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- PDB-8bce: Human Brr2 Helicase Region in complex with C-tail deleted Jab1 an... -

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Basic information

Entry
Database: PDB / ID: 8bce
TitleHuman Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 76
Components
  • Pre-mRNA-processing-splicing factor 8
  • U5 small nuclear ribonucleoprotein 200 kDa helicase
KeywordsHYDROLASE / helicase / complex / ligand
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
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 ...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 / Winged helix DNA-binding domain superfamily / Ribonuclease H-like superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
N-methoxybenzenesulfonamide / 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: 2.05 Å
AuthorsVester, K. / Loll, B. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)278001972 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Conformation-dependent ligand hot spots in the spliceosomal RNA helicase BRR2.
Authors: Vester, K. / Metz, A. / Huber, S. / Loll, B. / Wahl, M.C.
History
DepositionOct 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)230,73215
Polymers229,8002
Non-polymers93213
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-13 kcal/mol
Surface area84530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.054, 119.049, 188.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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-B09 / N-methoxybenzenesulfonamide


Mass: 187.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 49.52 %
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: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 139806 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.88 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.099 / Net I/σ(I): 13.63
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.03 / Num. unique obs: 21677 / CC1/2: 0.419 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S8Q

6s8q


Resolution: 2.05→48.51 Å / SU ML: 0.3251 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.5431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2668 2096 1.5 %
Rwork0.2204 137363 -
obs0.2211 139459 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.42 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15945 0 60 527 16532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009116353
X-RAY DIFFRACTIONf_angle_d1.005622148
X-RAY DIFFRACTIONf_chiral_restr0.05922486
X-RAY DIFFRACTIONf_plane_restr0.00972834
X-RAY DIFFRACTIONf_dihedral_angle_d16.65486152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.43271270.41138335X-RAY DIFFRACTION91.15
2.1-2.150.30541380.31729064X-RAY DIFFRACTION99.55
2.15-2.210.331400.29049169X-RAY DIFFRACTION99.92
2.21-2.270.44231340.38318752X-RAY DIFFRACTION95.21
2.27-2.350.28591400.25839188X-RAY DIFFRACTION99.89
2.35-2.430.25421400.23469160X-RAY DIFFRACTION99.92
2.43-2.530.28271400.23539180X-RAY DIFFRACTION99.89
2.53-2.640.24331400.23069211X-RAY DIFFRACTION99.97
2.64-2.780.30381410.24179227X-RAY DIFFRACTION99.9
2.78-2.960.30881400.23459191X-RAY DIFFRACTION99.9
2.96-3.190.27181420.23329257X-RAY DIFFRACTION99.91
3.19-3.510.26331410.22569256X-RAY DIFFRACTION99.86
3.51-4.010.22061420.19869319X-RAY DIFFRACTION99.73
4.01-5.050.25271430.17489400X-RAY DIFFRACTION99.93
5.05-48.510.24441480.19199654X-RAY DIFFRACTION99.46
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)
10.7063127302770.493170680859-0.296847320510.735860595242-0.1255515103850.477018677929-0.0185062811363-0.0133476904815-0.1701203919760.00386958374554-0.000660098188359-0.1778334263770.04333278629820.09492558737310.01995829704220.2002184223010.0385368033112-0.01265480134710.253444423042-0.002417534742150.296625116422.595210545920.416167697826-19.7627243795
22.060262496950.209343786774-0.461602791681.228130658110.4995473356651.806536175120.101896575109-0.1421785139510.3132089412630.208108367975-0.1228917055230.449813325652-0.103500987579-0.102862132105-0.04149205936810.303281244252-0.04143859412690.04472408694440.264041119169-0.07368114906350.502029114724-6.1524871985545.60929688387.04708302643
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 403 through 2121)BA403 - 21211 - 1719
22(chain 'J' and resid 2058 through 2320)JM2058 - 23201 - 263

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