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- PDB-4akv: Crystal structure of human sorting nexin 33 (SNX33) -

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Basic information

Entry
Database: PDB / ID: 4akv
TitleCrystal structure of human sorting nexin 33 (SNX33)
ComponentsSORTING NEXIN-33
KeywordsTRANSPORT PROTEIN / ORGANELLE BIOGENESIS
Function / homology
Function and homology information


plasma membrane tubulation / macropinocytosis / negative regulation of protein localization to cell surface / endosome organization / cleavage furrow formation / negative regulation of endocytosis / protein import / positive regulation of protein localization to cell surface / positive regulation of membrane protein ectodomain proteolysis / endosomal transport ...plasma membrane tubulation / macropinocytosis / negative regulation of protein localization to cell surface / endosome organization / cleavage furrow formation / negative regulation of endocytosis / protein import / positive regulation of protein localization to cell surface / positive regulation of membrane protein ectodomain proteolysis / endosomal transport / extrinsic component of membrane / mitotic cytokinesis / phosphatidylinositol binding / intracellular protein transport / cytoplasmic vesicle membrane / endocytosis / cytoplasmic vesicle / identical protein binding / membrane / cytosol
Similarity search - Function
Sorting nexin-33 / Sorting nexin-33, BAR domain / Sorting nexin 9 family / Sorting nexin protein, WASP-binding domain / WASP-binding domain of Sorting nexin protein / Arfaptin homology (AH) domain/BAR domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...Sorting nexin-33 / Sorting nexin-33, BAR domain / Sorting nexin 9 family / Sorting nexin protein, WASP-binding domain / WASP-binding domain of Sorting nexin protein / Arfaptin homology (AH) domain/BAR domain / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.651 Å
AuthorsOberholzer, A. / Froese, D.S. / Krojer, T. / Shrestha, L. / Filippakopoulos, P. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. ...Oberholzer, A. / Froese, D.S. / Krojer, T. / Shrestha, L. / Filippakopoulos, P. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Yue, W.W.
CitationJournal: To be Published
Title: Structure of Human Sorting Nexin 33
Authors: Oberholzer, A. / Froese, D.S. / Krojer, T. / Shrestha, L. / Filippakopoulos, P. / Muniz, J.R.C. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Yue, W.W.
History
DepositionFeb 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: SORTING NEXIN-33
B: SORTING NEXIN-33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3268
Polymers90,7492
Non-polymers5766
Water1,11762
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-132 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.650, 216.210, 58.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SORTING NEXIN-33 / SORTING NEXIN 33 / SH3 AND PX DOMAIN-CONTAINING PROTEIN 3


Mass: 45374.742 Da / Num. of mol.: 2 / Fragment: PH-BAR DOMAIN, RESIDUES 212-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q8WV41
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.38 Å3/Da / Density % sol: 48.31 % / Description: NONE

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Data collection

DiffractionMean temperature: 73 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.65→216.14 Å / Num. obs: 25956 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 72.32 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.3
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.651→65.431 Å / SU ML: 0.5 / σ(F): 1.37 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 1318 5.1 %
Rwork0.2105 --
obs0.2134 25895 99.68 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.597 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.396 Å20 Å20 Å2
2--4.1052 Å20 Å2
3---6.2908 Å2
Refinement stepCycle: LAST / Resolution: 2.651→65.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5713 0 30 62 5805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025877
X-RAY DIFFRACTIONf_angle_d0.6147902
X-RAY DIFFRACTIONf_dihedral_angle_d11.852215
X-RAY DIFFRACTIONf_chiral_restr0.047808
X-RAY DIFFRACTIONf_plane_restr0.0031025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6513-2.75740.4021250.34912632X-RAY DIFFRACTION98
2.7574-2.88290.40471550.3092662X-RAY DIFFRACTION100
2.8829-3.03490.37371460.292689X-RAY DIFFRACTION100
3.0349-3.22510.34261500.25892711X-RAY DIFFRACTION100
3.2251-3.47410.29081540.24692701X-RAY DIFFRACTION100
3.4741-3.82360.28391460.21532713X-RAY DIFFRACTION100
3.8236-4.37680.23241600.17942728X-RAY DIFFRACTION100
4.3768-5.51390.22681330.16842794X-RAY DIFFRACTION100
5.5139-65.45080.24251490.19922947X-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)
13.8045-0.23651.78272.68141.38336.21230.1649-0.6459-0.21860.7593-0.09560.1323-0.515-1.076-0.06610.96380.02120.13980.67860.05810.6043-13.5948-41.6518-20.6322
24.34010.52011.16773.96530.23073.45670.2842-0.4393-0.89410.7613-0.0316-0.25250.718-0.0429-0.28680.76130.073-0.03160.49320.07310.6622-6.2917-48.6943-21.6383
32.00783.66692.41767.0174.32793.51480.0510.3092-0.28530.28030.4069-0.52450.39720.5586-0.4830.44940.09180.01010.5382-0.02440.52319.68-23.9135-25.7457
41.77332.17421.61346.1673.72772.913-0.011-0.04210.33820.3118-0.41891.10430.37910.02930.44140.47680.01810.0360.4760.0960.4697-3.2419-31.4744-32.2554
53.19030.12620.36933.12291.86097.0031-0.18320.26930.2792-0.4387-0.084-0.0928-0.97240.13650.27130.4622-0.0294-0.07750.48890.05260.472430.5127.033-26.1562
69.044-1.3539-4.79276.14043.59093.936-0.21040.05-0.08230.7321-0.172-0.0623-0.22371.30170.38451.048-0.1655-0.25450.92750.1790.69136.513133.1202-4.5215
72.94663.43882.1564.79832.70812.5858-0.14060.4378-0.1379-0.05040.3663-0.31150.07210.5171-0.23190.3670.03270.04270.55410.00410.523821.2203-1.6837-22.7471
81.80522.52171.70865.10732.32833.0047-0.23720.00410.45030.06750.02270.4076-0.33720.34010.23010.44350.01680.04330.6149-0.00770.449426.243614.1901-11.1737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 211:265)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 266:371)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 372:502)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 503:573)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 207:350)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 351:369)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 370:496)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 497:573)

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