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

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Basic information

Entry
Database: PDB / ID: 7fmo
TitlePanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment P06D12 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
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 ...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. / Ribonuclease H-like superfamily
Similarity search - Domain/homology
N-(2-methoxyphenyl)-2-methyl-L-alanine / 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: 1.67 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)65,9984
Polymers65,7112
Non-polymers2872
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-3 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.744, 82.164, 94.216
Angle α, β, γ (deg.)90, 108.56, 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-VVK / N-(2-methoxyphenyl)-2-methyl-L-alanine


Type: L-peptide linking / Mass: 209.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15NO3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 50.36 %
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 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.67→44.75 Å / Num. obs: 74527 / % possible obs: 99.5 % / Redundancy: 6.89 % / CC1/2: 0.999 / Rrim(I) all: 0.086 / Net I/σ(I): 12.37 / Num. measured all: 513483
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
4.97-44.756.880.03350.071986619866288928890.9990.03699.4
3.53-44.757.060.03746.423612736127511951190.9990.03999.9
2.88-44.756.940.05330.384571045710658465840.9980.05899.9
2.5-44.757.060.117.825492754927778077800.9950.10799.8
2.23-44.757.120.17210.756257762577879287920.9870.186100
2.04-44.756.830.3325.76644566445973597350.9550.35999.9
1.89-44.756.810.6792.77716537165310522105220.8560.735100
1.77-44.756.811.4521.25771027710211325113250.571.57299.9
1.67-44.756.712.710.63790767907611781117810.2672.93797.6

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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: 1.67→44.75 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2449 2101 -
Rwork0.2123 --
obs0.2132 74503 99.56 %
Refinement stepCycle: LAST / Resolution: 1.67→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 19 116 4697
LS refinement shellResolution: 1.67→44.75 Å
RfactorNum. reflection% reflection
Rfree0.2449 2101 -
Rwork0.2123 --
obs--99.56 %
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)
10.9003-0.47630.05380.31850.17570.65950.07310.00650.00050.0065-0.024-0.04540.0005-0.0454-00.293-0.01110.03290.27120.02480.330937.83087.695426.1323
20.31110.117-0.04621.00550.34530.4535-0.0147-0.1116-0.0151-0.11160.018-0.1446-0.0151-0.1446-0.00010.2814-0.00650.00610.31980.0360.226728.132411.873421.0345
30.78120.4112-0.04670.60750.67361.24250.10480.1640.00260.164-0.02630.07690.00260.07690.00010.2788-0.02340.00340.3090.00380.365642.375916.125536.3721
40.556-0.26080.44911.2118-0.3960.39480.08020.1053-0.00390.1053-0.02350.1457-0.00390.14570.00010.3371-0.08960.00380.346-0.04290.441951.157824.281637.7085
50.762-0.6791-0.2730.6874-0.0260.77630.13310.02330.06920.0233-0.09490.01210.06920.012100.310.0117-0.02630.2726-0.03740.294312.149211.5277-30.1476
60.8450.60020.44830.8152-0.21040.98730.0586-0.15720.1057-0.1572-0.0157-0.12030.1057-0.1203-0.00020.30060.0041-0.02970.286-0.03660.31466.78917.0857-28.2662
70.1061-0.02460.33340.4573-0.26261.09790.01650.0190.01420.019-0.0126-0.17720.0142-0.177200.3118-0.0203-0.00180.3713-0.02340.256117.35664.5697-3.0972
80.2284-0.3753-0.24690.78280.80011.04480.0353-0.06630.1678-0.06630.14540.13370.16780.13370.00010.30150.0081-0.00220.3329-0.02920.310631.3789-0.8708-11.3425
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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