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- PDB-8ttv: Structure of SNX27 FERM complexed with Fam21A repeat 20 (1289-1302) -

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Basic information

Entry
Database: PDB / ID: 8ttv
TitleStructure of SNX27 FERM complexed with Fam21A repeat 20 (1289-1302)
Components
  • Fam21A repeat 20 peptide
  • Sorting nexin-27
KeywordsTRANSPORT PROTEIN / SNX27 / FAM21 / WASH / sorting nexin / endosome / protein transport
Function / homology
Function and homology information


establishment of natural killer cell polarity / WASH complex / phosphatidylinositol phosphate binding / retromer complex binding / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to endosome / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / retrograde transport, endosome to Golgi ...establishment of natural killer cell polarity / WASH complex / phosphatidylinositol phosphate binding / retromer complex binding / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to endosome / regulation of synapse maturation / endocytic recycling / phosphatidylinositol-3-phosphate binding / retrograde transport, endosome to Golgi / endosomal transport / endosome to lysosome transport / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / phosphatidylinositol binding / intracellular protein transport / Schaffer collateral - CA1 synapse / protein transport / early endosome membrane / early endosome / endosome / intracellular membrane-bounded organelle / glutamatergic synapse / nucleolus / signal transduction / plasma membrane / cytosol
Similarity search - Function
FAM21/CAPZIP domain / WASH complex subunit CAP-Z interacting, central region / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. ...FAM21/CAPZIP domain / WASH complex subunit CAP-Z interacting, central region / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / WASH complex subunit 2A / Sorting nexin-27
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGuo, Q. / Chen, K.-E. / Collins, B.M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1156493 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1136021 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structural basis for coupling of the WASH subunit FAM21 with the endosomal SNX27-Retromer complex.
Authors: Guo, Q. / Chen, K.E. / Gimenez-Andres, M. / Jellett, A.P. / Gao, Y. / Simonetti, B. / Liu, M. / Danson, C.M. / Heesom, K.J. / Cullen, P.J. / Collins, B.M.
History
DepositionAug 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-27
B: Fam21A repeat 20 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6183
Polymers32,5122
Non-polymers1061
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint0 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.965, 74.200, 105.189
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-27


Mass: 30947.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX27 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96L92
#2: Protein/peptide Fam21A repeat 20 peptide


Mass: 1563.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q641Q2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Sodium Cacodylate pH 6.5 and 22.5% PEG4000 / PH range: 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→42.91 Å / Num. obs: 20806 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.101 / Rrim(I) all: 0.26 / Χ2: 0.39 / Net I/σ(I): 6.7 / Num. measured all: 139518
Reflection shellResolution: 2→2.05 Å / % possible obs: 94.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 2.161 / Num. measured all: 8637 / Num. unique obs: 1385 / CC1/2: 0.205 / Rpim(I) all: 0.943 / Rrim(I) all: 2.366 / Χ2: 0.18 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.91 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 1998 10 %
Rwork0.2068 --
obs0.2124 19979 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 7 116 2294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092247
X-RAY DIFFRACTIONf_angle_d1.0093039
X-RAY DIFFRACTIONf_dihedral_angle_d7.492294
X-RAY DIFFRACTIONf_chiral_restr0.063322
X-RAY DIFFRACTIONf_plane_restr0.009384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.32151000.2847898X-RAY DIFFRACTION71
2.05-2.110.32061260.26941139X-RAY DIFFRACTION86
2.11-2.170.30081380.26971238X-RAY DIFFRACTION95
2.17-2.240.331470.25111323X-RAY DIFFRACTION99
2.24-2.320.31251440.24651289X-RAY DIFFRACTION99
2.32-2.410.29511430.24431299X-RAY DIFFRACTION100
2.41-2.520.3451490.27041337X-RAY DIFFRACTION100
2.52-2.660.33751450.27231305X-RAY DIFFRACTION100
2.66-2.820.27961450.22141309X-RAY DIFFRACTION100
2.82-3.040.26991480.22341327X-RAY DIFFRACTION100
3.04-3.350.27131490.1861345X-RAY DIFFRACTION100
3.35-3.830.23171520.17171359X-RAY DIFFRACTION100
3.83-4.820.18471520.14931370X-RAY DIFFRACTION100
4.82-42.910.24341600.18531443X-RAY DIFFRACTION100

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