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- PDB-4wal: Crystal structure of selenomethionine Msl5 protein in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4wal
TitleCrystal structure of selenomethionine Msl5 protein in complex with RNA at 2.2 A
Components
  • Branchpoint-bridging protein
  • RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
KeywordsPROTEIN BINDING/RNA / Msl5 / BBP / RNA binding / yeast pre-mRNA splicing / PROTEIN BINDING-RNA complex
Function / homology
Function and homology information


pre-mRNA branch point binding / regulation of mRNA splicing, via spliceosome / commitment complex / spliceosomal complex assembly / mRNA splicing, via spliceosome / mRNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / K Homology domain, type 1 / Clathrin adaptor, appendage, Ig-like subdomain superfamily / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily ...Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / K Homology domain, type 1 / Clathrin adaptor, appendage, Ig-like subdomain superfamily / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Branchpoint-bridging protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsJacewicz, A. / Smith, P. / Chico, L. / Schwer, B. / Shuman, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM52470 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM50288 United States
CitationJournal: Rna / Year: 2015
Title: Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs.
Authors: Jacewicz, A. / Chico, L. / Smith, P. / Schwer, B. / Shuman, S.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Source and taxonomy / Category: pdbx_audit_support / pdbx_entity_src_syn
Item: _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Branchpoint-bridging protein
B: RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3945
Polymers18,1702
Non-polymers2243
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-23 kcal/mol
Surface area8310 Å2
MethodPISA
2
A: Branchpoint-bridging protein
B: RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)147,15240
Polymers145,36316
Non-polymers1,78924
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area35600 Å2
ΔGint-248 kcal/mol
Surface area52190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.952, 81.952, 51.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein Branchpoint-bridging protein / Mud synthetic-lethal 5 protein / Splicing factor 1 / Zinc finger protein BBP


Mass: 14711.201 Da / Num. of mol.: 1 / Mutation: I222M, I227M, V238M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MSL5, BBP, SF1, YLR116W, L2949 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q12186
#2: RNA chain RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')


Mass: 3459.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 90 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.1-2.2M ammonium sulfate, 0.01M Mg Acetate, 0.05M MES
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97919 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.18→36.65 Å / Num. obs: 9666 / % possible obs: 100 % / Redundancy: 39.1 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 40.2
Reflection shellResolution: 2.18→2.3 Å / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.2→36.65 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.88 / Phase error: 20.86 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.215 452 4.82 %RANDOM
Rwork0.172 ---
obs0.174 9378 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→36.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 151 12 87 1212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071188
X-RAY DIFFRACTIONf_angle_d1.051637
X-RAY DIFFRACTIONf_dihedral_angle_d14.927491
X-RAY DIFFRACTIONf_chiral_restr0.038184
X-RAY DIFFRACTIONf_plane_restr0.005193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.51840.24411590.17892878X-RAY DIFFRACTION100
2.5184-3.17260.2451350.19222948X-RAY DIFFRACTION100
3.1726-36.65510.1921580.16143100X-RAY DIFFRACTION100
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)
12.1302-0.35760.12761.5531-1.07892.15120.04080.0641-0.0834-0.08720.01780.0078-0.0576-0.228-0.00010.1963-0.00320.0050.1430.01660.181716.459327.548117.2392
22.5709-0.310.15581.2544-0.32854.09850.0450.0124-0.03880.00710.05770.12160.0708-0.36340.01080.12310.00460.00050.15060.01230.186812.841323.774318.647
30.7531.0027-0.61541.884-0.12750.7569-0.30040.06340.1318-0.26290.1116-0.5474-0.68740.33730.00750.4729-0.03030.00920.26290.03210.331624.022143.55499.1707
40.3363-0.1277-0.32380.852-0.87021.9669-0.1858-0.32750.3232-0.702-0.01690.2783-0.3998-0.1585-0.00070.2876-0.0234-0.03160.21240.03720.22314.898137.934912.2566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 145 THROUGH 183 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 184 THROUGH 243 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 244 THROUGH 271 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 2 THROUGH 9 )

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