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- PDB-5j67: Structure of Astrotactin-2, a conserved vertebrate-specific and p... -

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Basic information

Entry
Database: PDB / ID: 5j67
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


inositol 1,3,4,5 tetrakisphosphate binding / cell pole / neuron cell-cell adhesion / clathrin-coated vesicle / neuron migration / late endosome / protein transport / cell cortex / perikaryon / early endosome ...inositol 1,3,4,5 tetrakisphosphate binding / cell pole / neuron cell-cell adhesion / 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 / SIRAS / Resolution: 3.16 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity_src_gen.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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 2.1Nov 13, 2024Group: Data collection / Database references ...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_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Astrotactin-2
D: Astrotactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,67116
Polymers260,2204
Non-polymers9,45112
Water00
1
A: Astrotactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4184
Polymers65,0551
Non-polymers2,3633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Astrotactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4184
Polymers65,0551
Non-polymers2,3633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Astrotactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4184
Polymers65,0551
Non-polymers2,3633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Astrotactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4184
Polymers65,0551
Non-polymers2,3633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.240, 108.190, 111.360
Angle α, β, γ (deg.)87.18, 84.50, 65.67
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22B
13A
23C
14A
24C
15A
25C
16A
26D
17B
27C
18B
28C
19B
29D
110B
210C
111B
211D
112C
212D
113C
213D
114C
214D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSSERSERAA717 - 12321 - 516
21LYSLYSSERSERBB717 - 12321 - 516
12TYRTYRLYSLYSAA1234 - 1286518 - 570
22TYRTYRLYSLYSBB1234 - 1286518 - 570
13LYSLYSTHRTHRAA717 - 11371 - 421
23LYSLYSTHRTHRCC717 - 11371 - 421
14CYSCYSSERSERAA1139 - 1232423 - 516
24CYSCYSSERSERCC1139 - 1232423 - 516
15TYRTYRGLYGLYAA1234 - 1287518 - 571
25TYRTYRGLYGLYCC1234 - 1287518 - 571
16LYSLYSGLUGLUAA717 - 12841 - 568
26LYSLYSGLUGLUDD717 - 12841 - 568
17LYSLYSTHRTHRBB717 - 11371 - 421
27LYSLYSTHRTHRCC717 - 11371 - 421
18CYSCYSSERSERBB1139 - 1232423 - 516
28CYSCYSSERSERCC1139 - 1232423 - 516
19LYSLYSSERSERBB717 - 12321 - 516
29LYSLYSSERSERDD717 - 12321 - 516
110TYRTYRLYSLYSBB1234 - 1286518 - 570
210TYRTYRLYSLYSCC1234 - 1286518 - 570
111TYRTYRGLUGLUBB1234 - 1284518 - 568
211TYRTYRGLUGLUDD1234 - 1284518 - 568
112LYSLYSTHRTHRCC717 - 11371 - 421
212LYSLYSTHRTHRDD717 - 11371 - 421
113CYSCYSSERSERCC1139 - 1232423 - 516
213CYSCYSSERSERDD1139 - 1232423 - 516
114TYRTYRGLUGLUCC1234 - 1284518 - 568
214TYRTYRGLUGLUDD1234 - 1284518 - 568

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

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Components

#1: Protein
Astrotactin-2


Mass: 65054.977 Da / Num. of mol.: 4
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.: 4
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)][b-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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) Homo sapiens (human) / Gene: ASTN2, KIAA0634 / 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


Mass: 420.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H15O15P3 / Source: (gene. exp.) Homo sapiens (human) / Gene: ASTN2, KIAA0634 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
Has protein modificationY

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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: 4.11 Å3/Da / Density % sol: 70.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12% PEG 20000, 150 mM KSCN, 0.1 M Bis-tris propane pH7.5 - 8.5
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.16→98.58 Å / Num. obs: 73362 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 17.1
Reflection shellHighest resolution: 3.16 Å / Rmerge(I) obs: 0.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
SHELXDEphasing
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.16→98.58 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 52.166 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25855 3722 5.1 %RANDOM
Rwork0.23343 ---
obs0.2347 69639 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 136.337 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å2-0.04 Å2-3.66 Å2
2--0.52 Å22.32 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 3.16→98.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18450 0 0 0 18450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01918909
X-RAY DIFFRACTIONr_bond_other_d0.0030.0217558
X-RAY DIFFRACTIONr_angle_refined_deg1.3572.00525729
X-RAY DIFFRACTIONr_angle_other_deg0.992340647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34252223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66223.878838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.479153193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.48715122
X-RAY DIFFRACTIONr_chiral_restr0.0670.22991
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02120511
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024179
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_it2.8359.5858934
X-RAY DIFFRACTIONr_mcbond_other2.8359.5858933
X-RAY DIFFRACTIONr_mcangle_it4.95314.37711143
X-RAY DIFFRACTIONr_mcangle_other4.95314.37711144
X-RAY DIFFRACTIONr_scbond_it2.69810.0639975
X-RAY DIFFRACTIONr_scbond_other2.69710.0589971
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.65114.99114581
X-RAY DIFFRACTIONr_long_range_B_refined7.97575.5419768
X-RAY DIFFRACTIONr_long_range_B_other7.97575.54719769
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A606620.04
12B606620.04
21A53020.04
22B53020.04
31A490220.03
32C490220.03
41A113440.04
42C113440.04
51A53320.04
52C53320.04
61A672440.04
62D672440.04
71B490000.03
72C490000.03
81B113580.03
82C113580.03
91B603980.04
92D603980.04
101B52920.05
102C52920.05
111B50320.07
112D50320.07
121C488880.04
122D488880.04
131C113240.04
132D113240.04
141C50480.07
142D50480.07
LS refinement shellResolution: 3.16→3.242 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 290 -
Rwork0.365 5089 -
obs--99.34 %
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)
10.54430.2316-0.16090.19720.01130.7428-0.0567-0.0166-0.22280.0607-0.0443-0.0899-0.07970.10990.1010.119-0.06070.01930.04720.02080.104429.596382.488515.6357
21.15940.33580.90631.33961.19692.07070.0333-0.41430.3502-0.0035-0.20350.0752-0.0795-0.38230.17030.2289-0.08350.09590.6752-0.02440.4272-3.66776.906660.4403
30.5635-0.28490.53842.17380.01330.756-0.06610.0717-0.00150.0631-0.03780.01140.0747-0.0750.10390.20030.0330.13640.29130.02280.1281-20.13468.36188.3759
41.64850.0237-0.35911.480.94791.17930.07580.0771-0.45230.1511-0.09570.11570.0372-0.20730.01990.059-0.0296-0.02020.76230.14610.260847.931585.599874.3594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A717 - 1288
2X-RAY DIFFRACTION2B717 - 1287
3X-RAY DIFFRACTION3C717 - 1288
4X-RAY DIFFRACTION4D717 - 1285

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