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- SASDAW8: 2:1 YopM:DDX3 complex (Yersinia outer protein M (34-481), YopM + ... -

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Basic information

Entry
Database: SASBDB / ID: SASDAW8
Sample2:1 YopM:DDX3 complex
  • Yersinia outer protein M (34-481) (protein), YopM, Yersinia enterocolitica
  • DEAD box RNA helicase DDX3 (51-418) (protein), DDX3, Yersinia enterocolitica
Biological speciesYersinia enterocolitica (bacteria)
CitationJournal: PLoS Pathog / Year: 2016
Title: Immunosuppressive Yersinia Effector YopM Binds DEAD Box Helicase DDX3 to Control Ribosomal S6 Kinase in the Nucleus of Host Cells.
Authors: Laura Berneking / Marie Schnapp / Andreas Rumm / Claudia Trasak / Klaus Ruckdeschel / Malik Alawi / Adam Grundhoff / Alexey G Kikhney / Friedrich Koch-Nolte / Friedrich Buck / Markus ...Authors: Laura Berneking / Marie Schnapp / Andreas Rumm / Claudia Trasak / Klaus Ruckdeschel / Malik Alawi / Adam Grundhoff / Alexey G Kikhney / Friedrich Koch-Nolte / Friedrich Buck / Markus Perbandt / Christian Betzel / Dmitri I Svergun / Moritz Hentschke / Martin Aepfelbacher /
Abstract: Yersinia outer protein M (YopM) is a crucial immunosuppressive effector of the plaque agent Yersinia pestis and other pathogenic Yersinia species. YopM enters the nucleus of host cells but neither ...Yersinia outer protein M (YopM) is a crucial immunosuppressive effector of the plaque agent Yersinia pestis and other pathogenic Yersinia species. YopM enters the nucleus of host cells but neither the mechanisms governing its nucleocytoplasmic shuttling nor its intranuclear activities are known. Here we identify the DEAD-box helicase 3 (DDX3) as a novel interaction partner of Y. enterocolitica YopM and present the three-dimensional structure of a YopM:DDX3 complex. Knockdown of DDX3 or inhibition of the exportin chromosomal maintenance 1 (CRM1) increased the nuclear level of YopM suggesting that YopM exploits DDX3 to exit the nucleus via the CRM1 export pathway. Increased nuclear YopM levels caused enhanced phosphorylation of Ribosomal S6 Kinase 1 (RSK1) in the nucleus. In Y. enterocolitica infected primary human macrophages YopM increased the level of Interleukin-10 (IL-10) mRNA and this effect required interaction of YopM with RSK and was enhanced by blocking YopM's nuclear export. We propose that the DDX3/CRM1 mediated nucleocytoplasmic shuttling of YopM determines the extent of phosphorylation of RSK in the nucleus to control transcription of immunosuppressive cytokines.
Contact author
  • Al Kikhney (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #346
Type: atomic / Software: SASREF / Radius of dummy atoms: 1.90 A / Chi-square value: 1.547
Search similar-shape structures of this assembly by Omokage search (details)
Model #349
Type: dummy / Software: DAMMIF (r5577) / Radius of dummy atoms: 3.10 A / Chi-square value: 1.344
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: 2:1 YopM:DDX3 complex / Specimen concentration: 0.66-10.60 / Entity id: 207 / 208
BufferName: HEPES / Concentration: 50.00 mM / pH: 7.5 / Composition: 150 mM NaCl
Entity #207Name: YopM / Type: protein / Description: Yersinia outer protein M (34-481) / Formula weight: 50.321 / Num. of mol.: 2 / Source: Yersinia enterocolitica
Sequence: KSKTEYYNAW SEWERNAPPG NGEQREMAVS RLRDCLDRQA HELELNNLGL SSLPELPPHL ERLVASCNSL TELPELPQSL KSLEVYENNL KALPDLPPLL VDLRVFNNQL EELPELQNLP FLTEIYANNN SLKTLPDLPP SLVDLNVREN YLTALPELPQ SLIFLDISDN ...Sequence:
KSKTEYYNAW SEWERNAPPG NGEQREMAVS RLRDCLDRQA HELELNNLGL SSLPELPPHL ERLVASCNSL TELPELPQSL KSLEVYENNL KALPDLPPLL VDLRVFNNQL EELPELQNLP FLTEIYANNN SLKTLPDLPP SLVDLNVREN YLTALPELPQ SLIFLDISDN ILSGLSELPP NLSCLDASRN GIRSLCDLPP SLVYLDVRDN QLIELPALPS GLERLIASFN HLAELPELPP NLYYLDASRN EISSLCDLPP SLVDLNVRKN QLIELPALPP DLERLIASFN HLAELPELPP NLSYLDASRN EISSLCDLPP SLVDLNVRKN QLIELPALPP DLERLIASFN HLAELPELPP NLSYLDASRN EISSLCDLPP SLVELDVRDN QLIELPALPP HLERLIASLN HLAEVPELPQ NLKQLHVEHN ALREFPDIPE SVEDLRMD
Entity #208Name: DDX3 / Type: protein / Description: DEAD box RNA helicase DDX3 (51-418) / Formula weight: 41.5 / Num. of mol.: 1 / Source: Yersinia enterocolitica

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Experimental information

BeamInstrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3.1 mm
DetectorName: Pilatus 2M
Scan
Title: DDX3_51-418 : YopM_34-481 complex / Measurement date: Jun 14, 2013 / Storage temperature: 23 °C / Cell temperature: 23 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /
MinMax
Q0.0768 4.5832
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 651 /
MinMax
Q0.0767596 1.78675
P(R) point1 651
R0 15
Result
Type of curve: extrapolated
Comments: A complex composed of two YopM_34-481 molecules and one DDX3_51-418
ExperimentalExperimental errorPorodPorod error
MW123 kDa12 119 kDa12
Volume--189.7 nm3-

GuinierP(R)Guinier error
Forward scattering, I07459 --
Radius of gyration, Rg3.97 nm4.033 nm0.12

MinMaxError
D-15 1.5
Guinier point15 95 -

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