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- PDB-8abq: Structure of the SNX1-SNX5 complex, Pt derivative -

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Basic information

Entry
Database: PDB / ID: 8abq
TitleStructure of the SNX1-SNX5 complex, Pt derivative
Components
  • Sorting nexin-1
  • Sorting nexin-5
KeywordsTRANSPORT PROTEIN / SNX / Membrane trafficking / PROTEIN TRANSPORT
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 / endosome membrane / 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
: / Sorting nexin-1 / Sorting nexin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.81 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
Ministry of Economy and Competitiveness (MINECO)PID2020-119132GB-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
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _struct.title
Revision 1.2Jul 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 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
C: Sorting nexin-5
B: Sorting nexin-1
D: Sorting nexin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,64512
Polymers102,0854
Non-polymers1,5618
Water724
1
A: Sorting nexin-1
C: Sorting nexin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6285
Polymers51,0422
Non-polymers5853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-92 kcal/mol
Surface area22840 Å2
2
B: Sorting nexin-1
D: Sorting nexin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0187
Polymers51,0422
Non-polymers9755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-138 kcal/mol
Surface area23580 Å2
Unit cell
Length a, b, c (Å)52.690, 51.470, 192.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number3
Space group name H-MP121

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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-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
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: 2.8→192.319 Å / Num. all: 24815 / Num. obs: 24815 / % possible obs: 96.2 % / Redundancy: 6.3 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.095 / Rsym value: 0.07 / Net I/av σ(I): 4.8 / Net I/σ(I): 10.3 / Num. measured all: 155315
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.956.20.9910.82220536090.4691.1820.9911.796.1
2.95-3.136.50.7612188733690.3470.90.762.396.1
3.13-3.356.10.4731.61948132090.2250.5650.4733.396.3
3.35-3.616.30.2353.21868029820.110.2790.2356.296.2
3.61-3.966.30.1245.81736027370.0580.1480.12410.695.8
3.96-4.436.10.0689.81528624970.0320.0820.06815.997
4.43-5.116.40.04512.81422222370.0220.0560.04519.696.9
5.11-6.266.40.05511.71197718740.030.0770.05519.796
6.26-8.856.40.03912931214610.0220.0590.0392695.5
8.85-51.4695.80.03311.349058400.0270.060.0333195.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.22data scaling
PHENIX1.18-3855-000refinement
PDB_EXTRACT3.25data extraction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.81→51.47 Å / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 33.72 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3055 1071 5.12 %
Rwork0.2521 19876 -
obs0.2571 20925 81.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 231.88 Å2 / Biso mean: 72.0214 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 2.81→51.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 8 4 6660
Biso mean--171.13 41.25 -
Num. residues----797
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.81-2.960.3242610.305188394424
2.96-3.140.40721090.29542325243465
3.14-3.380.35492040.27993168337287
3.38-3.720.32761950.2593327352290
3.73-4.260.32511540.25853336349092
4.26-5.370.27761530.23293398355192
5.37-51.470.27721730.25013439361290

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