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- PDB-4ow2: YopM from Yersinia enterocolitica WA-314 -

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Basic information

Entry
Database: PDB / ID: 4ow2
TitleYopM from Yersinia enterocolitica WA-314
ComponentsYop effector YopM
KeywordsTOXIN / leucine-rich repeat / LRR
Function / homologyLRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / extracellular region / Yop effector YopM / :
Function and homology information
Biological speciesYersinia enterocolitica subsp. enterocolitica WA-314 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsRumm, A. / Perbandt, M. / Aepfelbacher, M.
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.
History
DepositionJan 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Derived calculations
Revision 1.2Mar 7, 2018Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Yop effector YopM
B: Yop effector YopM
C: Yop effector YopM
D: Yop effector YopM


Theoretical massNumber of molelcules
Total (without water)201,4444
Polymers201,4444
Non-polymers00
Water1,06359
1
A: Yop effector YopM
C: Yop effector YopM


Theoretical massNumber of molelcules
Total (without water)100,7222
Polymers100,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Yop effector YopM
D: Yop effector YopM


Theoretical massNumber of molelcules
Total (without water)100,7222
Polymers100,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.847, 126.290, 139.933
Angle α, β, γ (deg.)90.00, 118.26, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 34 - 481 / Label seq-ID: 1 - 448

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Yop effector YopM


Mass: 50360.988 Da / Num. of mol.: 4 / Fragment: UNP residues 34-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica WA-314 (bacteria)
Gene: YWA314_20912 / Production host: Escherichia coli (E. coli) / References: UniProt: K1AZR9, UniProt: A0A0J9X1Z0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 4.07 Å3/Da / Density % sol: 69.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: BisTris Propane, sodium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97957 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 64045 / % possible obs: 97 % / Redundancy: 6.59 % / Biso Wilson estimate: 94.62 Å2 / Net I/σ(I): 14.2

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 35.165 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20124 2707 5.1 %RANDOM
Rwork0.18148 ---
obs0.18251 50515 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 201.09 Å2 / Biso mean: 101.759 Å2 / Biso min: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å2-0.79 Å2
2---0.76 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14167 0 0 59 14226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01914487
X-RAY DIFFRACTIONr_bond_other_d0.0040.0213998
X-RAY DIFFRACTIONr_angle_refined_deg1.2342.03119862
X-RAY DIFFRACTIONr_angle_other_deg1.169332456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3651788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68925.666683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.598152445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4941592
X-RAY DIFFRACTIONr_chiral_restr0.0660.22324
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02116300
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022836
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6137.4727164
X-RAY DIFFRACTIONr_mcbond_other2.6137.4727163
X-RAY DIFFRACTIONr_mcangle_it4.31211.2128948
X-RAY DIFFRACTIONr_mcangle_other4.31211.2128949
X-RAY DIFFRACTIONr_scbond_it3.0757.8537320
X-RAY DIFFRACTIONr_scbond_other3.0747.8537318
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.18911.65410914
X-RAY DIFFRACTIONr_long_range_B_refined7.8458.15914734
X-RAY DIFFRACTIONr_long_range_B_other7.82958.15714729
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A282290.1
12B282290.1
21A279950.11
22C279950.11
31A280880.11
32D280880.11
41B276630.11
42C276630.11
51B279240.11
52D279240.11
61C282380.1
62D282380.1
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 180 -
Rwork0.293 3710 -
obs--99.29 %
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)
10.6179-0.38270.53780.4642-0.61411.08020.17710.0059-0.1774-0.255-0.09840.09330.11510.1193-0.07860.35170.0229-0.09340.10170.02250.171379.5805-60.9324150.8392
20.4151-0.5335-0.14961.03650.61321.05830.1694-0.00290.2489-0.3854-0.0384-0.2524-0.1113-0.0059-0.1310.36520.01230.12090.0097-0.02790.2333369.1454-24.2145149.5053
30.56750.6809-0.24390.9421-0.40610.53030.00410.0071-0.0142-0.04090.07930.1234-0.15260.1134-0.08340.3124-0.08980.03770.17230.09070.2351406.6628-38.4064169.2198
40.51910.56880.35680.8650.24670.4813-0.0089-0.1775-0.0851-0.15640.0137-0.21940.0412-0.2837-0.00470.247-0.0880.10540.2958-0.00060.184342.9944-45.3397168.4611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 481
2X-RAY DIFFRACTION2B34 - 481
3X-RAY DIFFRACTION3C34 - 481
4X-RAY DIFFRACTION4D34 - 481

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