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- PDB-7wf9: Crystal structure of mouse SNX25 RGS domain in space group P41212 -

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Basic information

Entry
Database: PDB / ID: 7wf9
TitleCrystal structure of mouse SNX25 RGS domain in space group P41212
ComponentsSorting nexin-25
KeywordsPROTEIN TRANSPORT / Sorting nexin / SNX25 / RGS
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 membrane / endosome
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. / Regulator of G protein signaling domain / RGS, subdomain 2 ...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. / Regulator of G protein signaling domain / RGS, subdomain 2 / PX domain profile. / PX domain / Phox homology / RGS domain / PX domain superfamily / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhang, Y. / Xu, J. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171213 China
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Studies Reveal Unique Non-canonical Regulators of G Protein Signaling Homology (RH) Domains in Sorting Nexins.
Authors: Zhang, Y. / Chen, R. / Dong, Y. / Zhu, J. / Su, K. / Liu, J. / Xu, J.
History
DepositionDec 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-25
B: Sorting nexin-25


Theoretical massNumber of molelcules
Total (without water)30,1602
Polymers30,1602
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-60 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.877, 70.877, 148.539
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 283 - 402 / Label seq-ID: 4 - 123

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Sorting nexin-25


Mass: 15080.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snx25 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3ZT31
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.15M DL-Malic acid pH 7.0, 20%(w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.55→74.27 Å / Num. obs: 12971 / % possible obs: 99.5 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.022 / Rrim(I) all: 0.062 / Net I/σ(I): 13.7 / Num. measured all: 101520 / Scaling rejects: 922
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.55-2.668.10.71253915410.8620.2670.7522.599.5
8.82-74.276.50.04824653820.9980.0190.05123.397.6

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WF8

7wf8


Resolution: 2.55→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 30.224 / SU ML: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.419 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 631 4.9 %RANDOM
Rwork0.2228 ---
obs0.2248 12228 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.34 Å2 / Biso mean: 91.589 Å2 / Biso min: 59.32 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å20 Å20 Å2
2---2.83 Å20 Å2
3---5.65 Å2
Refinement stepCycle: final / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 0 0 2 2066
Biso mean---76.35 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132105
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181994
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.6462824
X-RAY DIFFRACTIONr_angle_other_deg1.2861.584596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0485243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95422.576132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.31515409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6221516
X-RAY DIFFRACTIONr_chiral_restr0.080.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02517
Refine LS restraints NCS

Ens-ID: 1 / Number: 3400 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.55→2.615 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 49 -
Rwork0.364 872 -
all-921 -
obs--99.35 %
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)
12.01791.86380.43324.58120.63090.5464-0.0402-0.1376-0.18310.24520.1162-0.2779-0.01720.1834-0.0760.1778-0.11690.01910.2393-0.01280.0589-41.2433-18.48843.1106
22.15192.91970.65474.38670.78160.80610.0483-0.1837-0.03640.01030.0211-0.00580.0582-0.0385-0.06940.0979-0.08690.02960.23120.00650.1048-49.0259-22.55195.5701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A283 - 405
2X-RAY DIFFRACTION2B282 - 403

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