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- PDB-6teo: Crystal structure of a yeast Snu114-Prp8 complex -

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Basic information

Entry
Database: PDB / ID: 6teo
TitleCrystal structure of a yeast Snu114-Prp8 complex
Components(Pre-mRNA-splicing factor ...) x 2
KeywordsSPLICING / Snu114-Prp8 / GTP
Function / homology
Function and homology information


generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 2 spliceosome / 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 ...generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 2 spliceosome / 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 / GTPase activity / GTP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Snu114, GTP-binding domain / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus ...Snu114, GTP-binding domain / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / 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 / Elongation factor Tu domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribonuclease H-like superfamily / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGanichkin, O. / Jia, J. / Loll, B. / Absmeier, E. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationTRR186 Germany
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: A Snu114-GTP-Prp8 module forms a relay station for efficient splicing in yeast.
Authors: Jia, J. / Ganichkin, O.M. / Preussner, M. / Absmeier, E. / Alings, C. / Loll, B. / Heyd, F. / Wahl, M.C.
History
DepositionNov 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
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 1.2May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor SNU114
B: Pre-mRNA-splicing factor 8
C: Pre-mRNA-splicing factor SNU114
D: Pre-mRNA-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,83310
Polymers273,5464
Non-polymers1,2876
Water905
1
A: Pre-mRNA-splicing factor SNU114
B: Pre-mRNA-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4175
Polymers136,7732
Non-polymers6443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-84 kcal/mol
Surface area45210 Å2
MethodPISA
2
C: Pre-mRNA-splicing factor SNU114
D: Pre-mRNA-splicing factor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4175
Polymers136,7732
Non-polymers6443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-89 kcal/mol
Surface area44630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.110, 158.590, 110.700
Angle α, β, γ (deg.)90.00, 116.54, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Pre-mRNA-splicing factor ... , 2 types, 4 molecules ACBD

#1: Protein Pre-mRNA-splicing factor SNU114 / 114 kDa U5 small nuclear ribonucleoprotein component / Growth inhibitory protein 10


Mass: 107416.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SNU114, GIN10, YKL173W, YKL637 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P36048
#2: Protein Pre-mRNA-splicing factor 8


Mass: 29357.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33334

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Non-polymers , 4 types, 11 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 50.5 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG8000, 200mM Lithium chloride, 50mM magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 48253 / % possible obs: 99.3 % / Redundancy: 4.2956 % / Biso Wilson estimate: 103.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.11 / Net I/σ(I): 12.32
Reflection shellResolution: 3.1→3.18 Å / Rmerge(I) obs: 1.517 / Mean I/σ(I) obs: 0.516 / Num. unique obs: 3522 / CC1/2: 0.516 / Rrim(I) all: 1.731

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JB9

3jb9


Resolution: 3.1→47.499 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 2410 5 %
Rwork0.2303 --
obs0.2324 48232 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→47.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16243 0 76 5 16324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316694
X-RAY DIFFRACTIONf_angle_d0.73722629
X-RAY DIFFRACTIONf_dihedral_angle_d10.02911910
X-RAY DIFFRACTIONf_chiral_restr0.0472555
X-RAY DIFFRACTIONf_plane_restr0.0072843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.16330.5041390.47682673X-RAY DIFFRACTION99
3.1633-3.2320.39421380.40692652X-RAY DIFFRACTION99
3.232-3.30720.39551400.34772661X-RAY DIFFRACTION99
3.3072-3.38990.40131420.32772693X-RAY DIFFRACTION99
3.3899-3.48150.33271420.2962682X-RAY DIFFRACTION100
3.4815-3.58390.35341420.27992701X-RAY DIFFRACTION100
3.5839-3.69960.33031410.27432667X-RAY DIFFRACTION100
3.6996-3.83170.32971430.26952698X-RAY DIFFRACTION100
3.8317-3.98510.30871410.23392687X-RAY DIFFRACTION100
3.9851-4.16630.27341410.2282699X-RAY DIFFRACTION100
4.1663-4.38580.27231430.21032708X-RAY DIFFRACTION100
4.3858-4.66040.27571430.20732711X-RAY DIFFRACTION100
4.6604-5.01990.24321410.19672688X-RAY DIFFRACTION100
5.0199-5.52440.24261440.22727X-RAY DIFFRACTION100
5.5244-6.32220.26251430.23292715X-RAY DIFFRACTION100
6.3222-7.95920.24681430.22122722X-RAY DIFFRACTION100
7.9592-47.4990.19451440.18152738X-RAY DIFFRACTION99

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