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- PDB-4pqp: Crystal structure of human SNX14 PX domain in space group P43212 -

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Basic information

Entry
Database: PDB / ID: 4pqp
TitleCrystal structure of human SNX14 PX domain in space group P43212
ComponentsSorting nexin-14
KeywordsPROTEIN TRANSPORT / sorting nexin / phox homology domain / phosphoinositide binding
Function / homology
Function and homology information


phosphatidylinositol-3,5-bisphosphate binding / autophagosome maturation / postsynaptic modulation of chemical synaptic transmission / phosphatidylinositol binding / late endosome membrane / late endosome / protein transport / lysosome / postsynapse / lysosomal membrane ...phosphatidylinositol-3,5-bisphosphate binding / autophagosome maturation / postsynaptic modulation of chemical synaptic transmission / phosphatidylinositol binding / late endosome membrane / late endosome / protein transport / lysosome / postsynapse / lysosomal membrane / intracellular membrane-bounded organelle / dendrite / cytosol
Similarity search - Function
Sorting nexin-14, PX domain / SNX14, RGS domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / Phox-like domain / PX Domain ...Sorting nexin-14, PX domain / SNX14, RGS domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / Phox-like domain / PX Domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMas, C. / Norwood, S. / Bugarcic, A. / Kinna, G. / Leneva, N. / Kovtun, O. / Teasdale, R. / Collins, B.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Different Phosphoinositide Specificities of the PX Domains of Sorting Nexins Regulating G-protein Signaling.
Authors: Mas, C. / Norwood, S.J. / Bugarcic, A. / Kinna, G. / Leneva, N. / Kovtun, O. / Ghai, R. / Ona Yanez, L.E. / Davis, J.L. / Teasdale, R.D. / Collins, B.M.
History
DepositionMar 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-14
B: Sorting nexin-14
C: Sorting nexin-14
D: Sorting nexin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0936
Polymers60,9094
Non-polymers1842
Water34219
1
A: Sorting nexin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3192
Polymers15,2271
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sorting nexin-14


Theoretical massNumber of molelcules
Total (without water)15,2271
Polymers15,2271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sorting nexin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3192
Polymers15,2271
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sorting nexin-14


Theoretical massNumber of molelcules
Total (without water)15,2271
Polymers15,2271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.670, 121.670, 82.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 563:575 or resseq 608:644 or resseq 649:686 )
21chain B and (resseq 563:575 or resseq 608:644 or resseq 649:686 )
31chain C and (resseq 563:575 or resseq 608:644 or resseq 649:686 )
41chain D and (resseq 563:575 or resseq 608:644 or resseq 649:686 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 563:575 or resseq 608:644 or resseq 649:686 )A563 - 575
121chain A and (resseq 563:575 or resseq 608:644 or resseq 649:686 )A608 - 644
131chain A and (resseq 563:575 or resseq 608:644 or resseq 649:686 )A649 - 686
211chain B and (resseq 563:575 or resseq 608:644 or resseq 649:686 )B563 - 575
221chain B and (resseq 563:575 or resseq 608:644 or resseq 649:686 )B608 - 644
231chain B and (resseq 563:575 or resseq 608:644 or resseq 649:686 )B649 - 686
311chain C and (resseq 563:575 or resseq 608:644 or resseq 649:686 )C563 - 575
321chain C and (resseq 563:575 or resseq 608:644 or resseq 649:686 )C608 - 644
331chain C and (resseq 563:575 or resseq 608:644 or resseq 649:686 )C649 - 686
411chain D and (resseq 563:575 or resseq 608:644 or resseq 649:686 )D563 - 575
421chain D and (resseq 563:575 or resseq 608:644 or resseq 649:686 )D608 - 644
431chain D and (resseq 563:575 or resseq 608:644 or resseq 649:686 )D649 - 686

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Components

#1: Protein
Sorting nexin-14 / SNX14


Mass: 15227.159 Da / Num. of mol.: 4 / Fragment: PX domain (UNP residues 561-686)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5W7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG4000, 0.1 M sodium citrate tribasic, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→68.2 Å / Num. all: 12933 / Num. obs: 12933 / % possible obs: 100 % / Observed criterion σ(I): 4.7 / Redundancy: 27.8 % / Biso Wilson estimate: 89.5 Å2 / Rmerge(I) obs: 0.14
Reflection shellHighest resolution: 3 Å

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.948 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 30.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 629 4.88 %RANDOM
Rwork0.2343 ---
obs0.2368 12883 99.95 %-
all-12883 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→48.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 12 19 3466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113563
X-RAY DIFFRACTIONf_angle_d1.4524818
X-RAY DIFFRACTIONf_dihedral_angle_d18.7441317
X-RAY DIFFRACTIONf_chiral_restr0.121494
X-RAY DIFFRACTIONf_plane_restr0.007611
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A748X-RAY DIFFRACTIONPOSITIONAL0.079
12B748X-RAY DIFFRACTIONPOSITIONAL0.079
13C748X-RAY DIFFRACTIONPOSITIONAL0.082
14D714X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30190.33131670.27632982X-RAY DIFFRACTION100
3.3019-3.77960.30961460.24023027X-RAY DIFFRACTION100
3.7796-4.76120.26581540.20863046X-RAY DIFFRACTION100
4.7612-48.95450.27691620.23983199X-RAY DIFFRACTION100
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)
19.9932-6.21460.4499.842-3.17997.9333-0.3643-1.1484-0.90210.16580.37180.12740.18040.48980.01730.6574-0.0187-0.06270.50830.09610.4822132.4762-33.272797.4746
24.97422.3148-2.87127.0084-1.86719.75650.0886-0.23680.73630.8053-0.037-0.2228-0.7939-0.4119-0.12010.58770.0804-0.10220.5335-0.10770.4678130.9221-25.163290.7785
34.76883.3335-1.02812.0102-7.83286.42131.41993.8653-2.2827-0.0451-3.1445-2.932-1.05522.3930.69781.3841.0804-0.56382.30610.08651.0732145.0649-34.668986.4862
410.1652.5363-4.13693.6969-0.79333.1413-0.4064-1.15-0.05471.40670.19160.0956-0.6006-0.24130.26060.87590.1252-0.07950.6757-0.1470.6272132.1924-24.185794.1685
56.88376.2241-2.18537.4902-1.49635.7929-0.4783-1.22970.4589-0.09880.31270.4308-1.89670.0387-0.05511.43940.0441-0.08120.5213-0.10440.6599149.0715-8.475381.0633
64.8153-1.5476-1.5673.48620.83763.66930.9471-1.2079-0.65542.8503-1.02720.4417-0.01760.2036-0.07621.4698-0.1304-0.01870.58360.10290.5972152.2991-4.352584.0642
76.41231.7558-3.43486.78240.97555.36860.4326-0.3591-0.02590.47-0.2271-0.0085-0.77450.734-0.20530.7926-0.0024-0.10460.5120.05590.498153.9188-12.829774.0452
86.2567-5.22574.2939.493-0.10995.3637-0.5985-0.1942-0.45180.66520.39590.8966-1.30650.27970.31971.48480.13680.23830.59520.11050.5925147.9502-45.713463.0334
95.7876-2.17330.99232.46230.23822.6230.77540.5295-0.4903-2.502-1.41150.28920.05610.66610.46931.47580.02140.19090.71730.21350.7954152.3677-51.380159.9207
106.829-2.22281.13547.34020.64336.0963-0.4908-0.15110.3928-0.63530.1801-0.31470.03910.50320.29030.6528-0.08240.10050.53980.06930.6668151.2335-39.744971.3215
118.47522.8665-2.70799.8781.99354.39370.1695-0.2347-0.8880.4450.0502-1.09791.61132.3586-0.29990.86930.32450.19760.88450.06170.9425158.2282-50.876371.9847
129.82245.6114-3.24333.94110.22285.1458-0.4191-0.18670.6238-2.12770.27070.51850.0812-0.2796-0.02690.88560.0196-0.24850.57650.10390.6759167.4454-30.644687.0583
133.76273.9449-3.17515.3655-0.54456.0168-0.68371.8191.1324-0.20210.74610.8721-0.4673-1.72760.11580.7731-0.1981-0.32481.440.27940.8193170.6713-28.998485.618
147.98041.8046-2.5974.5679-0.53225.16050.04820.43920.5171-0.57440.14151.0924-0.2205-0.3771-0.12670.730.2312-0.16770.87760.10630.7343167.0267-27.534696.9178
155.7054-5.9469-4.25969.84871.14666.17720.5427-0.1381-0.6385-0.8887-0.22450.9777-1.2339-0.4708-0.22230.66430.0965-0.09950.8017-0.02240.8706164.836-22.171793.0799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 563 through 590 )
2X-RAY DIFFRACTION2chain 'A' and (resid 591 through 641 )
3X-RAY DIFFRACTION3chain 'A' and (resid 642 through 649 )
4X-RAY DIFFRACTION4chain 'A' and (resid 650 through 686 )
5X-RAY DIFFRACTION5chain 'B' and (resid 562 through 587 )
6X-RAY DIFFRACTION6chain 'B' and (resid 588 through 609 )
7X-RAY DIFFRACTION7chain 'B' and (resid 610 through 686 )
8X-RAY DIFFRACTION8chain 'C' and (resid 563 through 587 )
9X-RAY DIFFRACTION9chain 'C' and (resid 588 through 610 )
10X-RAY DIFFRACTION10chain 'C' and (resid 611 through 668 )
11X-RAY DIFFRACTION11chain 'C' and (resid 669 through 686 )
12X-RAY DIFFRACTION12chain 'D' and (resid 562 through 577 )
13X-RAY DIFFRACTION13chain 'D' and (resid 586 through 609 )
14X-RAY DIFFRACTION14chain 'D' and (resid 610 through 630 )
15X-RAY DIFFRACTION15chain 'D' and (resid 631 through 686 )

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