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- PDB-9igy: Structure of a Chimeric Protein Composed of the SNX5 PhoX Domain ... -

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Basic information

Entry
Database: PDB / ID: 9igy
TitleStructure of a Chimeric Protein Composed of the SNX5 PhoX Domain and the N-terminal domain of NCOA7-AS,crystal form II
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 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,4904
Polymers82,4904
Non-polymers00
Water4,107228
1
A: Sorting nexin-5,Nuclear receptor coactivator 7
C: Sorting nexin-5,Nuclear receptor coactivator 7


Theoretical massNumber of molelcules
Total (without water)41,2452
Polymers41,2452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-34 kcal/mol
Surface area17940 Å2
2
B: Sorting nexin-5,Nuclear receptor coactivator 7
D: Sorting nexin-5,Nuclear receptor coactivator 7


Theoretical massNumber of molelcules
Total (without water)41,2452
Polymers41,2452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-32 kcal/mol
Surface area17730 Å2
Unit cell
Length a, b, c (Å)46.900, 76.990, 110.850
Angle α, β, γ (deg.)90.000, 100.181, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 20622.396 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 30% v/v Jeffamine ED-2001 pH 7.0

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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 PILATUS 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→46.16 Å / Num. obs: 33878 / % possible obs: 97.6 % / Redundancy: 6.79 % / Biso Wilson estimate: 38.59 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.162 / Net I/σ(I): 10.52
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 7.01 % / Mean I/σ(I) obs: 1.64 / Num. unique obs: 4141 / CC1/2: 0.695 / Rrim(I) all: 1.301 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5008refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.16 Å / SU ML: 0.3406 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2621 2015 5.95 %
Rwork0.2273 31843 -
obs0.2294 33858 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5437 0 0 228 5665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215573
X-RAY DIFFRACTIONf_angle_d0.40417538
X-RAY DIFFRACTIONf_chiral_restr0.0527837
X-RAY DIFFRACTIONf_plane_restr0.0032968
X-RAY DIFFRACTIONf_dihedral_angle_d11.32742114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.32311530.30242334X-RAY DIFFRACTION99.92
2.36-2.420.30711330.29642299X-RAY DIFFRACTION99.96
2.42-2.490.30261570.29192313X-RAY DIFFRACTION99.76
2.49-2.570.36661430.29142324X-RAY DIFFRACTION99.72
2.57-2.660.33091510.30462292X-RAY DIFFRACTION99.96
2.66-2.770.3321410.2832347X-RAY DIFFRACTION99.92
2.77-2.90.32341470.26532302X-RAY DIFFRACTION99.88
2.9-3.050.29041380.25542309X-RAY DIFFRACTION100
3.05-3.240.28481540.26732323X-RAY DIFFRACTION99.96
3.24-3.490.28741460.23072330X-RAY DIFFRACTION100
3.49-3.840.21251250.20881932X-RAY DIFFRACTION83.04
3.84-4.40.25071250.19151995X-RAY DIFFRACTION85.17
4.4-5.540.20911520.17162341X-RAY DIFFRACTION99.88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.02144661304-0.06875802656280.8421575885621.70969151321-0.5981904704633.44314292887-0.05505161409730.3461586013660.107006754568-0.0245059242856-0.0671447009984-0.1568521553070.05362015127670.3112257902490.118476361730.311302476032-0.05382763946110.01063307231280.334019757812-0.01364446029570.267165066828.91896466002-3.645434742536.09098629553
21.436905683530.543061095269-1.25188864261.13811045833-1.709386705174.06613268289-0.0351929960524-0.151256452308-0.07547568513970.00533634691007-0.0485920539322-0.0580718883168-0.2413193684210.004853663179250.08826536891460.3525517936260.0277073152837-0.03775375689340.3475503029460.000320597741940.3098415606893.642317166988.7743920185849.7017523486
31.38127262542-0.3127603825161.966587401061.64721117487-0.1009010328484.25264091325-0.118052152712-0.1256877593190.138093725123-0.0193905414276-0.1046567551040.139213167363-0.185500473466-0.2710286044450.2018992593910.256542850927-0.0805264638375-0.009513486186840.364283470102-0.02779113688970.30343269052-11.45279666996.29865979223-7.65893659782
42.5650860850.623967694479-3.557275741980.112946614611-1.84116353473.65110746321-0.1944981008140.305167744199-0.230231825792-0.00959164943286-0.09452706383120.03205895930790.108513669923-0.4628154540970.1885371283670.332537478839-0.0454132399286-0.01379437377820.502516182119-0.02962374781250.311985602387-19.0427630912-2.2600280645258.8247121679
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11Chain AAA29 - 1991 - 169
22Chain BBB29 - 1961 - 166
33Chain CCC29 - 1971 - 166
44Chain DDD29 - 1951 - 164

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