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- PDB-5tp1: The structure of the C-terminus of virulence protein IncE from Ch... -

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Basic information

Entry
Database: PDB / ID: 5tp1
TitleThe structure of the C-terminus of virulence protein IncE from Chlamydia trachomatis bound to Mus musculus SNX5-PX domain
Components
  • Inclusion membrane protein E
  • Sorting nexin-5
KeywordsPROTEIN TRANSPORT / host-pathogen
Function / homology
Function and homology information


pathogen-containing vacuole membrane / extrinsic component of endosome membrane / epidermal growth factor catabolic process / positive regulation of renal sodium excretion / pinocytosis / tubular endosome / macropinocytic cup / phosphatidylinositol-5-phosphate binding / retromer complex / Golgi Associated Vesicle Biogenesis ...pathogen-containing vacuole membrane / extrinsic component of endosome membrane / epidermal growth factor catabolic process / positive regulation of renal sodium excretion / pinocytosis / tubular endosome / macropinocytic cup / phosphatidylinositol-5-phosphate binding / retromer complex / Golgi Associated Vesicle Biogenesis / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / dynactin binding / phagocytic cup / brush border / : / host cell membrane / D1 dopamine receptor binding / positive regulation of insulin receptor signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / ruffle / negative regulation of blood pressure / phosphatidylinositol binding / intracellular protein transport / cytoplasmic vesicle membrane / early endosome membrane / membrane => GO:0016020 / endosome / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / extracellular region / cytosol
Similarity search - Function
Inclusion membrane protein E / Inclusion membrane protein E / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Phox-like domain / PX Domain / PX domain profile. / PX domain ...Inclusion membrane protein E / Inclusion membrane protein E / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Phox-like domain / PX Domain / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Inclusion membrane protein E / Sorting nexin-5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Chlamydia trachomatis D/UW-3/CX (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsRosenberg, O. / Czudnochowski, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K08 AI091656-04 United States
CitationJournal: Elife / Year: 2017
Title: Chlamydia interfere with an interaction between the mannose-6-phosphate receptor and sorting nexins to counteract host restriction.
Authors: Elwell, C.A. / Czudnochowski, N. / von Dollen, J. / Johnson, J.R. / Nakagawa, R. / Mirrashidi, K. / Krogan, N.J. / Engel, J.N. / Rosenberg, O.S.
History
DepositionOct 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-5
B: Sorting nexin-5
C: Sorting nexin-5
D: Sorting nexin-5
P: Inclusion membrane protein E
Q: Inclusion membrane protein E
R: Inclusion membrane protein E
S: Inclusion membrane protein E


Theoretical massNumber of molelcules
Total (without water)86,5218
Polymers86,5218
Non-polymers00
Water4,540252
1
A: Sorting nexin-5
P: Inclusion membrane protein E


Theoretical massNumber of molelcules
Total (without water)21,6302
Polymers21,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-11 kcal/mol
Surface area10260 Å2
MethodPISA
2
B: Sorting nexin-5
Q: Inclusion membrane protein E


Theoretical massNumber of molelcules
Total (without water)21,6302
Polymers21,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-12 kcal/mol
Surface area10160 Å2
MethodPISA
3
C: Sorting nexin-5
R: Inclusion membrane protein E


Theoretical massNumber of molelcules
Total (without water)21,6302
Polymers21,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-9 kcal/mol
Surface area10210 Å2
MethodPISA
4
D: Sorting nexin-5
S: Inclusion membrane protein E


Theoretical massNumber of molelcules
Total (without water)21,6302
Polymers21,6302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-11 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.730, 110.100, 86.130
Angle α, β, γ (deg.)90.00, 90.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Sorting nexin-5 /


Mass: 18938.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snx5 / Plasmid: pH3C
Details (production host): modified pET vector with n-terminal 8-his tag and precision protease site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9D8U8
#2: Protein/peptide
Inclusion membrane protein E


Mass: 2692.049 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Chlamydia trachomatis D/UW-3/CX (bacteria) / References: UniProt: P0DJI4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.01 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: SNX5/IncE in 20 mM Hepes pH 7.4, 100 mM NaCl, 1 mM TCEP was mixed with an equal volume of 26% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.31→67.84 Å / Num. obs: 29845 / % possible obs: 99.4 % / Redundancy: 3.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.5
Reflection shellResolution: 2.31→2.43 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.282 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.332 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Blu-Icedata collection
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HPC

3hpc


Resolution: 2.31→67.838 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 1441 4.84 %
Rwork0.2032 --
obs0.2058 29799 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→67.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5549 0 0 252 5801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045680
X-RAY DIFFRACTIONf_angle_d0.647678
X-RAY DIFFRACTIONf_dihedral_angle_d14.0432127
X-RAY DIFFRACTIONf_chiral_restr0.033865
X-RAY DIFFRACTIONf_plane_restr0.003989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.39260.34751360.28492814X-RAY DIFFRACTION98
2.3926-2.48840.31431460.25692788X-RAY DIFFRACTION99
2.4884-2.60170.26651610.24772813X-RAY DIFFRACTION99
2.6017-2.73880.32031790.21972763X-RAY DIFFRACTION99
2.7388-2.91040.2581280.22322847X-RAY DIFFRACTION99
2.9104-3.13510.31641210.21552867X-RAY DIFFRACTION99
3.1351-3.45060.25311440.20532848X-RAY DIFFRACTION99
3.4506-3.94990.22751280.18892857X-RAY DIFFRACTION100
3.9499-4.97620.24451530.17662863X-RAY DIFFRACTION100
4.9762-67.86680.22111450.17572898X-RAY DIFFRACTION99

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