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- PDB-7sr2: Crystal structure of the human SNX25 regulator of G-protein signa... -

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Basic information

Entry
Database: PDB / ID: 7sr2
TitleCrystal structure of the human SNX25 regulator of G-protein signalling (RGS) domain
ComponentsSorting nexin-25
KeywordsSIGNALING PROTEIN / endosome / sorting nexin / SNX / RGS / SNX25 / lipid droplet
Function / homology
Function and homology information


phosphatidylinositol binding / negative regulation of transforming growth factor beta receptor signaling pathway / membrane => GO:0016020 / intracellular membrane-bounded organelle
Similarity search - Function
Sorting nexin-25 / 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 ...Sorting nexin-25 / 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 / PX domain superfamily / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily
Similarity search - Domain/homology
ACETATE ION / LEUCINE / Sorting nexin-25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsCollins, B.M. / Paul, B. / Weeratunga, S.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200102551 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1136021 Australia
CitationJournal: Front Cell Dev Biol / Year: 2022
Title: Structural Predictions of the SNX-RGS Proteins Suggest They Belong to a New Class of Lipid Transfer Proteins.
Authors: Paul, B. / Weeratunga, S. / Tillu, V.A. / Hariri, H. / Henne, W.M. / Collins, B.M.
History
DepositionNov 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1345
Polymers29,8782
Non-polymers2563
Water54030
1
A: Sorting nexin-25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0042
Polymers14,9391
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sorting nexin-25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1293
Polymers14,9391
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.035, 75.864, 51.109
Angle α, β, γ (deg.)90.000, 109.270, 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-25 /


Mass: 14938.986 Da / Num. of mol.: 2 / Mutation: C526A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX25 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A494C0S0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 0.1 M calcium acetate, 0.1 M sodium cacodylate, pH 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: 0.95364 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.42→48.25 Å / Num. obs: 11882 / % possible obs: 97.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 43.54 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.07 / Net I/σ(I): 7.2
Reflection shellResolution: 2.42→2.52 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7264 / CC1/2: 0.631 / Rpim(I) all: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SR1

7sr1


Resolution: 2.42→41.57 Å / SU ML: 0.371 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247 1186 10 %
Rwork0.2108 10674 -
obs0.2144 11860 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.86 Å2
Refinement stepCycle: LAST / Resolution: 2.42→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 13 30 2026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072037
X-RAY DIFFRACTIONf_angle_d0.90362736
X-RAY DIFFRACTIONf_chiral_restr0.0583287
X-RAY DIFFRACTIONf_plane_restr0.0058348
X-RAY DIFFRACTIONf_dihedral_angle_d19.8216257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.530.37441350.32791216X-RAY DIFFRACTION90.61
2.53-2.670.3071470.26641330X-RAY DIFFRACTION98.27
2.67-2.830.28241500.24381340X-RAY DIFFRACTION98.48
2.83-3.050.27931490.23891344X-RAY DIFFRACTION98.42
3.05-3.360.24981500.20111347X-RAY DIFFRACTION98.55
3.36-3.840.25591490.18961348X-RAY DIFFRACTION99.07
3.85-4.840.20871510.17961360X-RAY DIFFRACTION98.95
4.84-41.570.21831550.20621389X-RAY DIFFRACTION99.29

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