r0j: PanDDA analysis group deposition -- Aar2/RNaseH in complex with f... -

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Basic information

Entry
Database: PDB / ID: 5r0j
TitlePanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry F08, DMSO-free
Components
  • A1 cistron-splicing factor AAR2
  • Pre-mRNA-splicing factor 8
KeywordsSPLICING / FragMAX / FragMAXapp / fragment screening / RNaseH like domain / VHS like domain / U5 snRNP assembly
Function / homology
Function and homology information


generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding ...generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / mRNA binding / nucleus / cytoplasm
Similarity search - Function
Aar2, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / A1 cistron-splicing factor, AAR2 / AAR2, N-terminal / AAR2, C-terminal / AAR2, C-terminal domain superfamily / AAR2, N-terminal domain superfamily / AAR2 C-terminal repeat region / AAR2 N-terminal domain ...Aar2, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / A1 cistron-splicing factor, AAR2 / AAR2, N-terminal / AAR2, C-terminal / AAR2, C-terminal domain superfamily / AAR2, N-terminal domain superfamily / AAR2 C-terminal repeat region / AAR2 N-terminal domain / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Ribonuclease H-like superfamily / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
4-[(methylamino)methyl]phenol / A1 cistron-splicing factor AAR2 / Pre-mRNA-splicing factor 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.81 Å
AuthorsWollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S.
CitationJournal: Structure / Year: 2020
Title: F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening.
Authors: Wollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 10, 2021Group: Data collection
Category: diffrn_detector / diffrn_radiation / diffrn_source
Item: _diffrn_detector.pdbx_collection_date / _diffrn_detector.type ..._diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.3Mar 6, 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: Pre-mRNA-splicing factor 8
B: A1 cistron-splicing factor AAR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8483
Polymers65,7112
Non-polymers1371
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.605, 82.428, 92.966
Angle α, β, γ (deg.)90.000, 107.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pre-mRNA-splicing factor 8


Mass: 29501.113 Da / Num. of mol.: 1 / Fragment: yPrp8 RNaseH (UNP Residues 1836-2096)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334
#2: Protein A1 cistron-splicing factor AAR2


Mass: 36209.836 Da / Num. of mol.: 1 / Fragment: GAMA - Aar2(1-152) - SSSSS - Aar2(171-317) / Mutation: L153_D170delinsSSSSS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: AAR2, YBL074C, YBL06.06, YBL0611 / Production host: Escherichia coli (E. coli) / References: UniProt: P32357
#3: Chemical ChemComp-RBJ / 4-[(methylamino)methyl]phenol


Mass: 137.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H11NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (w/v) PEG 4000, 0.2M Tris-HCl pH 8.5, 0.2M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.827 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.81→22.66 Å / Num. obs: 57984 / % possible obs: 99.8 % / Redundancy: 6.853 % / Biso Wilson estimate: 51.267 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.057 / Χ2: 1.038 / Net I/σ(I): 15.62 / Num. measured all: 397928
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obsCC1/2Rrim(I) allRejects% possible all
1.81-1.926.872.5320.5664267934992660.3352.735560.991
1.92-2.056.721.1541.3259068879687880.7371.2590.999
2.05-2.216.170.5432.9550776822582180.9060.59440.999
2.21-2.427.240.2387.2554901758275720.9820.25600.999
2.42-2.717.240.11814.2449306680868070.9950.12741
2.71-3.137.060.06226.1942737605060470.9980.06611
3.13-3.826.50.03941.1333321512851150.9990.04200.997
3.82-5.396.740.03153.5426872398639850.9990.03401
5.39-507.30.03258.2416680228522690.9990.03500.993

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMAC5.8.0238phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.81→22.66 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2812 2099 3.62 %
Rwork0.2287 55887 -
obs0.2306 57984 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 371.73 Å2 / Biso mean: 81.3734 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.81→22.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 26 92 4520
Biso mean--84.11 73.11 -
Num. residues----537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.850.57731370.5823646378398
1.85-1.90.45091400.495637423882100
1.9-1.950.42391370.416536783815100
1.95-20.34191400.337437103850100
2-2.070.32681400.294237213861100
2.07-2.140.34591390.29837053844100
2.14-2.230.33911400.272937163856100
2.23-2.330.32311400.249637313871100
2.33-2.450.27721390.255637093848100
2.45-2.610.34311400.258837413881100
2.61-2.810.32481400.267637303870100
2.81-3.090.33161400.27637293869100
3.09-3.540.32631410.252637573898100
3.54-4.450.22821410.194537583899100
4.45-22.660.22831430.169138143957100
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)
12.0359-0.3392-0.13850.55620.84911.48740.1260.061-0.0919-0.3085-0.1562-0.0376-0.1311-0.0622-0.00010.4510.00990.05610.38440.10220.417638.02157.990725.7944
21.2821-0.3480.86881.3949-0.15020.7530.02420.2441-0.2-0.4237-0.13430.0096-0.1016-0.2356-0.00010.50950.04820.03550.50020.05830.357828.079111.973120.8999
32.1495-0.76080.19160.94030.56992.08610.0069-0.06690.2364-0.024-0.0146-0.2139-0.04350.17560.00010.314-0.02890.02130.39870.1030.460142.892516.696735.5178
41.0212-0.09220.16750.35910.09041.08340.2761-0.35610.46810.0529-0.1652-0.2152-0.52370.7562-0.00030.4665-0.14610.00750.5520.06460.641951.343624.778136.6074
50.6949-0.80480.29910.8369-0.12461.2274-0.04210.04880.0863-0.2206-0.04070.26180.12-0.18010.00010.6287-0.0266-0.08910.516-0.13520.541911.889111.6183-29.5914
61.1795-0.17010.22611.6542-0.92.46290.01890.0360.0059-0.3898-0.12030.43890.2967-0.646300.4684-0.0591-0.10730.6115-0.16160.57136.4327.2933-27.6953
70.0042-0.27440.37890.53710.49512.0558-0.2136-0.27640.15460.1151-0.0560.1964-0.0141-0.62510.00020.541-0.0148-0.01250.5772-0.12830.45216.94814.5354-2.5713
80.71060.06850.71080.57170.84611.5197-0.0550.0230.05750.1180.0658-0.2226-0.00110.3227-0.00010.5939-0.02610.01780.5352-0.05940.561430.9282-0.7914-10.8131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1833:1904)A1833 - 1904
2X-RAY DIFFRACTION2(chain A and resid 1905:1964)A1905 - 1964
3X-RAY DIFFRACTION3(chain A and resid 1965:2027)A1965 - 2027
4X-RAY DIFFRACTION4(chain A and resid 2028:2069)A2028 - 2069
5X-RAY DIFFRACTION5(chain B and resid 1:66)B1 - 66
6X-RAY DIFFRACTION6(chain B and resid 67:137)B67 - 137
7X-RAY DIFFRACTION7(chain B and resid 138:251)B138 - 251
8X-RAY DIFFRACTION8(chain B and resid 252:317)B252 - 317

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