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- PDB-2yps: Crystal structure of the PX domain of human sorting nexin 3 -

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Basic information

Entry
Database: PDB / ID: 2yps
TitleCrystal structure of the PX domain of human sorting nexin 3
ComponentsSORTING NEXIN-3
KeywordsPROTEIN TRANSPORT / ENDOSOME
Function / homology
Function and homology information


negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / protein to membrane docking / negative regulation of protein transport / membrane invagination / WNT ligand biogenesis and trafficking / intralumenal vesicle formation / retromer complex binding / phosphatidylinositol-5-phosphate binding / retromer complex ...negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / protein to membrane docking / negative regulation of protein transport / membrane invagination / WNT ligand biogenesis and trafficking / intralumenal vesicle formation / retromer complex binding / phosphatidylinositol-5-phosphate binding / retromer complex / negative regulation of viral entry into host cell / phosphatidylinositol-3-phosphate binding / early phagosome / endocytic recycling / regulation of Wnt signaling pathway / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / negative regulation of phagocytosis / clathrin-coated vesicle / response to bacterium / negative regulation of protein catabolic process / positive regulation of neuron projection development / protein transport / early endosome membrane / protein phosphatase binding / early endosome / endosome membrane / Ub-specific processing proteases / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Vertebrate SNX3, PX domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCanning, P. / Kiyani, W. / Froese, D.S. / Krojer, T. / Strain-Damerell, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Yue, W.W.
CitationJournal: To be Published
Title: Crystal Structure of the Px Domain of Human Sorting Nexin 3
Authors: Canning, P. / Froese, D.S. / Krojer, T. / Strain-Damerell, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Yue, W.W.
History
DepositionOct 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SORTING NEXIN-3
B: SORTING NEXIN-3
C: SORTING NEXIN-3
D: SORTING NEXIN-3


Theoretical massNumber of molelcules
Total (without water)62,6114
Polymers62,6114
Non-polymers00
Water18010
1
A: SORTING NEXIN-3


Theoretical massNumber of molelcules
Total (without water)15,6531
Polymers15,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SORTING NEXIN-3


Theoretical massNumber of molelcules
Total (without water)15,6531
Polymers15,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SORTING NEXIN-3


Theoretical massNumber of molelcules
Total (without water)15,6531
Polymers15,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SORTING NEXIN-3


Theoretical massNumber of molelcules
Total (without water)15,6531
Polymers15,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.840, 81.700, 184.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2001-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1206, 0.992, -0.0367), (0.9923, 0.1215, 0.023), (0.0273, -0.0337, -0.9991)-0.4805, -0.015, -46.4175
2given(-0.3643, -0.559, 0.7449), (-0.5625, -0.5054, -0.6543), (0.7422, -0.6573, -0.1303)20.6694, -12.744, -27.2243
3given(-0.4764, -0.4581, -0.7504), (-0.4281, -0.6246, 0.6531), (-0.7679, 0.6324, 0.1015)-14.1557, 17.5823, -21.0993
4given(-0.4935, -0.443, -0.7485), (-0.4611, -0.5965, 0.657), (-0.7375, 0.6693, 0.0901)-14.8249, 18.3765, -20.1743
5given(-0.3843, -0.5469, 0.7438), (-0.5012, -0.553, -0.6656), (0.7753, -0.6286, -0.0616)19.847, -12.3475, -24.4821
6given(-0.151, 0.9884, -0.0146), (0.9881, 0.1513, 0.0262), (0.0281, -0.0105, -0.9995)0.2348, 0.0828, -46.5244

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Components

#1: Protein
SORTING NEXIN-3 / / PROTEIN SDP3


Mass: 15652.799 Da / Num. of mol.: 4 / Fragment: PX DOMAIN, RESIDUES 24-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MGC / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O60493
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.54 Å3/Da / Density % sol: 65.3 % / Description: NONE
Crystal growDetails: 3.5M FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2.6→51.02 Å / Num. obs: 16601 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 2.6→2.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CSK

2csk


Resolution: 2.6→51.02 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.894 / SU B: 20.64 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.54 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25511 836 5 %RANDOM
Rwork0.21092 ---
obs0.21308 15729 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.029 Å2
Baniso -1Baniso -2Baniso -3
1-3.61 Å20 Å20 Å2
2---1.58 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→51.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 0 10 3102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193151
X-RAY DIFFRACTIONr_bond_other_d0.0070.022918
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9614270
X-RAY DIFFRACTIONr_angle_other_deg1.17936635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19223.333135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52715485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5671524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213556
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02731
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 64 -
Rwork0.331 1153 -
obs--99.84 %
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)
12.0334-0.4630.3544.05320.59920.1793-0.0463-0.2010.04390.13170.0469-0.0030.0091-0.0382-0.00060.0554-0.02150.10220.13-0.02920.21840.599619.5605-29.1201
21.58390.1906-0.69020.8773-0.44420.89320.0002-0.08920.0926-0.0038-0.0925-0.06680.08630.04130.09230.0324-0.04140.03240.0982-0.0590.199918.99533.258-16.5252
32.48940.9533-1.0551.0951-0.43490.4618-0.04520.3306-0.04160.02490.0455-0.02080.0329-0.1799-0.00030.0722-0.11270.03660.2415-0.01010.0837-12.0235-3.3839-35.1579
41.56811.0415-0.09931.60130.31090.7111-0.0205-0.06120.01160.15390.0733-0.04940.1524-0.1169-0.05270.1609-0.0780.02760.1162-0.02050.0738-1.3505-12.9242-11.2757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 148
2X-RAY DIFFRACTION2B27 - 148
3X-RAY DIFFRACTION3C27 - 147
4X-RAY DIFFRACTION4D27 - 150

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