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

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Basic information

Entry
Database: PDB / ID: 5tgi
TitleStructure of the SNX5 PX domain in complex with chlamydial protein IncE in space group P212121
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: 1.98 Å
AuthorsCollins, B. / Paul, B.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1061574 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1058734 Australia
Australian Research Council (ARC)DP150100364 Australia
CitationJournal: To Be Published
Title: Structure of the SNX5 PX domain in complex with chlamydial protein IncE
Authors: Collins, B. / Paul, B.
History
DepositionSep 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 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 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: IncE
D: IncE


Theoretical massNumber of molelcules
Total (without water)39,3284
Polymers39,3284
Non-polymers00
Water4,972276
1
A: Sorting nexin-5
C: IncE


Theoretical massNumber of molelcules
Total (without water)19,6642
Polymers19,6642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area9700 Å2
MethodPISA
2
B: Sorting nexin-5
D: IncE


Theoretical massNumber of molelcules
Total (without water)19,6642
Polymers19,6642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-10 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.711, 67.540, 88.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sorting nexin-5


Mass: 17357.504 Da / Num. of mol.: 2 / 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: 2306.615 Da / Num. of mol.: 2 / Fragment: UNP residues 111-132
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.: 276 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M KSCN, 25% PEG 2K MME, 100 mM sodium acetate (pH 5.5)

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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: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.98→60.7 Å / Num. obs: 26075 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.4
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.868 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→45.151 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.72
RfactorNum. reflection% reflection
Rfree0.2259 2000 7.69 %
Rwork0.1812 --
obs0.1847 26021 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→45.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2579 0 0 276 2855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122640
X-RAY DIFFRACTIONf_angle_d1.3053567
X-RAY DIFFRACTIONf_dihedral_angle_d15.8531599
X-RAY DIFFRACTIONf_chiral_restr0.064396
X-RAY DIFFRACTIONf_plane_restr0.008460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.977-2.02640.27261410.20781690X-RAY DIFFRACTION100
2.0264-2.08120.25991390.19851669X-RAY DIFFRACTION100
2.0812-2.14250.27311400.18131686X-RAY DIFFRACTION100
2.1425-2.21160.23381400.18731690X-RAY DIFFRACTION100
2.2116-2.29070.25361410.18271692X-RAY DIFFRACTION100
2.2907-2.38240.22371420.18221710X-RAY DIFFRACTION100
2.3824-2.49080.23371420.19191697X-RAY DIFFRACTION100
2.4908-2.62210.22621420.18891702X-RAY DIFFRACTION100
2.6221-2.78640.23571420.18161709X-RAY DIFFRACTION100
2.7864-3.00150.22761430.18311709X-RAY DIFFRACTION100
3.0015-3.30340.21841430.18541718X-RAY DIFFRACTION100
3.3034-3.78120.20731440.16211745X-RAY DIFFRACTION100
3.7812-4.76310.19941460.15861754X-RAY DIFFRACTION100
4.7631-45.16270.23041550.19871850X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -1.3472 Å / Origin y: 26.5329 Å / Origin z: -19.9468 Å
111213212223313233
T0.0802 Å20.0263 Å20.0028 Å2-0.0863 Å2-0.015 Å2--0.0846 Å2
L0.1323 °20.0439 °20.1117 °2-0.2089 °2-0.1026 °2--0.1799 °2
S0.0483 Å °0.0408 Å °-0.0404 Å °-0.0024 Å °-0.0162 Å °0.0175 Å °0.0088 Å °0.0136 Å °0.0005 Å °
Refinement TLS groupSelection details: all

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