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- PDB-5m5p: S. cerevisiae spliceosomal helicase Brr2 (271-end) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5m5p
TitleS. cerevisiae spliceosomal helicase Brr2 (271-end) in complex with the Jab/MPN domain of S. cerevisiae Prp8
Components
  • Pre-mRNA-splicing factor 8
  • Pre-mRNA-splicing helicase BRR2
KeywordsHYDROLASE / splicing / helicase / complex
Function / homology
Function and homology information


spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly ...spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / nucleic acid binding / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
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 / 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 / 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
Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2 Å
AuthorsBecke, C. / Absmeier, E. / Wollenhaupt, J. / Santos, K.F. / Wahl, M.C.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationSFB 740 Germany
Bundesministerium fuer Bildung und Forschung05K10KEC Germany
Einstein Foundation BerlinA-2012-140 Germany
Freie Universitaet BerlinDahlem International Network PostDoc Fellowship Germany
CitationJournal: Cell Cycle / Year: 2017
Title: Interplay of cis- and trans-regulatory mechanisms in the spliceosomal RNA helicase Brr2.
Authors: Absmeier, E. / Becke, C. / Wollenhaupt, J. / Santos, K.F. / Wahl, M.C.
History
DepositionOct 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Data collection / Refinement description
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / pdbx_audit_support / software
Item: _diffrn.ambient_temp / _pdbx_audit_support.funding_organization
Revision 1.4Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_radiation / Item: _diffrn.ambient_temp
Revision 1.5Nov 21, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.6Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.7Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing helicase BRR2
B: Pre-mRNA-splicing factor 8
C: Pre-mRNA-splicing helicase BRR2
D: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)492,6154
Polymers492,6154
Non-polymers00
Water00
1
A: Pre-mRNA-splicing helicase BRR2
B: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)246,3072
Polymers246,3072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-15 kcal/mol
Surface area94760 Å2
MethodPISA
2
C: Pre-mRNA-splicing helicase BRR2
D: Pre-mRNA-splicing factor 8


Theoretical massNumber of molelcules
Total (without water)246,3072
Polymers246,3072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-19 kcal/mol
Surface area96290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.970, 196.870, 191.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLYSLYSchain AAA271 - 21635 - 1897
21SERSERLYSLYSchain CCC275 - 21639 - 1897
12SERSERPHEPHEchain BBB2148 - 23955 - 252
22SERSERPHEPHEchain DDD2148 - 23955 - 252

NCS ensembles :
ID
1
2

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Components

#1: Protein Pre-mRNA-splicing helicase BRR2 / Protein Snu246


Mass: 215817.031 Da / Num. of mol.: 2 / Fragment: UNP residues 271-2163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: BRR2, RSS1, SNU246, YER172C, SYGP-ORF66 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32639, RNA helicase
#2: Protein Pre-mRNA-splicing factor 8


Mass: 30490.338 Da / Num. of mol.: 2 / Fragment: UNP residues 2147-2413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33334

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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: 3.55 Å3/Da / Density % sol: 65.35 % / Description: needles
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 9.2% (w/v) PEG 4000 0.4 M MgCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.210.9184
SYNCHROTRONBESSY 14.120.9184
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 16, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 4.2→95.5 Å / Num. obs: 51802 / % possible obs: 99.9 % / Redundancy: 10.8 % / CC1/2: 0.995 / Rsym value: 0.315 / Net I/σ(I): 8.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bgd

4bgd


Resolution: 4.2→95.5 Å / SU ML: 0.74 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.06
RfactorNum. reflection% reflection
Rfree0.3349 2666 5.15 %
Rwork0.307 --
obs0.3085 51754 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 184.21 Å2 / Biso mean: 157.9082 Å2 / Biso min: 136.88 Å2
Refinement stepCycle: final / Resolution: 4.2→95.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33653 0 0 0 33653
Num. residues----4196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00334379
X-RAY DIFFRACTIONf_angle_d0.75746599
X-RAY DIFFRACTIONf_chiral_restr0.035277
X-RAY DIFFRACTIONf_plane_restr0.0045951
X-RAY DIFFRACTIONf_dihedral_angle_d10.1212777
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A21660X-RAY DIFFRACTION6.572TORSIONAL
12C21660X-RAY DIFFRACTION6.572TORSIONAL
21B2896X-RAY DIFFRACTION6.572TORSIONAL
22D2896X-RAY DIFFRACTION6.572TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.2-4.27640.43351400.380625352675100
4.2764-4.35860.38181330.386525812714100
4.3586-4.44760.40031460.376725372683100
4.4476-4.54430.39031350.358125372672100
4.5443-4.650.38961170.360825652682100
4.65-4.76630.39411540.354125632717100
4.7663-4.89510.40071510.35725412692100
4.8951-5.03920.36271450.349725662711100
5.0392-5.20180.3811250.349225672692100
5.2018-5.38770.37441440.357125532697100
5.3877-5.60340.35391280.347525972725100
5.6034-5.85840.34861390.343725712710100
5.8584-6.16720.40731300.344926132743100
6.1672-6.55350.37861480.337625562704100
6.5535-7.05940.35671460.312126042750100
7.0594-7.76950.28671270.296526222749100
7.7695-8.8930.2881440.254226312775100
8.893-11.20150.22571640.215526192783100
11.2015-95.53970.31821500.25732730288098

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