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- PDB-6s8q: Human Brr2 Helicase Region in complex with C-tail deleted Jab1 -

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Basic information

Entry
Database: PDB / ID: 6s8q
TitleHuman Brr2 Helicase Region 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 processing / mRNA splicing, via spliceosome / 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 / identical protein binding / membrane / nucleus
Similarity search - Function
Cytidine Deaminase, domain 2 / 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 / Sec63 domain / Sec63 Brl domain / JAB1/Mov34/MPN/PAD-1 ubiquitin protease ...Cytidine Deaminase, domain 2 / 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 / 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 / Ribonuclease H-like superfamily / Winged helix DNA-binding domain 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: 2.391 Å
AuthorsSantos, K.F. / Vester, K. / 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,9924
Polymers229,8002
Non-polymers1922
Water11,782654
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-43 kcal/mol
Surface area82660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.480, 118.632, 187.716
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: 199666.656 Da / Num. of mol.: 1
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.5 %
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: 0.91842 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 88725 / % possible obs: 99.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 56.6 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.144 / Net I/σ(I): 11.3
Reflection shellResolution: 2.4→2.53 Å / Num. unique obs: 14026 / CC1/2: 0.594 / Rrim(I) all: 1.446

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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: 2.391→48.08 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.32
RfactorNum. reflection% reflection
Rfree0.253 2100 2.38 %
Rwork0.1795 --
obs0.1812 88212 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 236.54 Å2 / Biso mean: 59.2729 Å2 / Biso min: 10.91 Å2
Refinement stepCycle: final / Resolution: 2.391→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15988 0 10 656 16654
Biso mean--121.06 49.28 -
Num. residues----1987
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.391-2.44630.36391350.2627555797
2.4463-2.50750.29331390.25035695100
2.5075-2.57530.30361390.23655683100
2.5753-2.65110.33281380.23225674100
2.6511-2.73660.31861390.22465715100
2.7366-2.83440.3461390.21825694100
2.8344-2.94790.28431400.20495719100
2.9479-3.08210.27381390.2045720100
3.0821-3.24450.28921400.20365722100
3.2445-3.44770.27351390.19725727100
3.4477-3.71390.24931400.17895744100
3.7139-4.08740.24711410.16075778100
4.0874-4.67850.21341410.13675771100
4.6785-5.89270.21051430.14675856100
5.8927-48.080.19951480.1546060100
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)
10.59270.064-0.02910.9274-0.00820.8523-0.0033-0.03080.1123-0.22860.00130.2224-0.0377-0.166200.18360.02110.01010.18240.00970.2041-28.0853-7.1651-10.1819
21.2799-0.8581-0.09551.2096-0.46761.68730.1904-0.23620.33410.7932-0.2958-0.2783-0.09460.4682-0.12820.5711-0.1723-0.14760.41190.10690.2153-9.3007-22.749923.8911
31.6118-0.14970.27481.76830.04181.39680.11740.0856-0.04260.0255-0.1371-0.26780.05550.2251-0.00080.14630.0340.01530.17680.02440.1339-4.6649-22.1802-7.6711
40.591-0.0409-0.06691.05570.36460.71420.1474-0.15510.0990.3886-0.19910.12060.0140.0444-0.02890.3734-0.11470.06230.236-0.05160.2077-12.937812.45859.2914
50.3761-0.4055-0.25360.44410.35150.57340.4433-0.55390.33740.2993-0.3042-0.7886-0.70120.61440.12320.4682-0.2387-0.19640.8160.14750.570816.270418.706413.5007
61.00890.6528-0.12590.4981-0.02890.71660.0504-0.0376-0.0218-0.02020.0403-0.1666-0.11820.18850.00030.2445-0.04270.03490.2762-0.04150.29267.00522.6814-12.086
71.69430.23620.92230.4412-0.23111.2059-0.03850.6061-0.0042-0.04220.3393-0.154-0.08610.14970.23320.2685-0.0490.09860.52910.12930.12228.29722.0198-55.1823
81.70120.5474-0.1242.0273-0.481.3542-0.04430.3479-0.0975-0.07840.1020.04010.1388-0.0544-0.00010.1796-0.0035-0.00870.3086-0.00230.1728-11.13256.1524-37.6715
90.62820.32610.1151.0124-0.1360.2174-0.0652-0.16730.23450.12810.1112-0.2568-0.060.0491-0.00010.3227-0.04030.03920.3727-0.03490.304126.782826.2712-34.8606
100.52580.09790.04560.4220.04050.3337-0.0307-0.6362-0.51230.7795-0.15130.00130.36260.0622-0.00020.6814-0.06270.11770.47220.10230.562925.1797-5.6985-33.8612
110.902-0.242-0.63890.22640.08620.5196-0.01990.795-0.2928-0.0357-0.4021-0.70960.4444-0.5338-0.00040.687-0.12550.25520.6027-0.28531.419623.3112-24.5726-56.9058
120.1676-0.00710.11830.58220.16420.6407-0.26260.2306-0.7890.30880.2347-0.24110.04710.23-0.00630.3497-0.01230.03550.5748-0.16360.68843.0432-4.4202-54.4703
131.47810.541-0.08921.74350.17881.01630.1446-0.07940.34660.2045-0.13370.3455-0.0373-0.003-0.06210.2062-0.04960.07650.1403-0.10590.4111-6.072845.35136.7391
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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