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

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Basic information

Entry
Database: PDB / ID: 8bcf
TitleHuman Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 78
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) / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / 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) / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / 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 / spliceosomal complex / helicase activity / mRNA splicing, via spliceosome / mRNA processing / osteoblast differentiation / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / RNA helicase activity / nuclear speck / cilium / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Sec63 domain / Sec63 Brl domain / C2 domain ...Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Sec63 domain / Sec63 Brl domain / C2 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. / C2 domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Arc Repressor Mutant, subunit A / 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 / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
~{N}-methoxy-~{N}-methyl-benzenesulfonamide / 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: 2.42 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)230,62213
Polymers229,8002
Non-polymers82211
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-12 kcal/mol
Surface area84040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.549, 118.698, 186.917
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-Q8Z / ~{N}-methoxy-~{N}-methyl-benzenesulfonamide


Mass: 201.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H11NO3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
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 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 85165 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 50.87 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.231 / Net I/σ(I): 9.14
Reflection shellResolution: 2.42→2.56 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 0.83 / Num. unique obs: 13518 / CC1/2: 0.365 / % possible all: 99.4

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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: 2.42→48.25 Å / SU ML: 0.4041 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.7346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2745 2100 2.47 %
Rwork0.2129 83052 -
obs0.2144 85152 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.86 Å2
Refinement stepCycle: LAST / Resolution: 2.42→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15984 0 53 325 16362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005216388
X-RAY DIFFRACTIONf_angle_d0.752422201
X-RAY DIFFRACTIONf_chiral_restr0.04822493
X-RAY DIFFRACTIONf_plane_restr0.00632841
X-RAY DIFFRACTIONf_dihedral_angle_d16.16776162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.470.34911370.33255389X-RAY DIFFRACTION98.68
2.47-2.540.36621380.30685453X-RAY DIFFRACTION99.96
2.54-2.60.37531390.29555514X-RAY DIFFRACTION99.96
2.6-2.680.35611380.28535472X-RAY DIFFRACTION99.95
2.68-2.770.331400.2855523X-RAY DIFFRACTION99.98
2.77-2.870.36461370.2675474X-RAY DIFFRACTION99.95
2.87-2.980.31561390.25375476X-RAY DIFFRACTION100
2.98-3.120.36361400.24675533X-RAY DIFFRACTION99.98
3.12-3.280.36131390.24095500X-RAY DIFFRACTION99.98
3.28-3.490.27971390.23275515X-RAY DIFFRACTION99.95
3.49-3.760.29791400.19935537X-RAY DIFFRACTION99.95
3.76-4.130.25391410.18535581X-RAY DIFFRACTION99.98
4.13-4.730.21431420.16765600X-RAY DIFFRACTION99.98
4.73-5.960.23941430.18785638X-RAY DIFFRACTION99.95
5.96-48.250.21381480.17995847X-RAY DIFFRACTION99.85
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)
10.5456840670970.384673087538-0.290498371840.466145499403-0.08640927792090.266556129296-0.0227147511831-0.00811709136713-0.1309982694560.02112642307450.0171945150662-0.1160465833410.0236295369580.0231969921959-0.00217819713280.2938750115830.0197721930927-0.02033319802690.3291585849650.006575816166330.322042399442.679064419960.39665574753-19.7517998526
20.9279158749210.2628251608170.1800196862920.9807827700330.212330300390.5239602222730.130698491836-0.09378050754850.3000055741240.155830118855-0.1178649726460.396705720155-0.114496855627-0.0441558662416-3.13419443802E-50.410069018192-0.04632405793280.04497360373090.409687257492-0.06649574460320.565467505572-6.2510797968145.55194395777.06765281467
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 2126)BA403 - 21261 - 1724
22(chain 'J' and resid 2058 through 2320)JE2058 - 23201 - 263

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