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- PDB-8a1g: Structure of the SNX1-SNX5 complex -

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Basic information

Entry
Database: PDB / ID: 8a1g
TitleStructure of the SNX1-SNX5 complex
Components
  • Sorting nexin-1
  • Sorting nexin-5
KeywordsPROTEIN TRANSPORT / SNX / Membrane trafficking. / TRANSPORT PROTEIN
Function / homology
Function and homology information


retromer, tubulation complex / lamellipodium morphogenesis / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / leptin receptor binding / tubular endosome / macropinocytic cup / early endosome to Golgi transport / phosphatidylinositol-5-phosphate binding ...retromer, tubulation complex / lamellipodium morphogenesis / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / leptin receptor binding / tubular endosome / macropinocytic cup / early endosome to Golgi transport / phosphatidylinositol-5-phosphate binding / transferrin receptor binding / retromer complex / phosphatidylinositol-4-phosphate binding / retrograde transport, endosome to Golgi / phosphatidylinositol-3,5-bisphosphate binding / epidermal growth factor receptor binding / Golgi Associated Vesicle Biogenesis / brush border / dynactin binding / regulation of macroautophagy / positive regulation of insulin receptor signaling pathway / D1 dopamine receptor binding / phagocytic cup / negative regulation of blood pressure / ruffle / phosphatidylinositol binding / insulin receptor binding / intracellular protein transport / receptor internalization / cytoplasmic side of plasma membrane / positive regulation of protein catabolic process / lamellipodium / early endosome membrane / vesicle / lysosome / endosome membrane / endosome / cadherin binding / protein heterodimerization activity / intracellular membrane-bounded organelle / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / protein-containing complex / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Sorting nexin, N-terminal / Sorting nexin-1 / Sorting Nexin 1, PX domain / Sorting nexin, N-terminal domain / SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Arfaptin homology (AH) domain/BAR domain ...Sorting nexin, N-terminal / Sorting nexin-1 / Sorting Nexin 1, PX domain / Sorting nexin, N-terminal domain / SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Arfaptin homology (AH) domain/BAR domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
N-PROPANOL / Sorting nexin-1 / Sorting nexin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsLopez-Robles, C. / Scaramuzza, S. / Astorga-Simon, E.N. / Banos-Mateos, S. / Vidaurrazaga, A. / Rojas, A.L. / Castano, D. / Hierro, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessPID2020-119132GB-I00 Spain
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Architecture of the ESCPE-1 membrane coat.
Authors: Carlos Lopez-Robles / Stefano Scaramuzza / Elsa N Astorga-Simon / Morié Ishida / Chad D Williamson / Soledad Baños-Mateos / David Gil-Carton / Miguel Romero-Durana / Ander Vidaurrazaga / ...Authors: Carlos Lopez-Robles / Stefano Scaramuzza / Elsa N Astorga-Simon / Morié Ishida / Chad D Williamson / Soledad Baños-Mateos / David Gil-Carton / Miguel Romero-Durana / Ander Vidaurrazaga / Juan Fernandez-Recio / Adriana L Rojas / Juan S Bonifacino / Daniel Castaño-Díez / Aitor Hierro /
Abstract: Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1) ...Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1), which rescues transmembrane proteins from the endolysosomal pathway for transport to the trans-Golgi network and the plasma membrane. This rescue entails the formation of recycling tubules through ESCPE-1 recruitment, cargo capture, coat assembly and membrane sculpting by mechanisms that remain largely unknown. Herein, we show that ESCPE-1 has a single-layer coat organization and suggest how synergistic interactions between ESCPE-1 protomers, phosphoinositides and cargo molecules result in a global arrangement of amphipathic helices to drive tubule formation. Our results thus define a key process of tubule-based endosomal sorting.
History
DepositionJun 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-1
B: Sorting nexin-1
C: Sorting nexin-5
D: Sorting nexin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,50511
Polymers102,0854
Non-polymers4217
Water37821
1
A: Sorting nexin-1
C: Sorting nexin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2235
Polymers51,0422
Non-polymers1803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-46 kcal/mol
Surface area22370 Å2
MethodPISA
2
B: Sorting nexin-1
D: Sorting nexin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2836
Polymers51,0422
Non-polymers2404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-45 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.780, 188.470, 51.600
Angle α, β, γ (deg.)90.000, 89.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sorting nexin-1


Mass: 26397.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13596
#2: Protein Sorting nexin-5


Mass: 24644.385 Da / Num. of mol.: 2
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
#3: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 11%PVA, 10% 1-propanol, 100mM Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.07158 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07158 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.5→49.77 Å / Num. obs: 32404 / % possible obs: 98.5 % / Redundancy: 5.173 % / Biso Wilson estimate: 61.213 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.137 / Rrim(I) all: 0.151 / Χ2: 0.707 / Net I/σ(I): 7.15 / Num. measured all: 167629
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.654.5830.8891.6922877528549920.6320.99894.5
2.65-2.834.7280.622.5323293499449270.80.69498.7
2.83-3.064.9140.3724.0422635464346060.9270.41599.2
3.06-3.355.3050.266.0522524426242460.960.28799.6
3.35-3.745.3370.169.120740390738860.980.17799.5
3.74-4.325.4840.11312.2518724342534140.990.12499.7
4.32-5.295.5640.10113.4315830288628450.9920.11198.6
5.29-7.475.830.10713.2213083225622440.9920.11799.5
7.47-49.776.3690.09617.137923125312440.9910.10599.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18-38555-000refinement
PDB_EXTRACT3.25data extraction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→49.77 Å / Cross valid method: THROUGHOUT / σ(F): 38.03 / Phase error: 30.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2845 1491 4.97 %
Rwork0.2427 28514 -
obs0.2492 29990 91.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.88 Å2 / Biso mean: 55.467 Å2 / Biso min: 13.72 Å2
Refinement stepCycle: final / Resolution: 2.5→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6702 0 84 21 6807
Biso mean--58.4 38.8 -
Num. residues----804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.580.3471660.31681158122439
2.58-2.670.3661250.31122089221471
2.67-2.780.35391520.29842728288092
2.78-2.910.29621400.28822807294795
2.91-3.060.35481070.28022829293695
3.06-3.250.34381270.27022861298895
3.25-3.50.2811430.24642787293095
3.5-3.860.25821700.22352807297794
3.86-4.410.26641520.20612797294994
4.42-5.560.26751410.24452815295694
5.56-49.770.31291530.2392836298994

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