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- PDB-9iae: Structure of a Chimeric Protein Composed of the SNX5 PX Domain an... -

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Basic information

Entry
Database: PDB / ID: 9iae
TitleStructure of a Chimeric Protein Composed of the SNX5 PX Domain and the N-Terminal Region of NCOA7-AS, crystal form I
ComponentsSorting nexin-5,Nuclear receptor coactivator 7
KeywordsUNKNOWN FUNCTION / SNX5 / NCOA7-AS / chimeric protein
Function / homology
Function and homology information


retromer, tubulation complex / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / phosphatidylinositol-5-phosphate binding / retromer complex / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding ...retromer, tubulation complex / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / phosphatidylinositol-5-phosphate binding / retromer complex / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / retrograde transport, endosome to Golgi / Golgi Associated Vesicle Biogenesis / dynactin binding / brush border / regulation of macroautophagy / positive regulation of insulin receptor signaling pathway / D1 dopamine receptor binding / phagocytic cup / negative regulation of blood pressure / ruffle / phosphatidylinositol binding / intracellular protein transport / cytoplasmic side of plasma membrane / endosome / cadherin binding / intracellular membrane-bounded organelle / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cytosol
Similarity search - Function
SNX5, PX domain / TLDc domain / Sorting nexin-5 / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / PX domain profile. ...SNX5, PX domain / TLDc domain / Sorting nexin-5 / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily
Similarity search - Domain/homology
Nuclear receptor coactivator 7 / Sorting nexin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsArnaud-Arnould, M. / Rebendenne, A. / Tauziet, M. / Urbach, S. / El Koulali, K. / Ricci, E. / Wencker, M. / Moncorge, O. / Blaise, M. / Goujon, C.
Funding support France, European Union, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE15-0010-02 France
European Research Council (ERC)759226European Union
CitationJournal: Biorxiv / Year: 2025
Title: SNX-BAR proteins 5 and 6 are required for NCOA7-AS antiviral activity against influenza A virus
Authors: Arnaud-Arnould, M. / Rebendenne, A. / Tauziet, M. / Urbach, S. / El Koulali, K. / Ricci, E. / Wencker, M. / Moncorge, O. / Blaise, M. / Goujon, C.
History
DepositionFeb 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-5,Nuclear receptor coactivator 7


Theoretical massNumber of molelcules
Total (without water)20,6991
Polymers20,6991
Non-polymers00
Water2,900161
1
A: Sorting nexin-5,Nuclear receptor coactivator 7

A: Sorting nexin-5,Nuclear receptor coactivator 7


Theoretical massNumber of molelcules
Total (without water)41,3972
Polymers41,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3280 Å2
ΔGint-22 kcal/mol
Surface area20340 Å2
Unit cell
Length a, b, c (Å)63.130, 63.130, 101.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-121-

PHE

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Components

#1: Protein Sorting nexin-5,Nuclear receptor coactivator 7


Mass: 20698.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This protein is a fusion protein and thus a chimeric protein made of the human Phox domain of the SNX5 protein and the N-terminal domain of the human NCOA7-AS protein. The first glycine is ...Details: This protein is a fusion protein and thus a chimeric protein made of the human Phox domain of the SNX5 protein and the N-terminal domain of the human NCOA7-AS protein. The first glycine is an additionnal residue coming from the TEV protease cleavage site,This protein is a fusion protein and thus a chimeric protein made of the human Phox domain of the SNX5 protein and the N-terminal domain of the human NCOA7-AS protein. The first glycine is an additionnal residue coming from the TEV protease cleavage site,This protein is a fusion protein and thus a chimeric protein made of the human Phox domain of the SNX5 protein and the N-terminal domain of the human NCOA7-AS protein. The first glycine is an additionnal residue coming from the TEV protease cleavage site,This protein is a fusion protein and thus a chimeric protein made of the human Phox domain of the SNX5 protein and the N-terminal domain of the human NCOA7-AS protein. The first glycine is an additionnal residue coming from the TEV protease cleavage site
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX5, NCOA7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y5X3, UniProt: H0Y6T0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.84 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Calcium acetate hydrate 0.1 M Sodium Cacodylate pH 6.5 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.13 Å / Num. obs: 10729 / % possible obs: 98.6 % / Redundancy: 19.6 % / Biso Wilson estimate: 37.38 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.193 / Net I/σ(I): 16.02
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 20.14 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1269 / CC1/2: 0.755 / Rrim(I) all: 1.66 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5008refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.13 Å / SU ML: 0.289 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.8117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2404 1076 10.03 %
Rwork0.2011 9651 -
obs0.2053 10727 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 0 161 1584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241472
X-RAY DIFFRACTIONf_angle_d0.45431991
X-RAY DIFFRACTIONf_chiral_restr0.056217
X-RAY DIFFRACTIONf_plane_restr0.004258
X-RAY DIFFRACTIONf_dihedral_angle_d11.9364564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.34621320.2471200X-RAY DIFFRACTION100
2.4-2.530.27091350.23871218X-RAY DIFFRACTION100
2.53-2.690.31591340.25911175X-RAY DIFFRACTION100
2.69-2.90.32581330.21921219X-RAY DIFFRACTION99.93
2.9-3.190.29321330.22461197X-RAY DIFFRACTION100
3.19-3.640.26681360.20111205X-RAY DIFFRACTION100
3.7-4.60.19111250.17481124X-RAY DIFFRACTION99.28
Refinement TLS params.Method: refined / Origin x: -14.1949430078 Å / Origin y: 4.29068930634 Å / Origin z: 7.24842229869 Å
111213212223313233
T0.208113452734 Å2-0.000287239450869 Å2-0.0324235281422 Å2-0.195205068989 Å20.0138581150453 Å2--0.337392236286 Å2
L0.696400967281 °2-0.0458311419498 °2-0.116390790953 °2-0.635432556345 °20.313275386798 °2--1.43539320383 °2
S0.000682964658419 Å °-0.0182033831126 Å °-0.0571614235663 Å °-0.0064757888592 Å °-0.02996971155 Å °0.0576199626006 Å °0.0813061098127 Å °0.00169086104558 Å °0.040027251924 Å °
Refinement TLS groupSelection details: Chain A

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