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- PDB-4f91: Brr2 Helicase Region -

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Basic information

Entry
Database: PDB / ID: 4f91
TitleBrr2 Helicase Region
ComponentsU5 small nuclear ribonucleoprotein 200 kDa helicase
KeywordsHYDROLASE / RNP remodeling / pre-mRNA splicing / spliceosome catalytic activation / DEXD/H-box RNA Helicase / RNA and ATP binding / Nucleus
Function / homology
Function and homology information


cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity ...cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / osteoblast differentiation / RNA helicase activity / cilium / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane
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 / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Sec63 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 / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Sec63 domain / Sec63 Brl domain / C2 domain / 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 / 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
U5 small nuclear ribonucleoprotein 200 kDa helicase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.697 Å
AuthorsSantos, K.F. / Jovin, S.M. / Weber, G. / Pena, V. / Luehrmann, R. / Wahl, M.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for functional cooperation between tandem helicase cassettes in Brr2-mediated remodeling of the spliceosome.
Authors: Santos, K.F. / Jovin, S.M. / Weber, G. / Pena, V. / Luhrmann, R. / Wahl, M.C.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: U5 small nuclear ribonucleoprotein 200 kDa helicase


Theoretical massNumber of molelcules
Total (without water)197,2381
Polymers197,2381
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.260, 150.500, 141.960
Angle α, β, γ (deg.)90.00, 120.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 ...Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 197238.234 Da / Num. of mol.: 1 / Fragment: Brr2 Helicase Region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP200, ASCC3L1, HELIC2, KIAA0788 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75643, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate, 1.2 M sodium Malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.127 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 23, 2011
RadiationMonochromator: Double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 140336 / % possible obs: 98.7 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6
Reflection shellResolution: 2.69→2.84 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 1.6 / % possible all: 93.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.697→48.394 Å / SU ML: 0.46 / σ(F): 0.73 / Phase error: 35.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2716 7158 5.1 %
Rwork0.2236 --
obs0.2261 140334 97.34 %
all-144169 -
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.161 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.1944 Å20 Å26.9023 Å2
2--37.9788 Å20 Å2
3----21.7844 Å2
Refinement stepCycle: LAST / Resolution: 2.697→48.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13859 0 0 6 13865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914153
X-RAY DIFFRACTIONf_angle_d1.32919177
X-RAY DIFFRACTIONf_dihedral_angle_d19.6095340
X-RAY DIFFRACTIONf_chiral_restr0.0912177
X-RAY DIFFRACTIONf_plane_restr0.0062454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.697-2.72770.54941440.49712614X-RAY DIFFRACTION57
2.7277-2.75970.46072470.40514515X-RAY DIFFRACTION98
2.7597-2.79340.43912560.39024415X-RAY DIFFRACTION98
2.7934-2.82880.44852360.37584587X-RAY DIFFRACTION99
2.8288-2.8660.42662080.35824450X-RAY DIFFRACTION99
2.866-2.90520.3812260.34974533X-RAY DIFFRACTION99
2.9052-2.94670.40872510.34624512X-RAY DIFFRACTION99
2.9467-2.99070.40772180.34454548X-RAY DIFFRACTION99
2.9907-3.03740.4052450.32774479X-RAY DIFFRACTION99
3.0374-3.08720.35732210.31584594X-RAY DIFFRACTION99
3.0872-3.14040.38272030.30384493X-RAY DIFFRACTION99
3.1404-3.19750.40392460.30294552X-RAY DIFFRACTION99
3.1975-3.2590.38662630.28984485X-RAY DIFFRACTION99
3.259-3.32550.30992910.27584435X-RAY DIFFRACTION99
3.3255-3.39780.37542380.27114559X-RAY DIFFRACTION99
3.3978-3.47680.32472240.25094500X-RAY DIFFRACTION99
3.4768-3.56380.312730.24384487X-RAY DIFFRACTION99
3.5638-3.66010.28972380.22764499X-RAY DIFFRACTION99
3.6601-3.76780.25862190.21244525X-RAY DIFFRACTION98
3.7678-3.88930.25742810.21114472X-RAY DIFFRACTION98
3.8893-4.02830.26312380.19664442X-RAY DIFFRACTION98
4.0283-4.18950.23122440.19174444X-RAY DIFFRACTION98
4.1895-4.380.23722210.18374508X-RAY DIFFRACTION98
4.38-4.61080.2452240.18684487X-RAY DIFFRACTION98
4.6108-4.89940.26042440.18624409X-RAY DIFFRACTION98
4.8994-5.27720.21162290.19054504X-RAY DIFFRACTION98
5.2772-5.80750.25052520.19784512X-RAY DIFFRACTION99
5.8075-6.6460.2632560.1924526X-RAY DIFFRACTION100
6.646-8.36630.15872500.13764559X-RAY DIFFRACTION100
8.3663-48.40150.18292720.1814533X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.3749 Å / Origin y: 0.978 Å / Origin z: 30.9515 Å
111213212223313233
T0.2614 Å2-0.1753 Å2-0.0171 Å2-0.0654 Å2-0.0155 Å2--0.2268 Å2
L0.8994 °20.1438 °2-0.4357 °2-0.3547 °2-0.0439 °2--1.0686 °2
S-0.0154 Å °0.0855 Å °0.1998 Å °0.0764 Å °0.0041 Å °0.0618 Å °-0.0859 Å °-0.2062 Å °0.0184 Å °
Refinement TLS groupSelection details: ALL

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