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- PDB-3elv: Crystal Structure of Full-Length Yeast Pml1p -

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Basic information

Entry
Database: PDB / ID: 3elv
TitleCrystal Structure of Full-Length Yeast Pml1p
ComponentsPre-mRNA leakage protein 1
KeywordsSPLICING / Intrinsically unstructured domain / forkhead-associated domain (FHA) domain / pre-mRNA retention and splicing / protein phosphorylation / RES complex / mRNA processing / mRNA splicing / Nucleus
Function / homology
Function and homology information


RES complex / maintenance of RNA location / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / miRNA processing / U2-type prespliceosome assembly / U2 snRNP / mRNA export from nucleus / spliceosomal complex / mRNA splicing, via spliceosome ...RES complex / maintenance of RNA location / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / miRNA processing / U2-type prespliceosome assembly / U2 snRNP / mRNA export from nucleus / spliceosomal complex / mRNA splicing, via spliceosome / nuclear speck / 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: 2.4 Å
AuthorsTrowitzsch, S. / Weber, G. / L hrmann, R. / Wahl, M.C.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the Pml1p subunit of the yeast precursor mRNA retention and splicing complex.
Authors: Trowitzsch, S. / Weber, G. / Luhrmann, R. / Wahl, M.C.
History
DepositionSep 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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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)47,7745
Polymers47,4852
Non-polymers2883
Water1,08160
1
A: Pre-mRNA leakage protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9353
Polymers23,7431
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pre-mRNA leakage protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8392
Polymers23,7431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.891, 86.891, 96.697
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-216-

HOH

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Components

#1: Protein Pre-mRNA leakage protein 1


Mass: 23742.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PML1, YLR016C, L1591 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q07930
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris-HCl, pH 7.5, 200 mM Li2SO4, 21-24 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9802 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 5, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9802 Å / Relative weight: 1
ReflectionResolution: 2.4→40.7 Å / Num. all: 16912 / Num. obs: 16896 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 71.7 Å2 / Rsym value: 0.083 / Net I/σ(I): 19.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2473 / Rsym value: 0.81 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 18.375 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.331 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26592 852 5.1 %RANDOM
Rwork0.21798 ---
all0.22027 16064 --
obs0.22027 16010 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.147 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å2-0.84 Å20 Å2
2---1.67 Å20 Å2
3---2.51 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 15 60 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222406
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.983253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16124.32125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26815436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8731521
X-RAY DIFFRACTIONr_chiral_restr0.0910.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021837
X-RAY DIFFRACTIONr_nbd_refined0.1890.2880
X-RAY DIFFRACTIONr_nbtor_refined0.30.21553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.217
X-RAY DIFFRACTIONr_mcbond_it0.531.51504
X-RAY DIFFRACTIONr_mcangle_it0.92322353
X-RAY DIFFRACTIONr_scbond_it1.03931028
X-RAY DIFFRACTIONr_scangle_it1.6974.5900
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 73 -
Rwork0.313 1102 -
obs-1102 96.79 %
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)
14.09570.596-1.18524.3051-0.38263.1962-0.3637-0.16510.11470.0405-0.04890.2254-0.2384-0.45670.4126-0.18650.1647-0.1436-0.3159-0.1675-0.156522.59511.67523.156
23.8997-0.1862-0.9224.52191.00243.4835-0.37670.4351-0.1028-0.25530.0705-0.25340.0656-0.0140.3062-0.2186-0.14880.0824-0.31930.0726-0.204747.0030.571-0.901
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A51 - 112
2X-RAY DIFFRACTION1A122 - 204
3X-RAY DIFFRACTION2B51 - 111
4X-RAY DIFFRACTION2B122 - 204

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