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- PDB-3im1: Structure of the C-terminal Sec63 unit of yeast Brr2, P212121 Form -

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Basic information

Entry
Database: PDB / ID: 3im1
TitleStructure of the C-terminal Sec63 unit of yeast Brr2, P212121 Form
ComponentsPre-mRNA-splicing helicase BRR2
KeywordsHYDROLASE / ATPase / RNA helicase / RNPase / RNA unwindase / molecular modeling / pre-mRNA splicing / spliceosome catalytic activation / U5-200K protein/Brr2 / ATP-binding / Helicase / mRNA processing / mRNA splicing / Nucleotide-binding / Nucleus / Phosphoprotein / Spliceosome
Function / homology
Function and homology information


spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U5 snRNP / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / nucleic acid binding / RNA helicase / ATP hydrolysis activity / ATP binding ...spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U5 snRNP / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / nucleic acid binding / RNA helicase / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus
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 / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / C2 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 / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / C2 domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Pre-mRNA-splicing helicase BRR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsPena, V. / Hrmann, R.L. / Wahl, M.C.
CitationJournal: To be Published
Title: Common Design Principles in the Spliceosomal RNA Helicase Brr2 and in the Hel308 DNA Helicase
Authors: Pena, V. / Jovin, S.M. / Fabrizio, P. / Orlowski, J. / Bujnicki, J.M. / Hrmann, R.L. / Wahl, M.C.
History
DepositionAug 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA-splicing helicase BRR2


Theoretical massNumber of molelcules
Total (without water)37,1551
Polymers37,1551
Non-polymers00
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.235, 76.504, 84.585
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: 37155.250 Da / Num. of mol.: 1 / Fragment: Sec63 unit (UNP residues 1839-2163)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BRR2, RSS1, SNU246, SYGP-ORF66, YER172C / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: P32639, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.4 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM sodium cacodylate, pH 6.0, 100mM Li2SO4, 15% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 43913 / Num. obs: 43474 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.06 / Net I/σ(I): 30.5
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3458 / Rsym value: 0.51 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.282 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23159 2181 5 %RANDOM
Rwork0.19305 ---
all0.19507 41613 --
obs0.19507 41201 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.622 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.93 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 0 412 3010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222790
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9763818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2125356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.56525.726124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5915509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5041510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022100
X-RAY DIFFRACTIONr_nbd_refined0.1890.21199
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21953
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.235
X-RAY DIFFRACTIONr_mcbond_it0.551.51786
X-RAY DIFFRACTIONr_mcangle_it0.92822841
X-RAY DIFFRACTIONr_scbond_it1.54231146
X-RAY DIFFRACTIONr_scangle_it2.3624.5977
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 149 -
Rwork0.345 3007 -
obs-3156 99.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1881-0.2122-4.18081.7815-0.999811.40170.08510.45590.127-0.26370.00170.1104-0.1612-0.5839-0.0868-0.0665-0.034-0.04150.05560.00590.01018.06271.5408-16.0598
23.9849-0.7961-0.84121.77970.4772.26860.0217-0.052-0.09910.22-0.10390.0659-0.01730.06510.0821-0.0343-0.00170.0047-0.0134-0.0082-0.073113.04768.520712.5004
317.9175-3.84867.32731.4933-0.21075.9819-0.1666-0.8945-0.12480.15820.10620.15510.0135-0.34120.0604-0.09340.00570.0310.0261-0.0046-0.04539.123363.51726.9341
46.2713-5.8472-1.76611.74852.66742.1036-0.0082-0.35780.02680.24720.02710.13510.2105-0.0634-0.0189-0.1035-0.04040.02150.0285-0.0121-0.00424.937951.7061-0.7415
54.64191.3851-0.16323.67711.58334.0189-0.0114-0.072-0.38920.10040.0991-0.27790.17790.2492-0.0877-0.10350.0405-0.0108-0.0103-0.01650.00219.794552.13190.3402
65.6662-3.36819.169817.23815.143222.2059-0.049-0.6429-0.02351.2270.2337-0.8031-0.08640.9758-0.18480.0442-0.1051-0.0430.25590.15620.113214.147351.61610.6143
71.71521.0561-0.77192.3726-0.65821.6498-0.07210.0139-0.0314-0.10860.0403-0.05970.0073-0.10650.0318-0.09590.00150.01140.003-0.0152-0.025716.01359.1672-3.185
80.8872-1.0707-1.011111.01995.17865.0228-0.02470.0868-0.0227-0.2294-0.04150.253-0.0563-0.41560.0663-0.1077-0.0177-0.00520.05610.0085-0.04588.04161.322-7.0717
90.84010.1203-0.51750.89280.65693.63930.0419-0.0846-0.00920.0945-0.03590.0373-0.26760.1604-0.0059-0.0372-0.0105-0.0046-0.0180.009-0.045218.646673.754.4686
106.57180.1759-0.65413.2929-3.53756.93190.0501-0.1115-0.3642-0.4379-0.2754-0.15760.42440.57620.2253-0.05310.04260.01760.01620.055-0.044228.493968.6325-16.4197
116.5957-5.0391-0.857125.40174.71345.71820.2692-0.16390.2088-0.8022-0.5223-1.1442-0.3320.77880.2531-0.1722-0.03880.03690.15760.123-0.017635.340675.9471-16.8077
1219.547936.322812.958481.770723.314423.8634-1.50521.2633-0.2751-3.41321.3403-1.4553-1.51221.29820.1649-0.07170.02770.07380.23780.1888-0.050634.701278.4123-26.2717
136.3434-1.2482-0.713.10472.96058.48140.2150.0116-0.4548-0.0238-0.0416-0.09360.40850.1588-0.17340.00350.0284-0.0533-0.03450.0367-0.056321.856173.2379-26.3858
141.71792.17482.68583.19874.07078.28560.1091-0.05480.17220.0186-0.27780.1757-1.13160.13660.16860.268-0.1569-0.00480.01850.0226-0.06725.617290.4711-3.5477
151.0368-0.66561.17621.45873.799834.6178-0.18510.01330.2817-0.61860.3418-0.0859-1.36290.5259-0.15660.2977-0.1808-0.0048-0.0711-0.0566-0.013324.590297.835112.3842
1650.461732.946815.574344.1968.24923.9264-2.20793.42581.9131-2.93322.25410.3054-2.49841.2724-0.04620.5795-0.0569-0.04970.15140.05180.034418.096190.6321-13.559
171.30480.95590.40712.42971.1054.73580.0448-0.07320.0434-0.0258-0.06-0.0088-0.54790.02240.0152-0.0577-0.0127-0.0095-0.07560.0209-0.092618.479.4072-0.937
183.8301-0.22842.86414.8811-3.330618.37490.0945-0.15290.2018-0.18220.02840.2277-1.293-0.3773-0.12290.1683-0.01530.0172-0.1851-0.0295-0.127417.40288.63623.4539
191.72910.31060.01421.20912.34954.82170.1025-0.1850.15-0.15760.0107-0.0227-0.83410.5221-0.11320.1799-0.154-0.0037-0.02390.0071-0.09424.465489.15636.6532
205.39384.91837.103110.030913.762219.79190.1735-0.30380.1494-0.05490.2039-0.2441-0.44560.7576-0.37740.1486-0.2610.01410.1135-0.058-0.113832.034190.84219.3806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1839 - 1856
2X-RAY DIFFRACTION2A1857 - 1880
3X-RAY DIFFRACTION3A1881 - 1889
4X-RAY DIFFRACTION4A1890 - 1900
5X-RAY DIFFRACTION5A1901 - 1914
6X-RAY DIFFRACTION6A1915 - 1921
7X-RAY DIFFRACTION7A1922 - 1938
8X-RAY DIFFRACTION8A1939 - 1955
9X-RAY DIFFRACTION9A1956 - 1990
10X-RAY DIFFRACTION10A1991 - 2006
11X-RAY DIFFRACTION11A2007 - 2020
12X-RAY DIFFRACTION12A2021 - 2031
13X-RAY DIFFRACTION13A2032 - 2043
14X-RAY DIFFRACTION14A2044 - 2060
15X-RAY DIFFRACTION15A2061 - 2076
16X-RAY DIFFRACTION16A2077 - 2084
17X-RAY DIFFRACTION17A2085 - 2110
18X-RAY DIFFRACTION18A2111 - 2121
19X-RAY DIFFRACTION19A2122 - 2151
20X-RAY DIFFRACTION20A2152 - 2163

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