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- PDB-6n5z: Crystal structure of the SNX5 PX domain in complex with the Sema4C -

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Basic information

Entry
Database: PDB / ID: 6n5z
TitleCrystal structure of the SNX5 PX domain in complex with the Sema4C
ComponentsSorting nexin-5,Semaphorin-4C
KeywordsENDOCYTOSIS / sorting nexin / SNX / endosome
Function / homology
Function and homology information


cell migration in hindbrain / retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / semaphorin receptor binding / macropinocytic cup / muscle cell differentiation / positive regulation of stress-activated MAPK cascade / negative regulation of axon extension involved in axon guidance ...cell migration in hindbrain / retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / semaphorin receptor binding / macropinocytic cup / muscle cell differentiation / positive regulation of stress-activated MAPK cascade / negative regulation of axon extension involved in axon guidance / retromer complex / chemorepellent activity / retrograde transport, endosome to Golgi / neural crest cell migration / phagocytic cup / negative chemotaxis / Golgi Associated Vesicle Biogenesis / dynactin binding / plasma membrane => GO:0005886 / semaphorin-plexin signaling pathway / regulation of macroautophagy / positive regulation of insulin receptor signaling pathway / ruffle / phosphatidylinositol binding / cerebellum development / neural tube closure / axon guidance / postsynaptic density membrane / intracellular protein transport / cytoplasmic side of plasma membrane / synaptic vesicle membrane / postsynaptic density / endosome / positive regulation of cell migration / cadherin binding / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / extracellular space / 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 / Semaphorin / PX domain profile. / PX domain / Phox homology / PX domain superfamily ...SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Semaphorin / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / AH/BAR domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Semaphorin-4C / Sorting nexin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-5,Semaphorin-4C
B: Sorting nexin-5,Semaphorin-4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6553
Polymers40,6202
Non-polymers351
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-19 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.520, 87.698, 100.487
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,Semaphorin-4C


Mass: 20309.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX5, SEMA4C, KIAA1739, SEMAI, UNQ5855/PRO34487 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X3, UniProt: Q9C0C4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 25% PEG3350, 0.1 M Tris (pH 8.0), 5% Cymal-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.45→43.6 Å / Num. obs: 14370 / % possible obs: 99.5 % / Redundancy: 7 % / Net I/σ(I): 14.2
Reflection shellResolution: 2.45→2.55 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→43.596 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.07
RfactorNum. reflection% reflection
Rfree0.2736 1345 9.96 %
Rwork0.2248 --
obs0.2297 13501 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→43.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 1 74 2656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092651
X-RAY DIFFRACTIONf_angle_d1.3333592
X-RAY DIFFRACTIONf_dihedral_angle_d8.3461601
X-RAY DIFFRACTIONf_chiral_restr0.069390
X-RAY DIFFRACTIONf_plane_restr0.01463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4493-2.53690.35131200.29971058X-RAY DIFFRACTION83
2.5369-2.63840.36671270.29431100X-RAY DIFFRACTION86
2.6384-2.75850.37011150.27871128X-RAY DIFFRACTION89
2.7585-2.90390.30391300.25741173X-RAY DIFFRACTION91
2.9039-3.08580.3561330.27671215X-RAY DIFFRACTION95
3.0858-3.32390.3121390.26291255X-RAY DIFFRACTION97
3.3239-3.65830.26391380.22761244X-RAY DIFFRACTION96
3.6583-4.18730.25151430.20071283X-RAY DIFFRACTION98
4.1873-5.27410.23651440.1851302X-RAY DIFFRACTION99
5.2741-43.60250.24191560.20791398X-RAY DIFFRACTION99

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