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- PDB-4w7s: Crystal structure of the yeast DEAD-box splicing factor Prp28 at ... -

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Basic information

Entry
Database: PDB / ID: 4w7s
TitleCrystal structure of the yeast DEAD-box splicing factor Prp28 at 2.54 Angstroms resolution
ComponentsPre-mRNA-splicing ATP-dependent RNA helicase PRP28
KeywordsHYDROLASE / splicing factor / DEAD-box protein / ATPase
Function / homology
Function and homology information


first spliceosomal transesterification activity / mRNA 5'-splice site recognition / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / mRNA binding ...first spliceosomal transesterification activity / mRNA 5'-splice site recognition / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily ...DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / 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 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pre-mRNA-splicing ATP-dependent RNA helicase PRP28
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.542 Å
AuthorsJacewicz, A. / Smith, P. / 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)GM102961 United States
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28.
Authors: Jacewicz, A. / Schwer, B. / Smith, P. / Shuman, S.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact
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_struct_oper_list.symmetry_operation
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing ATP-dependent RNA helicase PRP28
B: Pre-mRNA-splicing ATP-dependent RNA helicase PRP28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,88714
Polymers105,9822
Non-polymers2,90612
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-3 kcal/mol
Surface area42890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.719, 114.719, 156.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-725-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 / Helicase CA8


Mass: 52990.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRP28, YDR243C, YD8419.10C / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P23394, RNA helicase

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Non-polymers , 5 types, 261 molecules

#2: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 30% (v/v) PEG 400, 0.2 M MgCl2, 0.1 M Hepes-NaOH, pH 7.2-7.8, 0.1 M glycine
PH range: pH 7.2-7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.54→57 Å / Num. obs: 39724 / % possible obs: 99.8 % / Redundancy: 20.5 % / Net I/σ(I): 16.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 2.542→53.843 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.51 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2193 1949 4.91 %
Rwork0.1662 --
obs0.1688 39682 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.542→53.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7150 0 130 249 7529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097425
X-RAY DIFFRACTIONf_angle_d1.22710028
X-RAY DIFFRACTIONf_dihedral_angle_d16.0442868
X-RAY DIFFRACTIONf_chiral_restr0.0791156
X-RAY DIFFRACTIONf_plane_restr0.0051266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5416-2.60520.27281470.19682632X-RAY DIFFRACTION99
2.6052-2.67560.27751360.18912632X-RAY DIFFRACTION100
2.6756-2.75430.25131690.18172636X-RAY DIFFRACTION100
2.7543-2.84320.23161520.17852664X-RAY DIFFRACTION100
2.8432-2.94480.26731140.1882702X-RAY DIFFRACTION100
2.9448-3.06270.25361490.19212619X-RAY DIFFRACTION100
3.0627-3.20210.31291470.19812700X-RAY DIFFRACTION100
3.2021-3.37090.24151280.18442689X-RAY DIFFRACTION100
3.3709-3.58210.21081360.16632679X-RAY DIFFRACTION100
3.5821-3.85860.21161120.15962713X-RAY DIFFRACTION100
3.8586-4.24670.17241080.14472745X-RAY DIFFRACTION100
4.2467-4.86090.18231380.13072726X-RAY DIFFRACTION100
4.8609-6.12280.20511520.16512726X-RAY DIFFRACTION100
6.1228-53.85540.17461610.15872870X-RAY DIFFRACTION100

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