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- PDB-2jkd: Structure of the yeast Pml1 splicing factor and its integration i... -

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Basic information

Entry
Database: PDB / ID: 2jkd
TitleStructure of the yeast Pml1 splicing factor and its integration into the RES complex
ComponentsPRE-MRNA LEAKAGE PROTEIN 1
KeywordsGENE REGULATION / MRNA PROCESSING / PML1/SNU17/BUD13 / PRE-MRNA SPLICING / SACCHAROMYCES CEREVISIAE / PHOSPHO-PEPTIDE RECOGNITION / RES / NUCLEUS / MRNA SPLICING
Function / homology
Function and homology information


maintenance of RNA location / RES complex / U2-type prespliceosome assembly / U2 snRNP / mRNA export from nucleus / spliceosomal complex / mRNA splicing, via spliceosome / mRNA binding / nucleus / cytoplasm
Similarity search - Function
: / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pre-mRNA leakage protein 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBrooks, M.A. / Dziembowski, A. / Quevillon-Cheruel, S. / Henriot, V. / Faux, C. / van Tilbeurgh, H. / Seraphin, B.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Structure of the Yeast Pml1 Splicing Factor and its Integration Into the Res Complex
Authors: Brooks, M.A. / Dziembowski, A. / Quevillon-Cheruel, S. / Henriot, V. / Faux, C. / Van Tilbeurgh, H. / Seraphin, B.
History
DepositionAug 27, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRE-MRNA LEAKAGE PROTEIN 1
B: PRE-MRNA LEAKAGE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5557
Polymers43,0862
Non-polymers4685
Water82946
1
A: PRE-MRNA LEAKAGE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8234
Polymers21,5431
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PRE-MRNA LEAKAGE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7313
Polymers21,5431
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)85.720, 85.720, 97.840
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-2024-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.671, -0.7413, 0.0138), (0.7412, -0.6711, -0.0125), (0.0185, 0.0019, 0.9998)
Vector: 132.2827, 34.593, -11.3603)

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Components

#1: Protein PRE-MRNA LEAKAGE PROTEIN 1 / PML1


Mass: 21543.215 Da / Num. of mol.: 2 / Fragment: FHA DOMAIN, RESIDUES 25-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PET9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q07930
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 24-48 AND 113-121 OF CHAIN A AND 24-50 AND 112-121 OF CHAIN B WERE NOT MODELLED IN THE ...RESIDUES 24-48 AND 113-121 OF CHAIN A AND 24-50 AND 112-121 OF CHAIN B WERE NOT MODELLED IN THE STRUCTURE DUE TO LACK OF DENSITY.

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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: 3.04 Å3/Da / Density % sol: 59.22 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS-HCL, PH 8.5, 0.2 M LISO4 AND FROM 20 TO 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 14550 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 2.94 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 19.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.98 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 5.82 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.4.0065refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.5→40.86 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.602 / SU ML: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 721 5 %RANDOM
Rwork0.215 ---
obs0.217 13827 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0.53 Å20 Å2
2---1.06 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 28 46 2438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222425
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.983270
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0495291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.91924.355124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.07315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9421520
X-RAY DIFFRACTIONr_chiral_restr0.0990.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211834
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_it0.5531.51463
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06522364
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4333962
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3714.5906
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: 2.5→2.63 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.323 105
Rwork0.306 1985
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)
13.2670.08650.29893.8933-0.693.6945-0.07370.13760.15850.0447-0.17710.247-0.3701-0.3320.2508-0.22480.0504-0.07630.0269-0.1439-0.09444.014648.99425.8466
23.65270.56740.81053.32650.19573.9608-0.05160.2601-0.3043-0.283-0.1931-0.03850.2499-0.18370.2446-0.16240.01030.12170.0499-0.0833-0.042966.789634.007615.5615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 206
2X-RAY DIFFRACTION2B51 - 206

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