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- PDB-7fp6: PanDDA analysis group deposition -- Aar2/RNaseH in complex with f... -

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Basic information

Entry
Database: PDB / ID: 7fp6
TitlePanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment P08G05 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 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 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
(3R)-3-amino-3-phenylpropanenitrile / 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: 1.61 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
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)65,8573
Polymers65,7112
Non-polymers1461
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-7 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.007, 81.771, 93.303
Angle α, β, γ (deg.)90, 108.26, 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-W6L / (3R)-3-amino-3-phenylpropanenitrile


Mass: 146.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
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: May 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.61→44.7 Å / Num. obs: 81122 / % possible obs: 97.6 % / Redundancy: 6.87 % / CC1/2: 0.998 / Rrim(I) all: 0.079 / Net I/σ(I): 10.86 / Num. measured all: 556937
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
4.79-44.76.770.05232.492168321683320532050.9960.05699.4
3.39-44.76.910.05331.773925239252568456840.9970.05899.7
2.77-44.76.780.06425.14944449444729772970.9970.06999.5
2.4-44.76.830.09318.15836658366854485440.9940.199.3
2.15-44.76.890.14312.446681966819969496940.990.15598.9
1.96-44.76.730.2666.93714347143410608106080.9760.28997.9
1.82-44.76.910.5853.24790597905911438114380.9140.63297.9
1.7-44.771.2411.51858318583112270122700.7431.3497.7
1.6-44.76.872.5040.67850478504712381123810.3872.70792.4

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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: 1.61→44.7 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2288 2098 -
Rwork0.1965 --
obs0.1973 80991 98.11 %
Refinement stepCycle: LAST / Resolution: 1.61→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 11 117 4536
LS refinement shellResolution: 1.61→44.7 Å
RfactorNum. reflection% reflection
Rfree0.2288 2098 -
Rwork0.1965 --
obs--98.11 %
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)
10.6593-0.20690.06970.3733-0.02130.17410.0482-0.0252-0.0264-0.0252-0.0084-0.0757-0.0264-0.075700.38040.00390.03210.33850.02880.366538.16047.859325.8186
20.6696-0.14220.33561.09960.23810.6419-0.0017-0.12080.0251-0.1208-0.0548-0.11740.0251-0.1174-0.00010.39290.01980.01290.40630.03660.320528.276611.94420.8466
30.6689-0.1933-0.07380.76870.58531.44170.0950.31870.01640.3187-0.04170.05060.01640.05060.00010.3461-0.0092-0.02160.35470.03540.386342.922716.338335.7749
40.3915-0.09530.02451.1579-0.10050.48260.0910.2373-0.1050.2373-0.05240.1406-0.1050.1406-0.00010.3574-0.06930.00090.4087-0.02410.558651.744424.441537.0386
50.4318-0.23120.01120.6527-0.34040.80120.0781-0.07630.1394-0.0763-0.0633-0.04330.1394-0.043300.36240.0087-0.00690.3382-0.04630.390711.902311.711-29.7647
60.82750.06260.47580.4364-0.4871.45360.0131-0.18490.1522-0.18490.0171-0.21980.1522-0.2198-0.00020.375-0.0187-0.01460.3787-0.04020.4126.57267.2403-27.8512
70.112-0.01930.37090.81640.24081.3431-0.01820.13540.01640.1354-0.0496-0.2120.0164-0.2120.00010.3813-0.01510.00910.4541-0.02880.349617.29224.5676-2.8007
80.5704-0.3417-0.08710.54290.65551.0517-0.0366-0.0140.2463-0.0140.18070.21220.24630.212200.37270.0189-0.00310.4077-0.03820.410231.2973-0.7218-11.069
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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