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- PDB-5tgh: Structure of the SNX5 PX domain in complex with chlamydial protei... -

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Basic information

Entry
Database: PDB / ID: 5tgh
TitleStructure of the SNX5 PX domain in complex with chlamydial protein IncE in space group P32
Components
  • IncE
  • Sorting nexin-5
KeywordsPROTEIN TRANSPORT / host-pathogen endosome
Function / homology
Function and homology information


retromer, tubulation complex / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / retromer complex / phosphatidylinositol-5-phosphate binding / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding ...retromer, tubulation complex / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / retromer complex / phosphatidylinositol-5-phosphate binding / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / Golgi Associated Vesicle Biogenesis / brush border / dynactin binding / phagocytic cup / D1 dopamine receptor binding / regulation of macroautophagy / positive regulation of insulin receptor signaling pathway / ruffle / negative regulation of blood pressure / phosphatidylinositol binding / intracellular protein transport / cytoplasmic side of plasma membrane / endosome / cadherin binding / intracellular membrane-bounded organelle / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / membrane / cytosol
Similarity search - Function
Inclusion membrane protein E / Inclusion membrane protein E / SNX5, PX domain / 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. ...Inclusion membrane protein E / Inclusion membrane protein E / SNX5, PX domain / 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
IncE / Sorting nexin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
Chlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCollins, B. / Paul, B.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1058734 Australia
Australian Research Council (ARC)DP150100364 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1061574 Australia
CitationJournal: Elife / Year: 2017
Title: Structural basis for the hijacking of endosomal sorting nexin proteins byChlamydia trachomatis.
Authors: Paul, B. / Kim, H.S. / Kerr, M.C. / Huston, W.M. / Teasdale, R.D. / Collins, B.M.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 28, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.4Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 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: IncE
C: Sorting nexin-5
D: IncE
E: Sorting nexin-5
F: IncE
G: Sorting nexin-5
H: IncE


Theoretical massNumber of molelcules
Total (without water)79,1138
Polymers79,1138
Non-polymers00
Water181
1
A: Sorting nexin-5
B: IncE


Theoretical massNumber of molelcules
Total (without water)19,7782
Polymers19,7782
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area9630 Å2
MethodPISA
2
C: Sorting nexin-5
D: IncE


Theoretical massNumber of molelcules
Total (without water)19,7782
Polymers19,7782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-9 kcal/mol
Surface area9680 Å2
MethodPISA
3
E: Sorting nexin-5
F: IncE


Theoretical massNumber of molelcules
Total (without water)19,7782
Polymers19,7782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-9 kcal/mol
Surface area9600 Å2
MethodPISA
4
G: Sorting nexin-5
H: IncE


Theoretical massNumber of molelcules
Total (without water)19,7782
Polymers19,7782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-9 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.640, 100.640, 71.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Sorting nexin-5


Mass: 17357.504 Da / Num. of mol.: 4 / Fragment: UNP residues 22-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X3
#2: Protein/peptide
IncE


Mass: 2420.718 Da / Num. of mol.: 4 / Fragment: UNP residues 110-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: incE / Production host: Escherichia coli (E. coli) / References: UniProt: B7SCI5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 1.26 M (NH4)2SO4, acetate (pH 4.5), 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→50.3 Å / Num. obs: 20001 / % possible obs: 100 % / Redundancy: 5.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2923 / CC1/2: 0.683 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TGI

5tgi


Resolution: 2.8→41.179 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 1972 9.87 %
Rwork0.236 --
obs0.2378 19976 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→41.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 0 1 5190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155313
X-RAY DIFFRACTIONf_angle_d1.287168
X-RAY DIFFRACTIONf_dihedral_angle_d21.6721983
X-RAY DIFFRACTIONf_chiral_restr0.089804
X-RAY DIFFRACTIONf_plane_restr0.012919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.87010.37981440.32511301X-RAY DIFFRACTION100
2.8701-2.94770.33121400.31661265X-RAY DIFFRACTION100
2.9477-3.03440.32191420.28931283X-RAY DIFFRACTION100
3.0344-3.13230.3031360.30331315X-RAY DIFFRACTION100
3.1323-3.24420.3231370.28361315X-RAY DIFFRACTION100
3.2442-3.3740.26941360.27561244X-RAY DIFFRACTION100
3.374-3.52750.28281440.26191296X-RAY DIFFRACTION100
3.5275-3.71340.26461560.24521270X-RAY DIFFRACTION100
3.7134-3.94590.22731340.22991286X-RAY DIFFRACTION100
3.9459-4.25020.26161400.21091310X-RAY DIFFRACTION100
4.2502-4.67740.22041410.19461250X-RAY DIFFRACTION100
4.6774-5.3530.2011460.20331292X-RAY DIFFRACTION100
5.353-6.73940.24131420.23281296X-RAY DIFFRACTION100
6.7394-41.18370.21941340.2011281X-RAY DIFFRACTION100

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