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- PDB-8bc9: Human Brr2 Helicase Region in complex with C-tail deleted Jab1 an... -

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Basic information

Entry
Database: PDB / ID: 8bc9
TitleHuman Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 24
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 / 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 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PROCT domain ...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 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 / Ribonuclease H-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
N-hydroxybenzenesulfonamide / 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: 2.3 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)230,65614
Polymers229,8002
Non-polymers85612
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-13 kcal/mol
Surface area83300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.834, 119.219, 188.266
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-A09 / N-hydroxybenzenesulfonamide


Mass: 173.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 49.54 %
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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 100449 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 48.83 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.75
Reflection shellResolution: 2.3→2.43 Å / Mean I/σ(I) obs: 1.48 / Num. unique obs: 15822 / CC1/2: 0.57 / Rrim(I) all: 0.095

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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: 2.3→46.04 Å / SU ML: 0.309 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.8021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249 2101 2.09 %
Rwork0.198 98338 -
obs0.1991 100439 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15985 0 55 418 16458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007816390
X-RAY DIFFRACTIONf_angle_d0.917322200
X-RAY DIFFRACTIONf_chiral_restr0.0542492
X-RAY DIFFRACTIONf_plane_restr0.00812841
X-RAY DIFFRACTIONf_dihedral_angle_d15.73426164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.34271330.28596220X-RAY DIFFRACTION95.32
2.35-2.410.2941380.27076485X-RAY DIFFRACTION99.94
2.41-2.470.34731400.26326529X-RAY DIFFRACTION99.97
2.47-2.550.33081390.25166507X-RAY DIFFRACTION99.98
2.55-2.630.28871390.24086525X-RAY DIFFRACTION99.98
2.63-2.720.27941390.2316510X-RAY DIFFRACTION99.91
2.72-2.830.31471390.22916518X-RAY DIFFRACTION99.92
2.83-2.960.31151400.23586538X-RAY DIFFRACTION99.9
2.96-3.120.3251400.23366565X-RAY DIFFRACTION99.96
3.12-3.310.25181410.226571X-RAY DIFFRACTION99.9
3.31-3.570.27111400.20636564X-RAY DIFFRACTION99.93
3.57-3.930.25871400.18786574X-RAY DIFFRACTION99.73
3.93-4.490.20851420.16336638X-RAY DIFFRACTION99.96
4.49-5.660.2051430.16596679X-RAY DIFFRACTION99.77
5.66-46.040.20031480.1736915X-RAY DIFFRACTION99.52
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)
10.5194458850070.350143327152-0.2380696210470.533636520114-0.1099005141380.2852268813510.01846910483150.00151969259368-0.08696576983810.0570881603026-0.0163951754753-0.112337092160.006350304724790.063733955094-0.0001263435765170.2905951352010.0153647567068-0.02079129030750.348893740666-0.0001333625752820.3169842916142.869349167750.316678482452-19.9459092868
20.4218554188740.07718187034590.1118211763050.3410600009650.09535136166160.1814221177370.0966114929737-0.1251804434090.246811500040.171108003754-0.1388431755970.273446731378-0.1179040414950.0183081491434-0.003222864081060.431656529376-0.05385928538180.05539515710730.353630973882-0.1100830237850.568766879025-6.1809383538145.51905162556.94535341954
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 404 through 2127)BA404 - 21271 - 1724
22(chain 'J' and resid 2058 through 2320)JM2058 - 23201 - 263

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