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- PDB-4yhu: Yeast Prp3 C-terminal fragment 296-469 -

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Basic information

Entry
Database: PDB / ID: 4yhu
TitleYeast Prp3 C-terminal fragment 296-469
ComponentsU4/U6 small nuclear ribonucleoprotein PRP3
KeywordsRNA BINDING PROTEIN / Spliceosomal protein / DUF1115 / 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
YTTRIUM (III) ION / U4/U6 small nuclear ribonucleoprotein PRP3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsLiu, S. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 740 Germany
Citation
Journal: 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.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2012
Title: Structure determination by multiple-wavelength anomalous dispersion (MAD) at the Pr LIII edge
Authors: Pueringer, S. / Hellmig, M. / Liu, S. / Weiss, M. / Wahl, M.C. / Mueller, U.
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 2.0May 8, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / 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 / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
B: U4/U6 small nuclear ribonucleoprotein PRP3
C: U4/U6 small nuclear ribonucleoprotein PRP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4717
Polymers63,1153
Non-polymers3564
Water1,74797
1
A: U4/U6 small nuclear ribonucleoprotein PRP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2163
Polymers21,0381
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: U4/U6 small nuclear ribonucleoprotein PRP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1272
Polymers21,0381
Non-polymers891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: U4/U6 small nuclear ribonucleoprotein PRP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1272
Polymers21,0381
Non-polymers891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.663, 161.205, 105.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 21038.348 Da / Num. of mol.: 3 / Fragment: C-terminal fragment, UNP residues 296-469
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-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Y
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
Description: 0.02 M yittrium (III) chloride hexahydrate or 0.02 M praseodymium (III) acetate hydrate 0.08 M succinic acid, pH 7.0 13 % PEG 3350
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: 20036 / % possible obs: 99.3 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 24.96
Reflection shellResolution: 2→2.12 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 5.95 / % possible all: 96.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.5.0110refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 25.673 / SU ML: 0.245 / Cross valid method: FREE R-VALUE / ESU R: 0.441 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26241 1032 5.2 %RANDOM
Rwork0.20663 ---
obs0.20946 18932 95.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.411 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---2 Å20 Å2
3---1.87 Å2
Refinement stepCycle: 1 / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 4 97 3276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223297
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.944422
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8845388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.9124.545165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.64315646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.241515
X-RAY DIFFRACTIONr_chiral_restr0.1040.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022470
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3771.51922
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75723112
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.25231375
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0814.51310
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 55 -
Rwork0.37 1146 -
obs--80.5 %
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)
14.7468-0.08-0.05274.683-0.7846.60730.3776-0.1130.20040.2512-0.2711-0.44440.10390.7585-0.10660.1401-0.05290.02020.1589-0.09670.163551.06918.7357.397
22.4307-0.8056-0.65962.2115-1.61376.41810.13450.011-0.1563-0.2718-0.0534-0.08920.72970.2535-0.08110.17030.0017-0.03070.09-0.06260.096247.51812.3328.488
39.59862.06571.53775.08110.740212.73440.2193-0.07591.28390.4236-0.50480.1288-0.7086-0.31140.28550.2097-0.02620.09580.0666-0.08340.304345.66129.786.376
45.6691-0.3091-0.15815.37121.06165.9006-0.2451-0.0459-0.2607-0.16530.27970.1167-0.0211-0.0721-0.03460.11440.11470.08860.1950.07630.100435.65323.209-17.537
52.7219-7.55240.807220.8367-1.11283.7856-0.1318-0.244-0.60210.26870.21571.40190.8946-0.5801-0.08390.33820.03690.16060.40370.17380.416930.93110.802-14.873
67.3779-2.9633-1.08465.9084-0.77948.2019-0.495-0.87650.15970.62510.49450.356-0.8217-0.69630.00050.27110.27770.10190.38370.05790.138331.69630.598-6.301
79.9346-5.6577-0.155612.0938-1.77635.78281.06591.1084-0.6624-2.1366-1.1403-0.01520.14550.7070.07440.62550.4519-0.04730.4608-0.07370.35721.69244.432-22.082
812.0488-3.85744.14646.806-2.39475.82051.36032.08810.5299-2.0913-0.9761-0.1171-0.29380.5223-0.38431.09470.56720.14380.75690.03860.438919.1749.825-24.648
910.2371-5.5072-0.64212.80790.45685.65450.52490.2735-1.2926-0.5583-0.58171.22010.1524-0.16040.05680.23540.1863-0.13680.1386-0.06440.486515.70541.664-14.422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A335 - 375
2X-RAY DIFFRACTION2A376 - 430
3X-RAY DIFFRACTION3A431 - 467
4X-RAY DIFFRACTION4B335 - 406
5X-RAY DIFFRACTION5B407 - 428
6X-RAY DIFFRACTION6B429 - 466
7X-RAY DIFFRACTION7C335 - 373
8X-RAY DIFFRACTION8C374 - 404
9X-RAY DIFFRACTION9C405 - 466

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