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- PDB-6s8o: Human Brr2 Helicase Region M641C/A1582C -

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Basic information

Entry
Database: PDB / ID: 6s8o
TitleHuman Brr2 Helicase Region M641C/A1582C
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 / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus
Similarity search - Function
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 domain / DEAD/DEAH box helicase ...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 domain / DEAD/DEAH box helicase / 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
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: 3.172 Å
AuthorsVester, K. / Santos, K.F. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationTRR186 Germany
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The inactive C-terminal cassette of the dual-cassette RNA helicase BRR2 both stimulates and inhibits the activity of the N-terminal helicase unit.
Authors: Vester, K. / Santos, K.F. / Kuropka, B. / Weise, C. / Wahl, M.C.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: U5 small nuclear ribonucleoprotein 200 kDa helicase


Theoretical massNumber of molelcules
Total (without water)199,6711
Polymers199,6711
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area75260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.564, 152.531, 142.515
Angle α, β, γ (deg.)90.000, 120.690, 90.000
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: 199670.672 Da / Num. of mol.: 1 / Mutation: M641C, A1582C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRNP200, ASCC3L1, HELIC2, KIAA0788 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75643, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.45 Å3/Da / Density % sol: 64.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M sodium citrate, 1.5M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.17→50 Å / Num. obs: 44087 / % possible obs: 97 % / Redundancy: 3.4 % / Biso Wilson estimate: 94 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.121 / Net I/σ(I): 8.7
Reflection shellResolution: 3.17→3.36 Å / Num. unique obs: 6492 / CC1/2: 0.641 / Rrim(I) all: 1.316 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f91

4f91


Resolution: 3.172→48.383 Å / SU ML: 0.69 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 41.07
RfactorNum. reflection% reflection
Rfree0.3184 2094 4.76 %
Rwork0.264 --
obs0.2666 44032 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 230.86 Å2 / Biso mean: 118.8486 Å2 / Biso min: 52.58 Å2
Refinement stepCycle: final / Resolution: 3.172→48.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13858 0 0 20 13878
Biso mean---107.21 -
Num. residues----1724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.172-3.24550.58241060.5264212175
3.2455-3.32660.47911410.388283199
3.3266-3.41650.44731410.379285699
3.4165-3.5170.41741420.3392283699
3.517-3.63050.4361420.3549285599
3.6305-3.76020.42911420.358283799
3.7602-3.91070.41051420.3225282598
3.9107-4.08860.33311400.3049282499
4.0886-4.30410.36421410.2733283399
4.3041-4.57350.35541430.2565286799
4.5735-4.92630.29851410.236282399
4.9263-5.42150.28321410.2468282098
5.4215-6.20460.32841460.2698290199
6.2046-7.81190.27181400.2576280698
7.8119-48.3830.22441460.1832290398

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