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- PDB-5j68: Structure of Astrotactin-2, a conserved vertebrate-specific and p... -

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Basic information

Entry
Database: PDB / ID: 5j68
TitleStructure of Astrotactin-2, a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development
ComponentsAstrotactin-2
KeywordsMEMBRANE PROTEIN / MACPF / annexin-like / 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 / late endosome / protein transport ...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 / late endosome / protein transport / 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
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Astrotactin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.221 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: Advisory / Author supporting evidence
Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_residues
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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity_src_gen.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Astrotactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4184
Polymers65,0551
Non-polymers2,3633
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint37 kcal/mol
Surface area30300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.900, 103.900, 304.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Astrotactin-2 /


Mass: 65054.977 Da / Num. of mol.: 1
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: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-i1_g2-h1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
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
#4: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H15O15P3 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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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: 6.31 Å3/Da / Density % sol: 80.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 5.0 to 6.0, 5% PEG 6000 / PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 5.22→85.802 Å / Num. obs: 6915 / % possible obs: 100 % / Redundancy: 23.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.3
Reflection shellHighest resolution: 5.22 Å / Rmerge(I) obs: 3.047

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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: 5.221→85.802 Å / SU ML: 1.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 50.1
RfactorNum. reflection% reflection
Rfree0.3645 359 5.23 %
Rwork0.3476 --
obs0.3483 6866 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 5.221→85.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4610 0 0 0 4610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054725
X-RAY DIFFRACTIONf_angle_d0.8416431
X-RAY DIFFRACTIONf_dihedral_angle_d17.1592873
X-RAY DIFFRACTIONf_chiral_restr0.044749
X-RAY DIFFRACTIONf_plane_restr0.005795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.2206-5.97580.46151310.40832082X-RAY DIFFRACTION100
5.9758-7.52820.39941180.39842135X-RAY DIFFRACTION100
7.5282-85.81330.34131100.3312290X-RAY DIFFRACTION100

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