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- PDB-4alz: The Yersinia T3SS basal body component YscD reveals a different s... -

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Basic information

Entry
Database: PDB / ID: 4alz
TitleThe Yersinia T3SS basal body component YscD reveals a different structural periplasmatic domain organization to known homologue PrgH
ComponentsYOP PROTEINS TRANSLOCATION PROTEIN D
KeywordsMEMBRANE PROTEIN / T3SS / TYPE 3 SECRETION / EFFECTOR TRANSPORT
Function / homology
Function and homology information


: / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Histidine-containing Protein; Chain: A; - #30 / Yop protein translocation protein D, periplasmic domain / YscD/CdsD-like Bon-like domain 1 / Alpha-Beta Plaits - #1770 / Type III secretion system YscD/HrpQ / YscD, cytoplasmic domain / Inner membrane component of T3SS, cytoplasmic domain / Histidine-containing Protein; Chain: A; / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily ...Histidine-containing Protein; Chain: A; - #30 / Yop protein translocation protein D, periplasmic domain / YscD/CdsD-like Bon-like domain 1 / Alpha-Beta Plaits - #1770 / Type III secretion system YscD/HrpQ / YscD, cytoplasmic domain / Inner membrane component of T3SS, cytoplasmic domain / Histidine-containing Protein; Chain: A; / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Yop proteins translocation protein D
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 Å
AuthorsSchmelz, S. / Wisand, U. / Stenta, M. / Muenich, S. / Widow, U. / Cornelis, G.R. / Heinz, D.W.
CitationJournal: Elife / Year: 2013
Title: In situ structural analysis of the Yersinia enterocolitica injectisome.
Authors: Mikhail Kudryashev / Marco Stenta / Stefan Schmelz / Marlise Amstutz / Ulrich Wiesand / Daniel Castaño-Díez / Matteo T Degiacomi / Stefan Münnich / Christopher Ke Bleck / Julia Kowal / ...Authors: Mikhail Kudryashev / Marco Stenta / Stefan Schmelz / Marlise Amstutz / Ulrich Wiesand / Daniel Castaño-Díez / Matteo T Degiacomi / Stefan Münnich / Christopher Ke Bleck / Julia Kowal / Andreas Diepold / Dirk W Heinz / Matteo Dal Peraro / Guy R Cornelis / Henning Stahlberg /
Abstract: Injectisomes are multi-protein transmembrane machines allowing pathogenic bacteria to inject effector proteins into eukaryotic host cells, a process called type III secretion. Here we present the ...Injectisomes are multi-protein transmembrane machines allowing pathogenic bacteria to inject effector proteins into eukaryotic host cells, a process called type III secretion. Here we present the first three-dimensional structure of Yersinia enterocolitica and Shigella flexneri injectisomes in situ and the first structural analysis of the Yersinia injectisome. Unexpectedly, basal bodies of injectisomes inside the bacterial cells showed length variations of 20%. The in situ structures of the Y. enterocolitica and S. flexneri injectisomes had similar dimensions and were significantly longer than the isolated structures of related injectisomes. The crystal structure of the inner membrane injectisome component YscD appeared elongated compared to a homologous protein, and molecular dynamics simulations documented its elongation elasticity. The ring-shaped secretin YscC at the outer membrane was stretched by 30-40% in situ, compared to its isolated liposome-embedded conformation. We suggest that elasticity is critical for some two-membrane spanning protein complexes to cope with variations in the intermembrane distance. DOI:http://dx.doi.org/10.7554/eLife.00792.001.
History
DepositionMar 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YOP PROTEINS TRANSLOCATION PROTEIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7423
Polymers22,5541
Non-polymers1872
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.990, 51.550, 50.630
Angle α, β, γ (deg.)90.00, 106.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YOP PROTEINS TRANSLOCATION PROTEIN D / TYPE III SECRETION APPARATUS PROTEIN YSCD


Mass: 22554.447 Da / Num. of mol.: 1 / Fragment: PERIPLASMATIC DOMAIN, RESIDUES 150-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: E40 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: Q01245
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 283 TO PRO

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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: 2.12 Å3/Da / Density % sol: 42 %
Description: ANOMALOUS SIGNAL OF IODINE WAS USED TO OBTAIN EXPERIMENTAL PHASES. INITIAL PHASES WERE OBTAINED BY QUICK-SOAKING YSCD150-362 WT CRYSTALS WITH 0.5M KI AND COLLECTING OF AN ANOMALOUS ...Description: ANOMALOUS SIGNAL OF IODINE WAS USED TO OBTAIN EXPERIMENTAL PHASES. INITIAL PHASES WERE OBTAINED BY QUICK-SOAKING YSCD150-362 WT CRYSTALS WITH 0.5M KI AND COLLECTING OF AN ANOMALOUS DATASET USING THE CU KALPHA RADIATION OF A RIGAKU MICROMAX 7HF AND SATURN 944+ DETECTOR. FOR DATA PROCESSING XDS/XSCALE WAS USED. TO SOLVE THE WT STRUCTURE SAS AND MRSAD PROTOCOL OF AUTO-RICKSHAW WAS USED.AN INITIAL MODEL FROM AA 152-346 WAS BUILD BY ARP/WARP WHICH WAS USED AS AN MR MODEL FOR A WT DATASET(NON- ANOMALOUS). THE WT DATA SET WAS REFINED AND COMPLETED WITH REFMARC5 AND COOT, BUT STATISTICS WERE NOT SUFFICIENT FOR PUBLICATION. HENCE THE G283P MUTANT WAS GENERATED. FIRST TWO DOMAINS (AMINO ACIDS 150-280) OF WT MODEL WERE USED AS A MR MODEL FOR YSCD150-347 G283P. REMAINING DOMAIN WAS MANUALLY BUILD WITH COOT.
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: YSCD150-347 G283P CRYSTALS GREW FROM EQUAL VOLUMES OF PROTEIN (5.8 MG/ML IN 20 MM HEPES PH 7.0, 60 MM NACL) WITH PRECIPITANT SOLUTION (0.15 M NAH2PO4, 20 % (W/V) PEG 3350, 60 MM NACL) IN ...Details: YSCD150-347 G283P CRYSTALS GREW FROM EQUAL VOLUMES OF PROTEIN (5.8 MG/ML IN 20 MM HEPES PH 7.0, 60 MM NACL) WITH PRECIPITANT SOLUTION (0.15 M NAH2PO4, 20 % (W/V) PEG 3350, 60 MM NACL) IN HANGING-DROP VAPOR-DIFFUSION CRYSTALLIZATION TRAYS AT 292 K (EASYXTAL; QIAGEN).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2011
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.4→29.8 Å / Num. obs: 36930 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 13.94 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.4→29.791 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 1847 5 %
Rwork0.1894 --
obs0.1912 36927 99.55 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.945 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7547 Å20 Å2-0.4714 Å2
2--2.7898 Å20 Å2
3----2.0351 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 11 289 1862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091744
X-RAY DIFFRACTIONf_angle_d1.2382377
X-RAY DIFFRACTIONf_dihedral_angle_d15.041691
X-RAY DIFFRACTIONf_chiral_restr0.082258
X-RAY DIFFRACTIONf_plane_restr0.006324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.43790.3591420.28652689X-RAY DIFFRACTION100
1.4379-1.48020.30841410.25332680X-RAY DIFFRACTION100
1.4802-1.5280.24161430.222727X-RAY DIFFRACTION100
1.528-1.58260.23311410.19382684X-RAY DIFFRACTION100
1.5826-1.6460.24451430.20122701X-RAY DIFFRACTION100
1.646-1.72090.23541410.19442688X-RAY DIFFRACTION100
1.7209-1.81160.21031420.18192702X-RAY DIFFRACTION100
1.8116-1.92510.23411400.20472652X-RAY DIFFRACTION98
1.9251-2.07370.22111400.1962669X-RAY DIFFRACTION99
2.0737-2.28230.2331420.19432682X-RAY DIFFRACTION99
2.2823-2.61240.19681420.18372712X-RAY DIFFRACTION100
2.6124-3.29070.23241430.17752719X-RAY DIFFRACTION100
3.2907-29.79730.20861470.17122775X-RAY DIFFRACTION99

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