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- PDB-7ewf: Selenomethionine-substituted structure of S. cerevisiae Csn12 in ... -

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Basic information

Entry
Database: PDB / ID: 7ewf
TitleSelenomethionine-substituted structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1
Components
  • 26S proteasome complex subunit SEM1
  • Cop9 signalosome complex subunit 12
  • Protein THP3
KeywordsTRANSCRIPTION / Complex / Nucleic acid binding / mRNA splicing
Function / homology
Function and homology information


adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion / cellular response to pheromone / conjugation with cellular fusion / SAGA complex localization to transcription regulatory region / transcription export complex 2 / regulation of protein neddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle, lid subcomplex ...adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion / cellular response to pheromone / conjugation with cellular fusion / SAGA complex localization to transcription regulatory region / transcription export complex 2 / regulation of protein neddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle, lid subcomplex / proteasome storage granule / mRNA export from nucleus / proteasome assembly / protein folding chaperone / proteasome complex / euchromatin / double-strand break repair via homologous recombination / mRNA splicing, via spliceosome / double-stranded DNA binding / ubiquitin-dependent protein catabolic process / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of cell cycle / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #990 / Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / PCI domain ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #990 / Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
26S proteasome complex subunit SEM1 / Cop9 signalosome complex subunit 12 / Protein THP3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsKuang, Z. / Niu, L.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504903 to L.N. China
National Natural Science Foundation of China (NSFC)Grant Nos. 31621002 to L.N. China
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural assembly of the nucleic-acid-binding Thp3-Csn12-Sem1 complex functioning in mRNA splicing.
Authors: Kuang, Z. / Ke, J. / Hong, J. / Zhu, Z. / Niu, L.
History
DepositionMay 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein THP3
B: Cop9 signalosome complex subunit 12
C: 26S proteasome complex subunit SEM1


Theoretical massNumber of molelcules
Total (without water)94,9003
Polymers94,9003
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-43 kcal/mol
Surface area37380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.319, 116.319, 127.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Protein Protein THP3 / THO-related protein 3


Mass: 34475.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: THP3, YPR045C, YP9499.03c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12049
#2: Protein Cop9 signalosome complex subunit 12


Mass: 49980.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CSN12, YJR084W, J1860 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47130
#3: Protein 26S proteasome complex subunit SEM1


Mass: 10443.997 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SEM1, DSH1, YDR363W-A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94742
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 12% PEG3350, 100 mM Sodium malonate buffer (pH 5.0) and 3% Methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 23736 / % possible obs: 100 % / Redundancy: 16.6 % / Biso Wilson estimate: 64.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.147 / Net I/σ(I): 23.44
Reflection shellResolution: 2.85→2.9 Å / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 1168 / CC1/2: 0.897 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→33.58 Å / SU ML: 0.3657 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1181 5 %RANDOM
Rwork0.212 22449 --
obs0.2142 23630 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.95 Å2
Refinement stepCycle: LAST / Resolution: 2.85→33.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6115 0 0 8 6123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00536234
X-RAY DIFFRACTIONf_angle_d0.82258407
X-RAY DIFFRACTIONf_chiral_restr0.0495932
X-RAY DIFFRACTIONf_plane_restr0.00561071
X-RAY DIFFRACTIONf_dihedral_angle_d18.06233816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.980.35391260.30072803X-RAY DIFFRACTION99.97
2.98-3.140.33181450.25442761X-RAY DIFFRACTION99.97
3.14-3.330.29511880.25782726X-RAY DIFFRACTION100
3.33-3.590.3031700.22892763X-RAY DIFFRACTION100
3.59-3.950.25221410.20992812X-RAY DIFFRACTION99.97
3.95-4.520.20331110.1762850X-RAY DIFFRACTION99.97
4.52-5.690.22181430.19542841X-RAY DIFFRACTION99.9
5.69-33.580.241570.20392893X-RAY DIFFRACTION97.88
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)
10.1230419336720.0865055736723-0.02408499136320.0854079940061-0.03259560706750.1714766035390.01809283412610.0206992045669-0.0646942559303-0.115084444299-0.247227421352-0.0677775969292-0.05917157788030.0254761139306-1.81739627641E-90.361615438190.01691534302220.02908193020070.2510215224030.02544372258060.350964444535-36.0550359973-5.132989324658.08503030965
2-0.0199582853968-0.0327052141218-0.01142270544450.0597470687144-0.0213844497097-0.004342938049070.06494127540690.07061072471560.0358417439581-0.0328781352387-0.03527629398250.0709158859024-0.167529448771-0.06927547258572.41215579113E-80.440080024582-0.00104352676303-0.009901376648070.3008435722930.01200216401670.343572834768-50.25405074317.14209451028.76535188209
30.02492539976170.0163196925535-0.01649416940070.03687673083080.001187807885870.041479739862-0.05854534589650.0763983304853-0.1284038318460.1322265210910.1729993197670.05999791703210.0102182218315-0.176534076354.31305442013E-90.270031213662-0.002473582834260.08026268800980.3079830826520.03510156103130.292565534116-70.439674518820.561900229825.0418384055
40.00911484251027-0.0431954471455-0.0143484978963-0.005715146826890.0113675520907-0.00228101268173-0.07804318091420.07044233766880.0434965355563-0.0634551993012-0.09583529573120.01951859478880.07919680850210.12606139519-6.58913925582E-90.974125376372-0.218653492772-0.193031145021.26557799076-0.05168661248591.142283453711.1483935528428.60163118516.4695493724
50.0885467502290.01237246738320.03119095843950.0360128388133-0.103454752627-0.01145120504510.0794983352635-0.5730751405260.2268043988670.659609159085-0.0606241271649-0.610411374958-0.3340278899410.5963809569281.47944121816E-90.556286233572-0.629540559608-0.0378980922486-0.9209660453710.942473989037-0.0535917161951-25.737783853736.163859931417.1452102818
60.0523553733720.0365747760314-0.05341608627510.0650666693633-0.06806358324620.03965306771430.05285821000580.201247813346-0.01249163657560.3046655659380.03672869434420.120829890538-0.410858682302-0.01175566643811.84373107961E-90.5219944589660.08231446629010.09609887375250.2221924110170.04959846943540.324013989011-58.298744615437.015915132511.0531834804
70.009907131084230.01281082989310.0006470248211380.00840144189681-0.007459946344450.006129505151740.1040628099380.01517285919110.02127040460660.1002512722560.05713635649020.0375635939476-0.1344723964320.0231997485616-1.27666231189E-70.960418657406-0.158361173846-0.1137751332890.55688857710.07482358109040.862586623528-21.338273485146.614331699213.9294786218
80.000834447214820.00397126398428-0.001840958716050.000164514113438-0.00482354010474-0.00205045886511-0.0288509412768-0.006110906877830.03726068022030.001087011583190.0162352572473-0.02543706793450.002546536745230.03139609791832.12965016488E-60.83726674821-0.1181513040950.1667726724630.4754995001-0.0822485286450.755157344106-47.559058517851.72352816611.2143080314
90.00366078400313-0.005293483170410.004396376311960.00595541535658-0.003868753999730.001394886934070.02411917868360.02616809062020.00267218528289-0.006251094173750.05041438509040.05021980907270.0108286101822-0.00443635643412-1.25304889458E-70.7396041325110.2465397660040.1654196294110.6576071049210.255270018710.773434952966-67.357833065647.85619204760.924283782085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 187 through 314 )
2X-RAY DIFFRACTION2chain 'A' and (resid 315 through 391 )
3X-RAY DIFFRACTION3chain 'A' and (resid 392 through 458 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 121 )
5X-RAY DIFFRACTION5chain 'B' and (resid 122 through 309 )
6X-RAY DIFFRACTION6chain 'B' and (resid 310 through 423 )
7X-RAY DIFFRACTION7chain 'C' and (resid 32 through 57 )
8X-RAY DIFFRACTION8chain 'C' and (resid 58 through 71 )
9X-RAY DIFFRACTION9chain 'C' and (resid 72 through 89 )

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