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- PDB-7ewm: Native crystal structure of S. cerevisiae Csn12 in complex with T... -

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Basic information

Entry
Database: PDB / ID: 7ewm
TitleNative crystal structure of S. cerevisiae Csn12 in complex with Thp3 and Sem1
Components
  • 26S proteasome complex subunit SEM1Proteasome
  • 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 / SAGA complex localization to transcription regulatory region / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle, lid subcomplex / poly(A)+ mRNA export from nucleus ...adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion / SAGA complex localization to transcription regulatory region / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle, lid subcomplex / poly(A)+ mRNA export from nucleus / proteasome storage granule / proteasome assembly / mRNA export from nucleus / protein folding chaperone / proteasome complex / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / mRNA splicing, via spliceosome / ubiquitin-dependent protein catabolic process / double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / regulation of cell cycle / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Csn12 family / SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Winged helix-like DNA-binding domain superfamily
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)93,9153
Polymers93,9153
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-43 kcal/mol
Surface area37400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.575, 115.575, 126.825
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: 33959.320 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: 49558.391 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 / Proteasome


Mass: 10397.102 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 / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
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: 2.9→50 Å / Num. obs: 22217 / % possible obs: 99.9 % / Redundancy: 19.3 % / Biso Wilson estimate: 74.1 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Net I/σ(I): 29.77
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 1089 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EWF

7ewf


Resolution: 2.9→32.29 Å / SU ML: 0.3981 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.23
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1155 5.22 %RANDOM
Rwork0.222 20991 --
obs0.2236 22146 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.47 Å2
Refinement stepCycle: LAST / Resolution: 2.9→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6106 0 0 4 6110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00596225
X-RAY DIFFRACTIONf_angle_d0.87768395
X-RAY DIFFRACTIONf_chiral_restr0.051931
X-RAY DIFFRACTIONf_plane_restr0.0061069
X-RAY DIFFRACTIONf_dihedral_angle_d18.82963810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.030.37851230.30622625X-RAY DIFFRACTION99.96
3.03-3.190.34211640.28032535X-RAY DIFFRACTION100
3.19-3.390.28781510.26082603X-RAY DIFFRACTION99.96
3.39-3.650.29181280.24122610X-RAY DIFFRACTION99.96
3.65-4.020.26361460.22672609X-RAY DIFFRACTION99.93
4.02-4.60.22511600.19022598X-RAY DIFFRACTION100
4.6-5.790.22741200.21932688X-RAY DIFFRACTION100
5.79-32.290.22051630.20082723X-RAY DIFFRACTION99.04
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)
10.0152708699672-0.01441179091240.000165359496920.005817181576980.001539666140740.0093425589817-0.1234144023560.05536211493690.02485857586920.00753989304843-0.1444106572490.07047130943-0.0172843175116-0.0409779495784-3.93772802438E-80.3459932582280.01296979955220.008191777041970.581058821328-0.04711333160430.5364951188813.6048661850834.3595841128-12.3419763875
20.0112836605087-0.009430185158530.004306288562360.00603111257337-0.00137468941660.00999820807693-0.0852293373696-0.00506570949741-0.07565848190690.040028819185-0.08001650531450.104354769990.003990838778480.005882951752621.98445633423E-80.350025863451-0.04091301884710.01277958523860.3808054709640.01381717337210.33307760071515.602832602434.0289347921-11.7312876398
30.0194630399253-0.0198335230484-0.01473372745030.00530449756621-0.004302696636340.01223001896450.02787753418690.07105510029650.003807265403960.00343165319709-0.0809994541152-0.1373727282180.0466490727550.0152702124508-6.19844803659E-90.390745880822-0.005240500260490.03794661034280.434774139571-0.03328532975420.33786305754535.990580267431.5866719372-16.7855596562
40.00107859751584-0.00115385744709-0.00269574086920.003071269990220.005961164144470.003393135637950.027548738585-0.02292800713160.0542924653384-0.009802254756990.07448969775990.09704084873310.004417107749810.008384366550651.31244595416E-70.360075090693-0.0189305783907-0.006174900639420.4480242770110.01680195468390.35238534044139.378394216740.4172729063-3.71266948455
50.00371360306542-0.006365228203640.000303269583480.0122858102024-0.002213754880970.00460228460385-0.0410531782973-0.09507444928240.0938008663610.004108529454560.04470716948330.0122485243354-0.1309338502660.004027790854962.74825431791E-70.262886045484-0.157009335377-0.05946012401630.263251948919-0.09288937792550.22889840192550.147085758750.81047375282.71179449375
60.003140497841090.00119913323730.00129895189119-5.44456082437E-7-0.00240890981078-0.001326484453850.0823438006882-0.003833200125720.0228654225248-0.006431043012550.0608797007258-0.0121109460124-0.005172056593540.0263100644515-5.53183158858E-90.4672349268120.02330639565380.05280488465520.566945392888-0.03512414639330.65984709858656.749321579550.06344940995.27705221789
70.0008221322804080.0132799595745-0.0005172514851920.008194481242120.00555289659937-0.0053054745382-0.114947187411-0.046432114242-0.09665100505170.00746507707138-0.06475843029120.05818283761560.0241285441103-0.05468614877886.29862029065E-91.36178842508-0.02434311560280.05879651729041.080902658220.2629309748841.1465179049223.675239376-15.3790085993-4.69891729454
8-0.02901492931840.0131134674972-0.093923959652-0.03085795332850.0134301145655-0.05159969283770.0609574780067-0.196549519704-0.4738123262630.1841474912550.1822351320820.3646791620220.346803776762-0.1095264076581.36778044396E-9-0.9355725777271.627675497291.592984844-0.850390875642-1.18420347742-0.96689683135843.65575618534.13204330191-4.19714592158
90.01227814299630.000402047974098-0.004001361646520.0401278264995-0.001303601269990.01603850146690.0172073640605-0.1238072476130.130040475059-0.08218485554360.177084183413-0.1072787907170.0958849659070.195897347739-1.76619910804E-80.239615707218-0.0300171591091-0.05382882513290.690882598364-0.02352010537040.47888014604660.906410671731.4271415626-10.0452997913
100.001615325743080.00137335604798-0.001186099983410.00231055335159-0.00233261967094-0.00198071658009-0.032770793471-0.0133505224064-0.02118411478580.00437523268022-0.02154634444790.02761859806260.04236610272690.0158634576589-1.28433305297E-60.7866791999710.1930975946080.05829047392620.7285230881140.1809673979240.89125414885347.5595802869-5.39029872646-8.05266758259
110.002662957655820.00168937749975-0.006386569154230.0146695719092-0.01974188518630.0321456777034-0.002429119326863.23399982347E-50.0004867149863766.16025029627E-5-0.00364422168228.21604165022E-50.00274652846324-0.00419207083610.0001361417436571.169151909310.05959523672480.04341261311171.166444827470.013184344371.1478787263565.8732819306-2.95182688638-3.93766105746
120.00211822537535-0.004091364439840.0006734639075140.000407092564522-0.000625630464705-0.0005612828728030.0184797420126-0.0103722556713-0.02864382394330.003268669080780.0099627917095-0.001626609988650.0118799005754-0.0008621949648151.08697910749E-60.6256090070460.249980020183-0.1155360276610.735102340665-0.0236068278970.88928577862868.124625525315.0952271354-9.87369380592
130.00351385560618-0.001982895996-0.002824602115690.001986540993530.000154094028280.000419104267012-0.02321931571680.0259254142841-0.0200383039968-0.0148457732934-0.0188889632128-0.006562197811940.00532243062956-0.0180963404895-5.81197737746E-70.6641745172-0.06378106787080.1605198388450.850646708686-0.2082899644240.83864535198574.64771605934.3804845788-20.1071207344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 187 through 231 )
2X-RAY DIFFRACTION2chain 'A' and (resid 232 through 291 )
3X-RAY DIFFRACTION3chain 'A' and (resid 292 through 368 )
4X-RAY DIFFRACTION4chain 'A' and (resid 369 through 391 )
5X-RAY DIFFRACTION5chain 'A' and (resid 392 through 432 )
6X-RAY DIFFRACTION6chain 'A' and (resid 433 through 458 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 120 )
8X-RAY DIFFRACTION8chain 'B' and (resid 121 through 309 )
9X-RAY DIFFRACTION9chain 'B' and (resid 310 through 423 )
10X-RAY DIFFRACTION10chain 'C' and (resid 32 through 52 )
11X-RAY DIFFRACTION11chain 'C' and (resid 53 through 57 )
12X-RAY DIFFRACTION12chain 'C' and (resid 58 through 71 )
13X-RAY DIFFRACTION13chain 'C' and (resid 72 through 89 )

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