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- PDB-5dca: Crystal structure of yeast full length Brr2 in complex with Prp8 ... -

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Basic information

Entry
Database: PDB / ID: 5dca
TitleCrystal structure of yeast full length Brr2 in complex with Prp8 Jab1 domain
Components
  • Pre-mRNA-splicing factor 8
  • Pre-mRNA-splicing helicase BRR2
KeywordsHYDROLASE / protein complex / helicase / RNP remodeling / spliceosome activation
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 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding ...spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 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 / spliceosomal snRNP assembly / U6 snRNA binding / 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 / RNA helicase activity / nucleic acid binding / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / Cytidine Deaminase, domain 2 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Cytidine Deaminase; domain 2 / Sec63 domain ...Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / Cytidine Deaminase, domain 2 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Cytidine Deaminase; domain 2 / Sec63 domain / Sec63 Brl domain / C2 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 / DEAD/DEAH box helicase domain / C2 domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / Helicase conserved C-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / DNA polymerase; domain 1 / 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 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Ribonuclease H-like superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / 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: 2.8 Å
AuthorsAbsmeier, E. / Wollenhaupt, J. / Santos, K.F. / Wahl, M.C.
CitationJournal: Genes Dev. / Year: 2015
Title: The large N-terminal region of the Brr2 RNA helicase guides productive spliceosome activation.
Authors: Absmeier, E. / Wollenhaupt, J. / Mozaffari-Jovin, S. / Becke, C. / Lee, C.T. / Preussner, M. / Heyd, F. / Urlaub, H. / Luhrmann, R. / Santos, K.F. / Wahl, M.C.
History
DepositionAug 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 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
J: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)250,6582
Polymers250,6582
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-19 kcal/mol
Surface area99230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.850, 178.850, 181.110
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


Mass: 222147.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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


Mass: 28510.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES-NaOH, pH 6.5, 9 % (w/v) PEG 3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 85520 / Num. obs: 85520 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rsym value: 0.105 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BGD

4bgd


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 20.31 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R: 0.777 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25491 4257 5 %RANDOM
Rwork0.20224 ---
obs0.20484 81271 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.259 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å2-0 Å2
2---4.14 Å2-0 Å2
3---2.1 Å2
Refinement stepCycle: 1 / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17651 0 0 191 17842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01918020
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217309
X-RAY DIFFRACTIONr_angle_refined_deg0.9941.96424414
X-RAY DIFFRACTIONr_angle_other_deg0.706339920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6952191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71724.994841
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.634153253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6911582
X-RAY DIFFRACTIONr_chiral_restr0.0560.22766
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02120188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024042
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_it3.76310.0978788
X-RAY DIFFRACTIONr_mcbond_other3.75910.0968787
X-RAY DIFFRACTIONr_mcangle_it6.3515.13710971
X-RAY DIFFRACTIONr_mcangle_other6.35115.13810972
X-RAY DIFFRACTIONr_scbond_it3.35510.3339232
X-RAY DIFFRACTIONr_scbond_other3.35510.3349233
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.87115.3713444
X-RAY DIFFRACTIONr_long_range_B_refined1079.220528
X-RAY DIFFRACTIONr_long_range_B_other9.99879.21520514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 276 -
Rwork0.409 5472 -
obs--91.15 %

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