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- PDB-2ca5: MxiH needle protein of Shigella Flexneri (monomeric form, residue... -

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Basic information

Entry
Database: PDB / ID: 2ca5
TitleMxiH needle protein of Shigella Flexneri (monomeric form, residues 1- 78)
ComponentsMXIH
KeywordsTRANSPORT PROTEIN / MXIH / TYPE III SECRETION SYSTEM / NEEDLE COMPLEX / PROTEIN TRANSPORT / VIRULENCE
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / identical protein binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Type 3 secretion system needle filament protein
Similarity search - Component
Biological speciesSHIGELLA FLEXNERI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.1 Å
AuthorsDeane, J.E. / Roversi, P. / Cordes, F.S. / Johnson, S. / Kenjale, R. / Picking, W.L. / Picking, W.D. / Blocker, A.J. / Lea, S.M.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2006
Title: Molecular model of a type III secretion system needle: Implications for host-cell sensing.
Authors: Janet E Deane / Pietro Roversi / Frank S Cordes / Steven Johnson / Roma Kenjale / Sarah Daniell / Frank Booy / William D Picking / Wendy L Picking / Ariel J Blocker / Susan M Lea /
Abstract: Type III secretion systems are essential virulence determinants for many Gram-negative bacterial pathogens. The type III secretion system consists of cytoplasmic, transmembrane, and extracellular ...Type III secretion systems are essential virulence determinants for many Gram-negative bacterial pathogens. The type III secretion system consists of cytoplasmic, transmembrane, and extracellular domains. The extracellular domain is a hollow needle protruding above the bacterial surface and is held within a basal body that traverses both bacterial membranes. Effector proteins are translocated, via this external needle, directly into host cells, where they subvert normal cell functions to aid infection. Physical contact with host cells initiates secretion and leads to formation of a pore, thought to be contiguous with the needle channel, in the host-cell membrane. Here, we report the crystal structure of the Shigella flexneri needle subunit MxiH and a complete model for the needle assembly built into our three-dimensional EM reconstruction. The model, combined with mutagenesis data, reveals that signaling of host-cell contact is relayed through the needle via intersubunit contacts and suggests a mode of binding for a tip complex.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, Purification, Crystallization and Preliminary Crystallographic Analysis of Mxih, a Subunit of the Shigella Flexneri Type III Secretion System Needle.
Authors: Deane, J.E. / Cordes, F.S. / Roversi, P. / Johnson, S. / Kenjale, R. / Picking, W.D. / Picking, W.L. / Lea, S.M. / Blocker, A.
History
DepositionDec 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MXIH
B: MXIH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3497
Polymers19,0912
Non-polymers2585
Water86548
1
A: MXIH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7815
Polymers9,5461
Non-polymers2354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MXIH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5692
Polymers9,5461
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)183.203, 28.123, 27.723
Angle α, β, γ (deg.)90.00, 96.47, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99021, 0.10552, 0.09133), (-0.09519, 0.03213, 0.99494), (0.10205, -0.9939, 0.04186)
Vector: -30.92649, 55.95963, 4.19609)

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Components

#1: Protein MXIH


Mass: 9545.514 Da / Num. of mol.: 2 / Fragment: TRUNCATED C-TERMINUS, RESIDUES 1-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: PWR100 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A223
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT IS A 5-RESIDUES C-TERMINAL DELETION MUTANT. THE LEHHHHH SEQUENCE COMES FROM THE ...THIS CONSTRUCT IS A 5-RESIDUES C-TERMINAL DELETION MUTANT. THE LEHHHHH SEQUENCE COMES FROM THE EXPRESSION VECTOR.

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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: 1.9 Å3/Da / Density % sol: 0.34 %
Description: STRUCTURE DETERMINED BY MIRAS WITH URANYL ACETATE AND SEMET DERIVATIVES
Crystal growpH: 5.6
Details: 20% PEG 4000, 0.1 M SODIUM CITRATE PH 5.6, 20% ISOPROPANOL, 10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→28 Å / Num. obs: 8232 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 1.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SIGMAAmodel building
SCALAdata scaling
SHARPphasing
SOLOMONphasing
DMphasing
SIGMAAphasing
TNT5.6.1refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.1→28 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: REFINEMENT WAS DONE WITH MAXIMUM LIKELIHOOD IN BUSTER-TNT VERSION 1.3.0 THE REGIONS A1-A19, B1- B14 AND B76-B81 WERE DISORDERED IN THE CRYSTAL AND WERE NOT MODELLED
RfactorNum. reflection
Rwork0.194 -
all0.196 -
obs0.194 8232
Solvent computationSolvent model: BABINET SCALING / Bsol: 25 Å2 / ksol: 0.418 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 16 48 1026
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0069882
X-RAY DIFFRACTIONt_angle_deg0.87913322
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005362
X-RAY DIFFRACTIONt_gen_planes0.011335
X-RAY DIFFRACTIONt_it1.11598820
X-RAY DIFFRACTIONt_nbd0.044165
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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