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- PDB-6s9i: Human Brr2 Helicase Region D534C/N1866C in complex with C-tail de... -

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Basic information

Entry
Database: PDB / ID: 6s9i
TitleHuman Brr2 Helicase Region D534C/N1866C in complex with C-tail deleted Jab1
Components
  • Pre-mRNA-processing-splicing factor 8
  • U5 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 / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding ...cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / osteoblast differentiation / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / RNA helicase activity / RNA helicase / nuclear speck / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus
Similarity search - Function
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 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease ...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 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / 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 / 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 / Ribonuclease H-like superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing-splicing factor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 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 13, 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

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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
J: Pre-mRNA-processing-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)229,7772
Polymers229,7772
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-11 kcal/mol
Surface area83320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.240, 119.077, 187.913
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 199643.734 Da / Num. of mol.: 1 / Mutation: D534C, N1866C
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: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 30133.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPF8, PRPC8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P2Q9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Hepes-NaOH, 0.1M MgCl2, 8% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91677 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 68538 / % possible obs: 98.9 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rrim(I) all: 0.159 / Net I/σ(I): 9.6
Reflection shellResolution: 2.6→2.76 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 10962 / CC1/2: 0.474 / Rrim(I) all: 1.386 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.598→47.976 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.71
RfactorNum. reflection% reflection
Rfree0.278 2099 3.06 %
Rwork0.1967 --
obs0.1991 68531 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 210.54 Å2 / Biso mean: 69.6232 Å2 / Biso min: 17.3 Å2
Refinement stepCycle: final / Resolution: 2.598→47.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15815 0 0 102 15917
Biso mean---49.34 -
Num. residues----1964
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5982-2.65860.43121370.3263434098
2.6586-2.72510.31871390.28764414100
2.7251-2.79870.35421390.26964402100
2.7987-2.88110.32451320.2632414994
2.8811-2.97410.34621400.26024440100
2.9741-3.08030.35231400.26064429100
3.0803-3.20370.3651400.24184423100
3.2037-3.34940.31741400.23464436100
3.3494-3.5260.3431410.22224476100
3.526-3.74680.30071410.2054458100
3.7468-4.0360.25391410.17954454100
4.036-4.44180.23451360.1536431896
4.4418-5.0840.19791430.13854504100
5.084-6.40290.24251440.18144572100
6.4029-47.9760.23941460.162461797
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)
11.06-0.2597-0.07212.3581-0.44261.61790.02480.028-0.05990.2655-0.0530.2808-0.0272-0.12380.0440.2562-0.0324-0.00450.27430.01470.2718-77.19576.780610.3728
22.04850.1422-0.39982.924-0.29642.05180.17420.2693-0.1234-0.7722-0.1023-0.4608-0.03210.3268-0.0570.67630.07780.08930.50060.07010.4781-59.150722.7546-23.4495
32.72950.5984-0.22792.70160.18141.01710.2227-0.1798-0.03050.0582-0.2369-0.4369-0.11350.28090.03330.3767-0.07220.010.41640.07540.4012-54.228422.25347.6839
41.4395-0.2116-0.31882.282-0.06981.6250.20910.2568-0.0566-0.5881-0.18010.220.180.0924-0.01040.47210.0972-0.07530.3703-0.00590.3441-62.1029-12.2765-9.4023
52.70640.6246-0.70610.58760.63871.849-0.02920.5933-0.2449-0.63-0.0089-0.75880.1660.36820.09420.59210.20430.17730.93380.0750.732-32.6914-18.2138-13.1301
62.0961-0.58340.26891.0861-0.31651.6165-0.02690.05360.0670.06440.0375-0.26550.11540.2041-0.00670.30180.0508-0.02250.3634-0.03010.3236-42.2755-22.721212.1068
72.4077-0.1632-0.76830.9327-0.15051.6983-0.1235-0.66160.04320.12750.1921-0.0320.11590.2848-0.06520.43950.0753-0.06760.66160.06820.3096-41.1077-22.1755.2269
82.116-0.7701-0.52373.1656-0.0641.8230.0071-0.25950.12970.05090.04850.0468-0.21790.0926-0.03570.26460.0121-0.02050.37870.04080.2978-60.5644-6.334537.66
92.09060.4195-0.48371.68310.5490.839-0.16470.0743-0.0786-0.20980.1094-0.2223-0.01320.10270.07750.43150.062-0.04740.49640.02640.3484-22.588-26.57534.9307
101.9399-1.3053-1.04531.74811.16821.13110.37830.5570.7801-0.8613-0.26740.0059-0.4448-0.195-0.1050.75970.082-0.01930.53350.1490.7454-24.43745.298733.4965
111.8677-0.07380.09110.8622-0.81782.4319-0.1409-0.25840.21190.13660.2431-0.6887-0.7224-0.4182-0.1730.97030.0695-0.09190.7329-0.24861.4511-26.090124.980155.7416
122.0491-0.65010.34851.6091-0.10241.7776-0.2508-0.56130.7283-0.01670.3464-0.2623-0.24970.416-0.08820.6001-0.0432-0.00130.7632-0.14151.0005-7.14974.622853.9675
131.6679-0.16940.28811.8672-0.1751.26010.0627-0.0046-0.3043-0.1645-0.03740.32490.1017-0.0011-0.05010.35120.0577-0.07330.3405-0.03050.5067-54.8926-45.1026-7.0178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1:419 or resid 886:995)B1 - 419
2X-RAY DIFFRACTION1chain 'B' and (resid 1:419 or resid 886:995)B886 - 995
3X-RAY DIFFRACTION2chain 'B' and (resid 429:455 or resid 682:885)B429 - 455
4X-RAY DIFFRACTION2chain 'B' and (resid 429:455 or resid 682:885)B682 - 885
5X-RAY DIFFRACTION3chain 'B' and (resid 459:681)B459 - 681
6X-RAY DIFFRACTION4chain 'B' and (resid 996:1123)B996 - 1123
7X-RAY DIFFRACTION5chain 'B' and (resid 1124:1181)B1124 - 1181
8X-RAY DIFFRACTION6chain 'B' and (resid 1182:1294)B1182 - 1294
9X-RAY DIFFRACTION7chain 'B' and (resid 1295:1520)B1295 - 1520
10X-RAY DIFFRACTION8chain 'B' and (resid 1521:1723)B1521 - 1723
11X-RAY DIFFRACTION9chain 'B' and (resid 1724:1825)B1724 - 1825
12X-RAY DIFFRACTION10chain 'B' and (resid 1826:1956)B1826 - 1956
13X-RAY DIFFRACTION11chain 'B' and (resid 1957:2013)B1957 - 2013
14X-RAY DIFFRACTION12chain 'B' and (resid 2014:3000)B2014 - 3000
15X-RAY DIFFRACTION13chain J and (resid 2000:3000)J2000 - 3000

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