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- PDB-5m52: Crystal structure of yeast Brr2 full-lenght in complex with Prp8 ... -

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Basic information

Entry
Database: PDB / ID: 5m52
TitleCrystal structure of yeast Brr2 full-lenght in complex with Prp8 Jab1 domain
Components
  • Pre-mRNA-splicing factor 8
  • Pre-mRNA-splicing helicase BRR2
KeywordsHYDROLASE / Protein Complex / Helicase
Function / homology
Function and homology information


spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / Prp19 complex / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding ...spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / Prp19 complex / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / nucleic acid binding / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Cytidine Deaminase, domain 2 / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Cytidine Deaminase; domain 2 / Sec63 domain ...Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Cytidine Deaminase, domain 2 / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Cytidine Deaminase; domain 2 / Sec63 domain / Sec63 Brl 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. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / C2 domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H-like superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsWollenhaupt, J. / Absmeier, E. / Becke, C. / Santos, K.F. / Wahl, M.C.
CitationJournal: Cell Cycle / Year: 2017
Title: Interplay of cis- and trans-regulatory mechanisms in the spliceosomal RNA helicase Brr2.
Authors: Absmeier, E. / Becke, C. / Wollenhaupt, J. / Santos, K.F. / Wahl, M.C.
History
DepositionOct 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 helicase BRR2
C: Pre-mRNA-splicing factor 8
B: Pre-mRNA-splicing helicase BRR2
D: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)553,9214
Polymers553,9214
Non-polymers00
Water18010
1
A: Pre-mRNA-splicing helicase BRR2
C: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)276,9612
Polymers276,9612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-22 kcal/mol
Surface area97750 Å2
MethodPISA
2
B: Pre-mRNA-splicing helicase BRR2
D: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)276,9612
Polymers276,9612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-23 kcal/mol
Surface area94980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.335, 181.158, 210.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pre-mRNA-splicing helicase BRR2 / Protein Snu246 / yeast Brr2


Mass: 246470.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BRR2, RSS1, SNU246, YER172C, SYGP-ORF66 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32639, RNA helicase
#2: Protein Pre-mRNA-splicing factor 8 / yeast Prp8 Jab1 domain


Mass: 30490.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 7.5, 10.5 % (w/v) PEG 3350, 0.2 M MgCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 94451 / % possible obs: 99.6 % / Redundancy: 6.75 % / Rsym value: 0.327 / Net I/σ(I): 7.1
Reflection shellResolution: 3.4→3.6 Å / Rsym value: 1.56

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DCA

5dca


Resolution: 3.4→48.72 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.844 / SU B: 38.53 / SU ML: 0.564 / Cross valid method: THROUGHOUT / ESU R Free: 0.621
RfactorNum. reflection% reflectionSelection details
Rfree0.29629 2100 2.2 %RANDOM
Rwork0.25204 ---
obs0.25301 92351 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 94.292 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å2-0 Å20 Å2
2---3.18 Å20 Å2
3---1.45 Å2
Refinement stepCycle: 1 / Resolution: 3.4→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34512 0 0 10 34522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01935241
X-RAY DIFFRACTIONr_bond_other_d0.0010.0233819
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.96447767
X-RAY DIFFRACTIONr_angle_other_deg0.821377982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.79754289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41324.9791637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.201156313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.29615157
X-RAY DIFFRACTIONr_chiral_restr0.0530.25421
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02139492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027909
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2959.52517207
X-RAY DIFFRACTIONr_mcbond_other1.2959.52517206
X-RAY DIFFRACTIONr_mcangle_it2.41114.27921479
X-RAY DIFFRACTIONr_mcangle_other2.41114.27921480
X-RAY DIFFRACTIONr_scbond_it0.6879.52518034
X-RAY DIFFRACTIONr_scbond_other0.6879.52518033
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.42514.25826288
X-RAY DIFFRACTIONr_long_range_B_refined4.03574.11738844
X-RAY DIFFRACTIONr_long_range_B_other4.03574.11738845
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.398→3.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 147 -
Rwork0.373 6480 -
obs--96.2 %

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