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- PDB-8bch: Human Brr2 Helicase Region in complex with Sulfaguanidine -

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Basic information

Entry
Database: PDB / ID: 8bch
TitleHuman Brr2 Helicase Region in complex with Sulfaguanidine
ComponentsU5 small nuclear ribonucleoprotein 200 kDa helicase
KeywordsHYDROLASE / helicase / 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 / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex ...cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / helicase activity / mRNA splicing, via spliceosome / osteoblast differentiation / RNA helicase activity / 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 / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / C2 domain superfamily / 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 / 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 / Arc Repressor Mutant, subunit A / Helicase superfamily 1/2, ATP-binding domain / 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
1-(4-aminophenyl)sulfonylguanidine / U5 small nuclear ribonucleoprotein 200 kDa helicase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,8812
Polymers199,6671
Non-polymers2141
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area76690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.290, 149.530, 141.490
Angle α, β, γ (deg.)90.000, 120.320, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: Chemical ChemComp-QA9 / 1-(4-aminophenyl)sulfonylguanidine


Mass: 214.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.35 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M sodium citrate, 1.5M sodium malonate

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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: Apr 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.87→50 Å / Num. obs: 58705 / % possible obs: 97.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 82.9 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.201 / Net I/σ(I): 10.19
Reflection shellResolution: 2.87→3.04 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.63 / Num. unique obs: 9524 / CC1/2: 0.38 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F91

4f91


Resolution: 2.87→47.2 Å / SU ML: 0.7015 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 46.6319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3374 2010 3.58 %
Rwork0.2815 54180 -
obs0.2835 56190 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 119.71 Å2
Refinement stepCycle: LAST / Resolution: 2.87→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13859 0 14 11 13884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314167
X-RAY DIFFRACTIONf_angle_d0.6119197
X-RAY DIFFRACTIONf_chiral_restr0.04362177
X-RAY DIFFRACTIONf_plane_restr0.00522456
X-RAY DIFFRACTIONf_dihedral_angle_d15.48265342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-2.940.63981230.60633286X-RAY DIFFRACTION79.48
2.94-3.020.46281510.45814049X-RAY DIFFRACTION99.15
3.02-3.10.55871030.50882791X-RAY DIFFRACTION70.71
3.11-3.210.54981370.45813692X-RAY DIFFRACTION99.33
3.21-3.320.44491540.37684158X-RAY DIFFRACTION99.65
3.32-3.450.37731520.34234106X-RAY DIFFRACTION99.3
3.45-3.610.43521500.34554108X-RAY DIFFRACTION98.79
3.61-3.80.44331440.37293876X-RAY DIFFRACTION93.93
3.8-4.040.33071490.29684016X-RAY DIFFRACTION96.39
4.04-4.350.37911410.28293802X-RAY DIFFRACTION91.72
4.35-4.790.30631490.23984015X-RAY DIFFRACTION96.72
4.79-5.480.28581510.22364052X-RAY DIFFRACTION97.25
5.48-6.90.30231520.2674111X-RAY DIFFRACTION98.38
6.9-47.20.23691540.18814118X-RAY DIFFRACTION97.29
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)
10.06937630824970.0030991868961-0.1551517396040.502042057362-0.2942909028490.5613148023130.417824355974-0.6731611866490.02262939410240.217048658478-0.380558982122-0.272378326671-0.4370149039110.887670732150.01387028028750.574813598863-0.502466749639-0.04827674194660.733030817612-0.044809713940.56587438520324.812375559616.314342159530.3964063104
20.4788334857690.176176069438-0.4527940560560.28662877739-0.08641000214681.53657874465-0.1022980861220.211566913993-0.01396827593250.102432557554-0.03075742017960.04889015370460.270263734761-0.156065290085-0.1428279624440.444095242229-0.124747979611-0.01861363732210.271919385061-0.0903843664590.438700739147-12.0238088835-10.608715307133.1117446228
30.123689974328-0.0250682057412-0.06800912535790.559298519392-0.06133826111450.1970688846190.2243732170710.7001038102950.220041842898-0.0830354960905-0.019309334280.183518860176-0.0455554073535-0.346223441114-6.46553641584E-50.6994160747360.1027161517580.08189188490111.367635834530.1830075350550.94309801583-50.62713734916.874054158523.9743404631
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 402 through 812 )402 - 8121 - 411
22chain 'B' and (resid 813 through 1813 )813 - 1813412 - 1412
33chain 'B' and (resid 1814 through 2125 )1814 - 21251413 - 1724

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