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- PDB-5j69: Structure of Astrotactin-2, a conserved vertebrate-specific and p... -

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Basic information

Entry
Database: PDB / ID: 5j69
TitleStructure of Astrotactin-2, a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development
ComponentsAstrotactin-2
KeywordsMEMBRANE PROTEIN / MACPF domain / annexin-like domain / fibronectin / neural guidance
Function / homology
Function and homology information


establishment of body hair planar orientation / cell pole / inositol 1,3,4,5 tetrakisphosphate binding / neuron cell-cell adhesion / negative regulation of protein localization to cell surface / protein localization to cell surface / clathrin-coated vesicle / neuron migration / protein transport / late endosome ...establishment of body hair planar orientation / cell pole / inositol 1,3,4,5 tetrakisphosphate binding / neuron cell-cell adhesion / negative regulation of protein localization to cell surface / protein localization to cell surface / clathrin-coated vesicle / neuron migration / protein transport / late endosome / cell cortex / perikaryon / early endosome / endosome / calcium ion binding / membrane
Similarity search - Function
Astrotactin / Astrotactin-2, C-terminal beta-hairpin domain / Annexin-like domain / Astrotactin-1/2, EGF-like and Fn(III) domains / Astrotactin-1/2, N-terminal / Annexin-like domain / Astrotactin-2 C-terminal beta-hairpin domain / Astrotactin 1/2 N-terminal / ASTN1/2 Fn3 domain / membrane-attack complex / perforin ...Astrotactin / Astrotactin-2, C-terminal beta-hairpin domain / Annexin-like domain / Astrotactin-1/2, EGF-like and Fn(III) domains / Astrotactin-1/2, N-terminal / Annexin-like domain / Astrotactin-2 C-terminal beta-hairpin domain / Astrotactin 1/2 N-terminal / ASTN1/2 Fn3 domain / membrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / Fibronectin type III superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.63 Å
AuthorsNi, T. / Harlos, K. / Gilbert, R.J.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N000331/1 United Kingdom
CitationJournal: Open Biology / Year: 2016
Title: Structure of astrotactin-2: a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development.
Authors: Ni, T. / Harlos, K. / Gilbert, R.
History
DepositionApr 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Oct 2, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Astrotactin-2
B: Astrotactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7176
Polymers60,8322
Non-polymers8854
Water00
1
A: Astrotactin-2
hetero molecules

A: Astrotactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7176
Polymers60,8322
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
2
B: Astrotactin-2
hetero molecules

B: Astrotactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7176
Polymers60,8322
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
Unit cell
Length a, b, c (Å)98.700, 86.600, 108.360
Angle α, β, γ (deg.)90.00, 111.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Astrotactin-2


Mass: 30415.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASTN2, KIAA0634 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O75129
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 65.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric buffer pH 4.0 to 4.5 20% PEG 1000 / PH range: 4-4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3.63→60.77 Å / Num. obs: 9653 / % possible obs: 99.4 % / Redundancy: 49.3 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 19.3
Reflection shellHighest resolution: 3.63 Å / Rmerge(I) obs: 1.547

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Processing

Software
NameVersionClassification
PHENIX(dev_2283: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J67

5j67


Resolution: 3.63→60.77 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 42.89
RfactorNum. reflection% reflection
Rfree0.3017 476 4.94 %
Rwork0.2795 --
obs0.2807 9645 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.63→60.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 56 0 4094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034180
X-RAY DIFFRACTIONf_angle_d0.6695658
X-RAY DIFFRACTIONf_dihedral_angle_d18.7521597
X-RAY DIFFRACTIONf_chiral_restr0.039646
X-RAY DIFFRACTIONf_plane_restr0.004718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6302-4.15540.37761320.36233042X-RAY DIFFRACTION99
4.1554-5.23490.33671710.32343018X-RAY DIFFRACTION100
5.2349-60.78280.2731730.24113109X-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)
14.9466-1.09593.83433.9362-0.1087.7960.1033-0.73380.16910.34210.9458-1.0155-0.2796-3.0149-0.65740.9252-0.1937-0.12631.256-0.25121.1145-38.1745-21.5481120.7187
25.2895-0.47291.83061.1264-0.05334.28950.7331-0.4693-0.3512-0.68410.38860.3519-0.7197-1.5317-0.64871.3053-0.2899-0.11621.7270.26521.3811-60.8836-19.1433106.2316
32.81750.0074-1.23112.4724-0.13455.11351.19131.31130.6063-0.52070.1471-0.3352-1.1276-0.2846-0.71351.2275-0.15640.20731.053-0.19230.9591-30.9452-13.3673120.1929
42.8816-1.8598-1.49291.7005-0.66043.64120.02220.9463-0.7683-0.65981.3803-0.8939-0.42630.0913-0.94070.4774-1.46660.50041.3204-0.13451.1767-39.9393-16.7358109.7692
55.8363-1.37970.0181.15341.72455.28121.08290.7057-1.2161-0.42730.44580.93061.7497-2.671-0.38761.7025-0.0408-0.49223.6959-0.15841.6359-77.0542-24.4947102.8288
63.47190.2049-0.7027-0.1612-0.80316.16620.8725-0.84540.48180.4222-0.00160.4966-0.5565-1.3313-0.13051.4669-0.1334-0.17261.41020.30111.0663-49.0504-20.5001111.8778
77.6978-2.77770.07147.11892.55727.7534-0.4352-0.2981-0.60880.159-0.26591.0443-1.76971.66920.87431.0032-0.2367-0.31870.7320.15051.0848-58.8626-47.8288131.7557
85.0069-0.49481.8962.99160.99575.4128-1.91043.1130.2833-2.28830.337-0.77771.55940.94080.07972.191-0.56010.59081.7643-0.02431.1514-43.455-48.0671127.381
93.8308-0.1004-3.97353.37390.85444.1724-1.11410.08350.1978-0.2854-0.4862-0.57831.11160.46190.17541.46970.09870.03031.67220.08211.2949-37.2999-46.1361157.7103
109.63428.06243.06579.24075.41926.0393-0.5153-5.4479-2.51632.2285-0.4845-1.08365.11990.33390.12771.44070.37470.25471.95810.14250.9655-36.6679-48.5961173.8051
116.5250.6811-2.0724-0.39010.96375.8108-0.18722.3474-0.2343-0.24010.06890.64350.47180.20510.34091.2145-0.38870.00860.87390.17591.0588-57.1565-43.7161138.8422
122.1-1.8318-2.60671.82373.58327.15921.30710.82791.5354-0.460.0512-1.43641.63972.864-0.06431.37851.5638-0.31084.25210.22681.3687-23.802-51.9149157.0676
136.3204-0.816.61716.3825-1.01216.8130.77642.5249-1.8273-1.57950.4579-0.63271.9273.2440.09071.88240.0974-0.02771.73940.57541.6605-32.8299-58.989150.7188
146.2531-3.59662.56342.4722-1.60729.17590.5867-0.5151.6240.13530.7092-2.14591.12223.85920.93111.5527-1.1890.24080.25460.42651.0582-50.5583-47.498136.204
153.1681.11490.10140.64990.04740.007-0.50751.1001-0.4003-3.95330.22150.6077-1.19830.52980.07983.39490.49130.85010.69780.37532.0469-71.3541-29.497141.0381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 718 through 757 )
2X-RAY DIFFRACTION2chain 'A' and (resid 758 through 810 )
3X-RAY DIFFRACTION3chain 'A' and (resid 811 through 838 )
4X-RAY DIFFRACTION4chain 'A' and (resid 839 through 868 )
5X-RAY DIFFRACTION5chain 'A' and (resid 869 through 911 )
6X-RAY DIFFRACTION6chain 'A' and (resid 912 through 982 )
7X-RAY DIFFRACTION7chain 'B' and (resid 719 through 752 )
8X-RAY DIFFRACTION8chain 'B' and (resid 753 through 774 )
9X-RAY DIFFRACTION9chain 'B' and (resid 775 through 788 )
10X-RAY DIFFRACTION10chain 'B' and (resid 789 through 801 )
11X-RAY DIFFRACTION11chain 'B' and (resid 802 through 869 )
12X-RAY DIFFRACTION12chain 'B' and (resid 870 through 912 )
13X-RAY DIFFRACTION13chain 'B' and (resid 913 through 939 )
14X-RAY DIFFRACTION14chain 'B' and (resid 940 through 968 )
15X-RAY DIFFRACTION15chain 'B' and (resid 969 through 982 )

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