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- PDB-3im2: Structure of the C-terminal Sec63 unit of yeast Brr2, P41212 Form -

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Basic information

Entry
Database: PDB / ID: 3im2
TitleStructure of the C-terminal Sec63 unit of yeast Brr2, P41212 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 / nucleic acid binding / RNA helicase activity / 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 / nucleic acid binding / RNA helicase activity / 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 / DEAD/DEAH box helicase ...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 / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily / Helicase conserved C-terminal domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pre-mRNA-splicing helicase BRR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3492
Polymers37,1551
Non-polymers1941
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.090, 104.090, 77.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-73-

HOH

21A-255-

HOH

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Components

#1: Protein Pre-mRNA-splicing helicase BRR2


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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.82 Å3/Da / Density % sol: 56.39 %
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: 1.99→30 Å / Num. all: 29754 / Num. obs: 29516 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.1 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 4644 / Rsym value: 0.56 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3IM1

3im1


Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.968 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23655 1503 5.1 %RANDOM
Rwork0.18765 ---
all0.19009 28257 --
obs0.19009 27975 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 13 352 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222773
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.9753786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5715351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.08625.556126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49915504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4821511
X-RAY DIFFRACTIONr_chiral_restr0.080.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022089
X-RAY DIFFRACTIONr_nbd_refined0.180.21177
X-RAY DIFFRACTIONr_nbtor_refined0.2890.21908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.246
X-RAY DIFFRACTIONr_mcbond_it0.3811.51758
X-RAY DIFFRACTIONr_mcangle_it0.61522795
X-RAY DIFFRACTIONr_scbond_it0.97231158
X-RAY DIFFRACTIONr_scangle_it1.5394.5991
LS refinement shellResolution: 1.988→2.039 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 98 -
Rwork0.259 1924 -
obs-2022 93.87 %
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)
12.66912.06252.08281.62942.162810.2211-0.2606-0.03761.15790.326-0.0016-0.6278-0.8989-0.5750.26220.0716-0.0935-0.0023-0.06730.03640.101818.0166-18.2943-10.5366
25.29151.4165-0.53592.0631-0.56972.5188-0.09420.13180.2225-0.07680.11420.1094-0.39380.0916-0.0199-0.0223-0.05740.0107-0.1-0.0079-0.067210.5393-25.85-19.2096
319.2318-3.9499-8.58925.0437-0.92465.54410.11820.24610.5547-0.105-0.0039-0.1922-0.20920.1388-0.1144-0.0423-0.07140.0227-0.0918-0.0342-0.088813.9764-32.4964-23.5646
48.21543.2690.13394.73332.48585.3224-0.09020.32840.6578-0.41010.2180.0313-0.25810.2632-0.1278-0.0204-0.00030.0316-0.0729-0.0024-0.043515.5869-43.4557-32.6175
52.09140.0421-1.15860.64341.59995.25620.02370.1295-0.14980.028-0.04260.04850.1261-0.14430.0189-0.0977-0.0075-0.0214-0.0678-0.0193-0.03863.4559-46.1247-24.2484
617.2861-17.8656-9.901819.387212.446711.72020.28640.633-1.4213-0.3327-0.50061.7655-0.7723-1.37810.21420.07050.07920.04780.16050.07150.14012.7552-35.5262-31.0453
71.74450.8227-1.10071.7592-1.87095.8097-0.03020.0344-0.0921-0.0783-0.0127-0.03150.12210.12580.0429-0.0896-0.01660.0164-0.0549-0.0387-0.020410.8562-44.6219-19.8992
82.38813.28022.224715.35857.51226.29470.0870.1243-0.1893-0.29820.082-0.4114-0.09620.5286-0.169-0.14830.00480.0177-0.0048-0.0139-0.067519.6238-45.381-21.5896
91.4282-0.0950.1031.7631-0.17270.56470.03370.00470.07590.1409-0.00620.0352-0.15180.0232-0.0275-0.036-0.04420.0198-0.0527-0.0076-0.077711.5723-31.6511-9.6883
105.32372.4688-2.18945.37710.03993.9954-0.12940.0429-0.1866-0.31710.1644-0.29270.10850.1495-0.035-0.09160.00460.0202-0.0782-0.0016-0.051210.2381-54.0417-1.8695
1113.12392.0707-3.25048.53761.40499.13740.4207-0.41260.5554-0.15670.03280.0016-0.26880.4746-0.4534-0.12830.00520.0473-0.0625-0.0211-0.08887.6275-52.31117.6816
127.6903-17.4891-15.201439.773534.570830.0487-1.0588-1.8497-0.66993.37011.6725-2.57563.09351.2376-0.61380.33310.1269-0.16030.34730.16740.157513.8188-59.620611.6596
131.6542-0.6503-0.356847.25852.77028.2002-0.4499-0.5131-0.71710.142-0.193-1.97640.71190.6130.6429-0.26030.07730.0552-0.0640.07120.129121.7183-58.96011.1441
144.5793-6.7112-1.461629.55611.99518.3374-0.3582-0.53530.37421.96820.3411-0.53540.1183-0.10040.01710.0972-0.0559-0.0071-0.05570.0279-0.22516.2303-31.92859.9857
158.2157-9.07791.450927.4071-2.45748.6672-0.3908-0.50621.130.02160.20470.0972-1.539-0.03610.18610.427-0.0987-0.1277-0.1483-0.19960.017613.4248-14.76819.7183
166.3452-4.1345-11.110225.184413.984921.4765-0.0942-1.2454-1.10632.3221.3402-1.18391.40052.6144-1.2460.28880.1574-0.27170.7098-0.07080.08827.3389-38.90648.5684
173.8292-3.043-0.88866.93982.38675.0990.0002-0.2127-0.04360.25770.0516-0.0618-0.13330.1209-0.0518-0.17-0.0954-0.0056-0.1220.0172-0.190216.4907-33.646-3.7492
1811.6193-11.10196.610818.0443-7.486312.6958-0.0269-0.22540.76160.7576-0.1108-1.1667-0.14910.52840.1377-0.0187-0.1635-0.0568-0.2089-0.1053-0.14119.5087-25.45031.5619
193.1384-1.5218-0.66785.68151.24554.447-0.2547-0.27080.32870.87890.206-0.0082-0.5746-0.06330.04860.1249-0.0194-0.0211-0.067-0.0569-0.149712.5085-23.75014.9144
203.9717-4.0719-1.46917.69934.06117.8504-0.2766-0.11520.04471.8292-0.13041.1482-0.761-0.80810.40690.28850.08380.12320.0064-0.0751-0.14355.9265-22.03679.6129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1844 - 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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