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

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Basic information

Entry
Database: PDB / ID: 5sti
TitlePanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment P02H11 from the F2X-Universal Library
Components
  • A1 cistron-splicing factor AAR2
  • Pre-mRNA-splicing factor 8
KeywordsSPLICING / FRAGMAX / FRAGMAXAPP / fragment screening / RNaseH like domain / U5 SNRNP assembly
Function / homology
Function and homology information


generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-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 3'-splice site recognition / mRNA 5'-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 N-terminal domain / 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 / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain ...AAR2 N-terminal domain / 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 / 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. / Ribonuclease H-like superfamily
Similarity search - Domain/homology
1-(3-methoxy-4-methylphenyl)methanamine / A1 cistron-splicing factor AAR2 / Pre-mRNA-splicing factor 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.76 Å
AuthorsBarthel, T. / Wollenhaupt, J. / Lima, G.M.A. / Wahl, M.C. / Weiss, M.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: J.Med.Chem. / Year: 2022
Title: Large-Scale Crystallographic Fragment Screening Expedites Compound Optimization and Identifies Putative Protein-Protein Interaction Sites.
Authors: Barthel, T. / Wollenhaupt, J. / Lima, G.M.A. / Wahl, M.C. / Weiss, M.S.
History
DepositionAug 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)66,0134
Polymers65,7112
Non-polymers3022
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-6 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.972, 81.825, 93.749
Angle α, β, γ (deg.)90, 108.21, 90
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: UNP residues 1836-2090
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: AAR2, YBL074C, YBL06.06, YBL0611 / Production host: Escherichia coli (E. coli) / References: UniProt: P32357
#3: Chemical ChemComp-W8F / 1-(3-methoxy-4-methylphenyl)methanamine


Mass: 151.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 19% PEG4000, 3% DMSO, 0.1 M Tris, pH 8.5, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.76→44.53 Å / Num. obs: 63229 / % possible obs: 97.2 % / Redundancy: 6.93 % / CC1/2: 0.999 / Rrim(I) all: 0.079 / Net I/σ(I): 11.61 / Num. measured all: 438118
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2Rrim(I) all% possible all
5.22-44.536.820.03641.551712217122251125110.9990.03999.2
3.7-44.536.920.04239.563081230812445044500.9980.04599.3
3.03-44.536.770.05828.443836338363566356630.9980.06399.2
2.62-44.536.770.10616.544537845378670267020.9950.11598.9
2.35-44.537.040.17410.585303253032753375330.9890.18898.8
2.14-44.537.110.36.285911859118831483140.9760.32498.3
1.98-44.536.890.5843.246173461734895989590.9180.63297.7
1.86-44.537.021.2931.486721167211957195710.7091.39697.3
1.75-44.536.862.620.696534665346952595250.3562.83390.9

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Processing

Software
NameVersionClassificationNB
xdsapp3.1.5ddata processing
XDSJan 10, 2022data reduction
Aimlessdata scaling
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.76→44.53 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2598 2096 -
Rwork0.2209 --
obs0.2222 63076 97.8 %
Refinement stepCycle: LAST / Resolution: 1.76→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 22 84 4514
LS refinement shellResolution: 1.76→44.53 Å
RfactorNum. reflection% reflection
Rfree0.2598 2096 -
Rwork0.2209 --
obs--97.8 %
Refinement TLS params.

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)
11.2734-0.4952-0.14810.56950.41550.88810.0373-0.0043-0.0825-0.0043-0.0395-0.0367-0.0825-0.0367-0.00010.35830.00070.01710.28050.04770.330938.68047.654325.9923
21.33480.0235-0.1451.25820.37380.25590.01-0.2653-0.1115-0.2653-0.093-0.1165-0.1115-0.1165-0.00010.4320.0102-0.01240.37310.05960.242428.812811.745321.0035
30.5475-0.1865-0.39841.19031.35161.53460.10070.1534-0.09530.1534-0.06810.0684-0.09530.06840.00030.3577-0.0369-0.02680.3660.06570.391443.39316.168136.0292
41.01020.0020.27921.4611-0.44370.87680.44380.389-0.33450.389-0.31870.6544-0.33450.6544-0.04450.3246-0.06710.00870.40910.03990.599652.218824.292537.3686
50.7051-0.8903-0.04190.8967-0.45391.14450.0741-0.07360.1437-0.0736-0.1019-0.14920.1437-0.1492-00.40550.0002-0.0310.3197-0.03850.39912.126711.4555-29.8841
60.70030.84130.5541.2152-0.3221.72320.0531-0.21910.1731-0.2191-0.0454-0.1820.1731-0.182-0.00010.306-0.0231-0.01280.3308-0.04850.35516.80086.9463-27.9579
70.0546-0.39740.7690.813-0.24271.3823-0.03340.1688-0.05070.1688-0.0061-0.3555-0.0507-0.35550.00020.3927-0.02290.00210.4426-0.03010.319617.77684.382-2.8416
80.7355-0.0105-0.19390.57641.07441.41990.10210.09870.39270.09870.09470.22440.39270.22440.00010.33530.0243-0.01820.4141-0.03230.397431.7186-0.9127-11.2707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1833:1904)
2X-RAY DIFFRACTION2(chain A and resid 1905:1964)
3X-RAY DIFFRACTION3(chain A and resid 1965:2027)
4X-RAY DIFFRACTION4(chain A and resid 2028:2069)
5X-RAY DIFFRACTION5(chain B and resid 1:66)
6X-RAY DIFFRACTION6(chain B and resid 67:137)
7X-RAY DIFFRACTION7(chain B and resid 138:251)
8X-RAY DIFFRACTION8(chain B and resid 252:317)

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