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- PDB-6n5x: Crystal structure of the SNX5 PX domain in complex with the CI-MP... -

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Basic information

Entry
Database: PDB / ID: 6n5x
TitleCrystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121 - Form 1)
ComponentsSorting nexin-5,Cation-independent mannose-6-phosphate receptor
KeywordsENDOCYTOSIS / sorting nexin / SNX / endosome
Function / homology
Function and homology information


retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity ...retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / retromer complex / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding / retrograde transport, endosome to Golgi / lysosomal transport / phagocytic cup / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / dynactin binding / mannose binding / endocytic vesicle / G-protein alpha-subunit binding / regulation of macroautophagy / animal organ regeneration / response to retinoic acid / positive regulation of insulin receptor signaling pathway / transport vesicle / ruffle / receptor-mediated endocytosis / phosphatidylinositol binding / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / intracellular protein transport / trans-Golgi network / cytoplasmic side of plasma membrane / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome membrane / endosome / cadherin binding / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / MRH domain / MRH domain profile. ...SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / AH/BAR domain superfamily / Kringle-like fold
Similarity search - Domain/homology
Chem-JEF / Cation-independent mannose-6-phosphate receptor / Sorting nexin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
AuthorsCollins, B. / Paul, B. / Weeratunga, S.
CitationJournal: Nat.Cell Biol. / Year: 2019
Title: Molecular identification of a BAR domain-containing coat complex for endosomal recycling of transmembrane proteins.
Authors: Simonetti, B. / Paul, B. / Chaudhari, K. / Weeratunga, S. / Steinberg, F. / Gorla, M. / Heesom, K.J. / Bashaw, G.J. / Collins, B.M. / Cullen, P.J.
History
DepositionNov 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-5,Cation-independent mannose-6-phosphate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7143
Polymers21,0241
Non-polymers6902
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.653, 64.730, 69.251
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,Cation-independent mannose-6-phosphate receptor / M6PR / 300 kDa mannose 6-phosphate receptor / MPR 300 / Insulin-like growth factor 2 receptor / ...M6PR / 300 kDa mannose 6-phosphate receptor / MPR 300 / Insulin-like growth factor 2 receptor / Insulin-like growth factor II receptor / IGF-II receptor / M6P/IGF2 receptor / M6P/IGF2R


Mass: 21024.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX5, IGF2R, MPRI / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X3, UniProt: P11717
#2: 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
#3: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H63NO10
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 75% of 0.2 M (NH4)SO4, 0.1 M MES pH 6.5, 30% (w/v) PEG5000 MME + 15% glycerol + 40% v/v Polypropylene glycol P400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97803 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97803 Å / Relative weight: 1
ReflectionResolution: 2.05→48.6 Å / Num. obs: 14255 / % possible obs: 99.7 % / Redundancy: 13.2 % / Net I/σ(I): 15.9
Reflection shellResolution: 2.05→2.11 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.051→47.289 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.2342 710 5.01 %
Rwork0.2004 --
obs0.2021 14181 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.051→47.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 15 81 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031433
X-RAY DIFFRACTIONf_angle_d0.6541934
X-RAY DIFFRACTIONf_dihedral_angle_d17.704870
X-RAY DIFFRACTIONf_chiral_restr0.041210
X-RAY DIFFRACTIONf_plane_restr0.004249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0508-2.20910.27631280.22592622X-RAY DIFFRACTION98
2.2091-2.43140.2621560.21072643X-RAY DIFFRACTION100
2.4314-2.78320.28171510.20612653X-RAY DIFFRACTION100
2.7832-3.50640.25451330.20342709X-RAY DIFFRACTION100
3.5064-47.30110.19881420.19172844X-RAY DIFFRACTION100

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