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- PDB-7rdn: Crystal structure of S. cerevisiae pre-mRNA leakage protein 39 (Pml39) -

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Basic information

Entry
Database: PDB / ID: 7rdn
TitleCrystal structure of S. cerevisiae pre-mRNA leakage protein 39 (Pml39)
ComponentsPre-mRNA leakage protein 39
KeywordsNUCLEAR PROTEIN / mRNA nuclear export / nuclear pore complex / nuclear basket / BIR domain / ZN ion binding
Function / homologyZinc finger, C3HC-like / NuBaID N-terminal domain (aka zf-C3HC) / maintenance of RNA location / nuclear pore nuclear basket / mRNA transport / nuclear membrane / zinc ion binding / Pre-mRNA leakage protein 39
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å
AuthorsHashimoto, H. / Ramirez, D.H. / Pawlak, N. / Blobel, G. / Palancade, B. / Debler, E.W.
CitationJournal: Sci Rep / Year: 2022
Title: Structure of the pre-mRNA leakage 39-kDa protein reveals a single domain of integrated zf-C3HC and Rsm1 modules.
Authors: Hashimoto, H. / Ramirez, D.H. / Lautier, O. / Pawlak, N. / Blobel, G. / Palancade, B. / Debler, E.W.
History
DepositionJul 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA leakage protein 39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2193
Polymers29,0881
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.010, 53.010, 171.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Pre-mRNA leakage protein 39 / 39 kDa pre-mRNA leakage protein


Mass: 29087.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PML39, YML107C, YM8339.12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03760
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: PEG 8000, HEPES-HCl pH 7.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.49→44.34 Å / Num. obs: 18812 / % possible obs: 99.6 % / Redundancy: 11.3 % / Biso Wilson estimate: 67.5 Å2 / CC1/2: 0.954 / CC star: 0.988 / Rmerge(I) obs: 0.045 / Net I/σ(I): 30.4
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 3.16 / Num. unique obs: 1837 / % possible all: 99.67

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.49→44.34 Å / SU ML: 0.373 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.2152
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2625 941 5 %
Rwork0.2327 17871 -
obs0.2341 18812 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.49 Å2
Refinement stepCycle: LAST / Resolution: 2.49→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 2 0 1781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261820
X-RAY DIFFRACTIONf_angle_d0.49152461
X-RAY DIFFRACTIONf_chiral_restr0.0374272
X-RAY DIFFRACTIONf_plane_restr0.0036305
X-RAY DIFFRACTIONf_dihedral_angle_d13.1881672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.620.36391380.31282552X-RAY DIFFRACTION99.7
2.62-2.790.34141340.30012574X-RAY DIFFRACTION99.71
2.79-30.36731220.29822518X-RAY DIFFRACTION99.77
3-3.30.35811420.28942588X-RAY DIFFRACTION99.85
3.3-3.780.24381340.27222535X-RAY DIFFRACTION99.93
3.78-4.760.22141340.20532555X-RAY DIFFRACTION100
4.76-44.340.24511370.19472549X-RAY DIFFRACTION99.7
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)
16.71801209994-2.010548035421.621208897646.97299543662-0.5106350724016.910613055960.08168844078070.332517836703-0.4382551297-0.590718108023-0.166641433743-0.3112624724340.8096820162930.3709694219920.05246148676570.573636898414-0.0549332238435-0.01774731791730.745873727457-0.07128081325970.596353231496-3.3602735857823.021054418348.9484844441
25.765812941751.422836350891.516173593753.178294712160.4324850913385.30592821033-0.0992115979613-0.3574978192210.3193993583990.0573492829295-0.238250357490.0835706321752-0.4037637486870.6499702214710.4150520537680.492661751925-0.0811370790186-0.008549423940170.639999481013-0.01010671243190.432479422324-2.0736263947229.842832867953.3552398012
32.779605235720.6608273432971.973175563194.744333807873.867793705094.094958215260.320136699660.895571764909-0.038294393256-1.63524878356-0.456799120045-0.9793534344091.03805401581-0.56610606589-0.2390090333711.24202401478-0.09875660553390.03514877024131.040376938330.0445478637440.738012632592-15.859666432715.601791527930.2528060394
47.53073541583.368039146923.566475221886.113474153382.006554549587.463956895510.888983871466-0.0110892294159-1.339833000080.193173918321-0.9575693445731.194657230381.56140738675-0.9860803432840.02478332508770.976322242427-0.345458287536-0.05457228288861.146184693460.03214225813811.0711866295-27.95827169037.4416926003836.5292434748
55.321363163991.899098745861.736035332366.287655462163.502280952535.384308968920.5059080530850.721310349246-0.8594197518120.09585779871090.221441069863-0.3539462617721.84600742770.538315917885-0.542356947421.078437500140.0692454232463-0.04394951296840.633169096008-0.1333552470520.571948137759-12.20434147277.1153051527239.2898228265
66.395751339960.1660487753481.244956758514.825277110952.479878381274.594543260010.303815169473-0.2798100899940.0885430956621-0.131308539644-0.4524314219110.5510973277870.454463206676-0.9952407598340.01932061149370.704798615256-0.2773493821530.056901718790.795235099439-0.06658781063780.597342638885-21.52356939614.949163346344.4237621392
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 79 through 110 )79 - 1101 - 32
22chain 'A' and (resid 111 through 195 )111 - 19533 - 113
33chain 'A' and (resid 196 through 211 )196 - 211114 - 129
44chain 'A' and (resid 212 through 241 )212 - 241130 - 145
55chain 'A' and (resid 242 through 281 )242 - 281146 - 185
66chain 'A' and (resid 282 through 311 )282 - 311186 - 215

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