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- PDB-8hql: Crystal structure of mouse SNX25 PX domain -

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Basic information

Entry
Database: PDB / ID: 8hql
TitleCrystal structure of mouse SNX25 PX domain
ComponentsSorting nexin-25
KeywordsPROTEIN TRANSPORT / PX domain / Sorting nexins / SNX25
Function / homology
Function and homology information


receptor catabolic process / type I transforming growth factor beta receptor binding / phosphatidylinositol binding / negative regulation of transforming growth factor beta receptor signaling pathway / protein transport / endosome / endosome membrane
Similarity search - Function
SNX25, PX domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain ...SNX25, PX domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily
Similarity search - Domain/homology
ACETIC ACID / Sorting nexin-25
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYu, Z. / Xu, J. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171213 China
CitationJournal: Redox Biol / Year: 2024
Title: Redox-modulated SNX25 as a novel regulator of GPCR-G protein signaling from endosomes.
Authors: Zhang, Y. / Yu, Z. / Sun, M. / Du, R. / Gao, H. / Dai, Q. / Dong, Y. / Liu, C. / Yin, M. / Xu, T. / Zhang, X. / Liu, J. / Xu, J.
History
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 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-25
B: Sorting nexin-25
C: Sorting nexin-25
D: Sorting nexin-25
E: Sorting nexin-25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,85743
Polymers74,2205
Non-polymers5,63738
Water2,414134
1
A: Sorting nexin-25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,29311
Polymers14,8441
Non-polymers1,44910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sorting nexin-25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3098
Polymers14,8441
Non-polymers1,4657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sorting nexin-25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6389
Polymers14,8441
Non-polymers7948
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sorting nexin-25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9858
Polymers14,8441
Non-polymers1,1417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sorting nexin-25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6327
Polymers14,8441
Non-polymers7886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: Sorting nexin-25
B: Sorting nexin-25
hetero molecules

A: Sorting nexin-25
B: Sorting nexin-25
hetero molecules

D: Sorting nexin-25
hetero molecules

D: Sorting nexin-25
hetero molecules

C: Sorting nexin-25
E: Sorting nexin-25
hetero molecules

C: Sorting nexin-25
E: Sorting nexin-25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,71486
Polymers148,43910
Non-polymers11,27576
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation10_564-y,-x+1,-z-1/61
crystal symmetry operation5_554y,-x+y,z-1/61
crystal symmetry operation8_555x-y,-y,-z1
Buried area28670 Å2
ΔGint-133 kcal/mol
Surface area59350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.680, 92.680, 449.521
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11D-706-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Sorting nexin-25


Mass: 14843.917 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snx25 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZT31

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Non-polymers , 5 types, 172 molecules

#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.8 M Magnesium sulfate hydrate, 0.1 M Sodium acetate trihydrate pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→39.97 Å / Num. obs: 46187 / % possible obs: 99.9 % / Redundancy: 7.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.029 / Rrim(I) all: 0.084 / Net I/σ(I): 16.6 / Num. measured all: 360104
Reflection shellResolution: 2.4→2.48 Å / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.78 / Num. measured all: 35765 / Num. unique obs: 4398 / CC1/2: 0.804 / Rpim(I) all: 0.285 / Rrim(I) all: 0.832 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→39 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.357 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24186 2319 5 %RANDOM
Rwork0.19858 ---
obs0.20074 43809 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.4→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4851 0 224 134 5209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135135
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175040
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.6386844
X-RAY DIFFRACTIONr_angle_other_deg1.3761.57511617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73222.463272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26515916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1311535
X-RAY DIFFRACTIONr_chiral_restr0.0910.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021186
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.0195.3552399
X-RAY DIFFRACTIONr_mcbond_other7.025.352396
X-RAY DIFFRACTIONr_mcangle_it9.7688.0082984
X-RAY DIFFRACTIONr_mcangle_other9.7678.012985
X-RAY DIFFRACTIONr_scbond_it7.966.1732736
X-RAY DIFFRACTIONr_scbond_other7.9596.1732737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.9348.8463861
X-RAY DIFFRACTIONr_long_range_B_refined13.65360.9765393
X-RAY DIFFRACTIONr_long_range_B_other13.65260.995394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35450.12
12B35450.12
21A36500.13
22C36500.13
31A35830.11
32D35830.11
41A36520.11
42E36520.11
51B35210.12
52C35210.12
61B36700.09
62D36700.09
71B35490.12
72E35490.12
81C35530.12
82D35530.12
91C36290.12
92E36290.12
101D36010.1
102E36010.1
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 175 -
Rwork0.29 3132 -
obs--99.79 %

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