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- PDB-4bgd: Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8 -

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Basic information

Entry
Database: PDB / ID: 4bgd
TitleCrystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8
Components(PRE-MRNA-SPLICING ...) x 2
KeywordsTRANSCRIPTION / SPLICEOSOME / RNA HELICASE / U5 SNRNP / RETINITIS PIGMENTOSA
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
Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / 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 / : ...Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / 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 / 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 domain / DEAD/DEAH box helicase / C2 domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helicase conserved C-terminal 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 / Ribonuclease H-like superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å
AuthorsNguyen, T.H.D. / Li, J. / Nagai, K.
CitationJournal: Structure / Year: 2013
Title: Structural Basis of Brr2-Prp8 Interactions and Implications for U5 Snrnp Biogenesis and the Spliceosome Active Site
Authors: Nguyen, T.H.D. / Li, J. / Galej, W.P. / Oshikane, H. / Newman, A.J. / Nagai, K.
History
DepositionMar 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,7605
Polymers223,9102
Non-polymers8503
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-33 kcal/mol
Surface area83910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.640, 178.640, 180.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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PRE-MRNA-SPLICING ... , 2 types, 2 molecules AC

#1: Protein PRE-MRNA-SPLICING HELICASE BRR2 / PROTEIN SNU246


Mass: 195729.453 Da / Num. of mol.: 1 / Fragment: RESIDUES 442-2163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32639, RNA helicase
#2: Protein PRE-MRNA-SPLICING FACTOR 8 / PRP8 / JAB1/MPN


Mass: 28180.924 Da / Num. of mol.: 1 / Fragment: RESIDUES 2148-2395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P33334

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Non-polymers , 4 types, 18 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.77 Å3/Da / Density % sol: 67 %
Description: THE TWO KNOWN FRAGMENTS COULD ALSO BE FOUND BY MOLECULAR REPLACEMENT, BUT IT WAS NOT SUFFICIENT FOR STRUCTURE DETERMINATION. THE STRUCTURE WAS SOLVED BY SIRAS.
Crystal growpH: 7.5 / Details: 100 MM HEPESNA PH 7.5, 200 MM MGCL2, 32-40% PEG400

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→92.2 Å / Num. obs: 63788 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.8
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: PDB ENTRIES 3HIB AND 2OG4

3hib

2og4


Resolution: 3.1→92.37 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.956 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.436
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26993 3206 5 %RANDOM
Rwork0.21373 ---
obs0.21664 60299 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 121.282 Å2
Baniso -1Baniso -2Baniso -3
1-5.73 Å20 Å20 Å2
2---7.84 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 3.1→92.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15663 0 55 15 15733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01916074
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215378
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.96521795
X-RAY DIFFRACTIONr_angle_other_deg0.798335451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08551954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91924.77740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.349152848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7291574
X-RAY DIFFRACTIONr_chiral_restr0.0750.22457
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023646
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_it8.54911.8747819
X-RAY DIFFRACTIONr_mcbond_other8.54811.8747818
X-RAY DIFFRACTIONr_mcangle_it12.73917.8089769
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.78212.4698255
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 231 -
Rwork0.306 4224 -
obs--95.23 %

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