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- PDB-5m59: Crystal structure of Chaetomium thermophilum Brr2 helicase core i... -

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Basic information

Entry
Database: PDB / ID: 5m59
TitleCrystal structure of Chaetomium thermophilum Brr2 helicase core in complex with Prp8 Jab1 domain
Components
  • Pre-mRNA splicing helicase-like protein
  • Putative pre-mRNA splicing factor
KeywordsSPLICING / Brr2 / pre-mRNA splicing / RNA-helicase / Prp8
Function / homology
Function and homology information


: / U5 snRNA binding / U6 snRNA binding / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / metallopeptidase activity / nucleic acid binding / ATP hydrolysis activity / ATP binding
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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
ACETATE ION / Pre-mRNA splicing helicase-like protein / Putative pre-mRNA splicing factor
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAbsmeier, E. / Becke, C. / Wollenhaupt, J. / 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 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 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

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Assembly

Deposited unit
B: Putative pre-mRNA splicing factor
A: Pre-mRNA splicing helicase-like protein
D: Putative pre-mRNA splicing factor
C: Pre-mRNA splicing helicase-like protein
F: Putative pre-mRNA splicing factor
E: Pre-mRNA splicing helicase-like protein
H: Putative pre-mRNA splicing factor
G: Pre-mRNA splicing helicase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)931,29412
Polymers931,0588
Non-polymers2364
Water54030
1
D: Putative pre-mRNA splicing factor
C: Pre-mRNA splicing helicase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,8243
Polymers232,7652
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-17 kcal/mol
Surface area86260 Å2
MethodPISA
2
F: Putative pre-mRNA splicing factor
E: Pre-mRNA splicing helicase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,8243
Polymers232,7652
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-16 kcal/mol
Surface area84440 Å2
MethodPISA
3
H: Putative pre-mRNA splicing factor
G: Pre-mRNA splicing helicase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,8243
Polymers232,7652
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-16 kcal/mol
Surface area87460 Å2
MethodPISA
4
B: Putative pre-mRNA splicing factor
A: Pre-mRNA splicing helicase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,8243
Polymers232,7652
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-14 kcal/mol
Surface area84480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.540, 269.589, 231.689
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative pre-mRNA splicing factor


Mass: 31083.316 Da / Num. of mol.: 4 / Fragment: Jab1 domain, UNP residues 2037-2309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0071250 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SFL3
#2: Protein
Pre-mRNA splicing helicase-like protein


Mass: 201681.250 Da / Num. of mol.: 4 / Fragment: UNP residues 426-2193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0009470 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0S0B9
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.2 mM spermine-tetrahydrochloride 3 % (v/v) Tacsimate, pH 7.0 2% (w/v) PEG MME5000 0.1 M HEPES-NaOH, pH 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 184926 / % possible obs: 98.8 % / Redundancy: 7 % / CC1/2: 0.991 / Rrim(I) all: 0.295 / Net I/σ(I): 8.1
Reflection shellResolution: 3.2→3.39 Å / Redundancy: 6.8 % / Num. unique all: 29309 / CC1/2: 0.266

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KIT

4kit


Resolution: 3.2→49.134 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2868 9215 5 %
Rwork0.2443 --
obs0.2464 184298 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→49.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms63621 0 16 30 63667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00265080
X-RAY DIFFRACTIONf_angle_d0.51788300
X-RAY DIFFRACTIONf_dihedral_angle_d11.88924401
X-RAY DIFFRACTIONf_chiral_restr0.0219904
X-RAY DIFFRACTIONf_plane_restr0.00311372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.37483010.36775729X-RAY DIFFRACTION99
3.2364-3.27440.38023070.35645854X-RAY DIFFRACTION99
3.2744-3.31430.38423120.35525920X-RAY DIFFRACTION99
3.3143-3.35630.36423010.34985718X-RAY DIFFRACTION98
3.3563-3.40040.40283020.35295741X-RAY DIFFRACTION97
3.4004-3.4470.38673040.33885777X-RAY DIFFRACTION98
3.447-3.49620.34283070.33735809X-RAY DIFFRACTION99
3.4962-3.54840.38453130.32815946X-RAY DIFFRACTION100
3.5484-3.60390.35083060.31315806X-RAY DIFFRACTION99
3.6039-3.66290.34683080.31465864X-RAY DIFFRACTION100
3.6629-3.72610.32643090.30535872X-RAY DIFFRACTION99
3.7261-3.79380.35933070.29935828X-RAY DIFFRACTION100
3.7938-3.86670.33593070.29735870X-RAY DIFFRACTION99
3.8667-3.94560.34463060.28585810X-RAY DIFFRACTION99
3.9456-4.03140.3183100.28175886X-RAY DIFFRACTION99
4.0314-4.12510.31833080.26615844X-RAY DIFFRACTION100
4.1251-4.22820.31052990.25745686X-RAY DIFFRACTION96
4.2282-4.34250.30983080.24575832X-RAY DIFFRACTION100
4.3425-4.47020.27483100.23255894X-RAY DIFFRACTION100
4.4702-4.61430.26293110.22915918X-RAY DIFFRACTION100
4.6143-4.77910.23163070.22025838X-RAY DIFFRACTION100
4.7791-4.97030.28683090.21635856X-RAY DIFFRACTION100
4.9703-5.19630.2613110.2235923X-RAY DIFFRACTION100
5.1963-5.46990.27753070.22465815X-RAY DIFFRACTION99
5.4699-5.81210.25773040.23355778X-RAY DIFFRACTION97
5.8121-6.260.31063090.23595872X-RAY DIFFRACTION100
6.26-6.88850.25623080.22885858X-RAY DIFFRACTION100
6.8885-7.88170.2593120.20595931X-RAY DIFFRACTION99
7.8817-9.91670.19753070.15835821X-RAY DIFFRACTION98
9.9167-49.14010.21613050.16455787X-RAY DIFFRACTION96

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