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- PDB-4yhv: Yeast Prp3 C-terminal fragment 325-469 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4yhv
TitleYeast Prp3 C-terminal fragment 325-469
ComponentsU4/U6 small nuclear ribonucleoprotein PRP3
KeywordsRNA BINDING PROTEIN / Spliceosomal protein / DUF1115 / RNA-binding domain / ferredoxin-like fold
Function / homology
Function and homology information


U4/U6 snRNP / U4 snRNP / spliceosomal complex assembly / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / nucleus
Similarity search - Function
Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / pre-mRNA processing factor 3 domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain
Similarity search - Domain/homology
ACETIC ACID / U4/U6 small nuclear ribonucleoprotein PRP3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, S. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 740 Germany
CitationJournal: Elife / Year: 2015
Title: A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing.
Authors: Liu, S. / Mozaffari-Jovin, S. / Wollenhaupt, J. / Santos, K.F. / Theuser, M. / Dunin-Horkawicz, S. / Fabrizio, P. / Bujnicki, J.M. / Luhrmann, R. / Wahl, M.C.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U4/U6 small nuclear ribonucleoprotein PRP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4813
Polymers17,3611
Non-polymers1202
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.079, 56.079, 86.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein U4/U6 small nuclear ribonucleoprotein PRP3 / Pre-mRNA-splicing factor 3 / Prp3


Mass: 17361.094 Da / Num. of mol.: 1 / Fragment: C-terminal fragment, UNP residues 325-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP3, RNA3, YDR473C, D8035.16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03338
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 10 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 10459 / % possible obs: 99.3 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.96
Reflection shellResolution: 2→2.12 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 5.94 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YHU

4yhu


Resolution: 2→24.283 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 522 4.99 %
Rwork0.1612 --
obs0.164 10454 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→24.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 8 67 1196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131201
X-RAY DIFFRACTIONf_angle_d1.2781617
X-RAY DIFFRACTIONf_dihedral_angle_d14.57460
X-RAY DIFFRACTIONf_chiral_restr0.064164
X-RAY DIFFRACTIONf_plane_restr0.006210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9963-2.19710.2191270.1662424X-RAY DIFFRACTION97
2.1971-2.51480.20741310.17022481X-RAY DIFFRACTION100
2.5148-3.16720.25771310.18822498X-RAY DIFFRACTION100
3.1672-24.28470.20931330.14622529X-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)
14.4956-1.07370.06393.3905-0.02643.6782-0.00220.0683-0.08160.00830.12580.138-0.0550.0679-0.10530.1651-0.0635-0.01350.19980.03770.168911.1225-20.3338-2.224
26.2384-0.0378-0.7591.8615-0.00090.52990.2197-0.0386-0.32680.1594-0.1406-0.24990.01940.2713-0.08550.2381-0.0193-0.04520.47220.04810.238821.7656-21.38582.5486
35.0125-0.2526-0.26395.82860.74177.11290.5055-0.42090.78630.6753-0.09050.1247-0.7029-0.2139-0.42450.4438-0.11170.13290.2834-0.00070.33139.9223-7.35081.9192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 332 through 405 )
2X-RAY DIFFRACTION2chain 'A' and (resid 406 through 432 )
3X-RAY DIFFRACTION3chain 'A' and (resid 433 through 466 )

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