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- PDB-8fia: The structure of fly Teneurin self assembly -

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Basic information

Entry
Database: PDB / ID: 8fia
TitleThe structure of fly Teneurin self assembly
ComponentsTeneurin-m
KeywordsCELL ADHESION / adhesion / extracellular
Function / homology
Function and homology information


regulation of homotypic cell-cell adhesion / compound eye corneal lens development / postsynaptic spectrin-associated cytoskeleton organization / maintenance of alignment of postsynaptic density and presynaptic active zone / synaptic target attraction / compound eye photoreceptor development / synaptic vesicle membrane organization / positive regulation of locomotion / R7 cell development / maintenance of presynaptic active zone structure ...regulation of homotypic cell-cell adhesion / compound eye corneal lens development / postsynaptic spectrin-associated cytoskeleton organization / maintenance of alignment of postsynaptic density and presynaptic active zone / synaptic target attraction / compound eye photoreceptor development / synaptic vesicle membrane organization / positive regulation of locomotion / R7 cell development / maintenance of presynaptic active zone structure / presynaptic membrane organization / postsynaptic membrane organization / compound eye morphogenesis / filamin binding / chaeta development / regulation of terminal button organization / synaptic target recognition / neuromuscular synaptic transmission / positive regulation of heterotypic cell-cell adhesion / synaptic assembly at neuromuscular junction / motor neuron axon guidance / cytoplasmic microtubule organization / extracellular matrix / synapse organization / neuromuscular junction / postsynaptic membrane / cell adhesion / neuron projection / protein heterodimerization activity / neuronal cell body / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / : / RHS repeat / RHS Repeat / YD repeat / Carboxypeptidase-like, regulatory domain superfamily / Six-bladed beta-propeller, TolB-like / Epidermal growth factor-like domain. / EGF-like domain profile. ...Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / : / RHS repeat / RHS Repeat / YD repeat / Carboxypeptidase-like, regulatory domain superfamily / Six-bladed beta-propeller, TolB-like / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Teneurin-m
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBandekar, S.J. / Li, J. / Arac, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM134035 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM142266 United States
CitationJournal: Embo Rep. / Year: 2023
Title: The structure of fly Teneurin-m reveals an asymmetric self-assembly that allows expansion into zippers.
Authors: Li, J. / Bandekar, S.J. / Arac, D.
History
DepositionDec 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Teneurin-m
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,63016
Polymers222,5831
Non-polymers5,04815
Water5,567309
1
A: Teneurin-m
hetero molecules

A: Teneurin-m
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,26132
Polymers445,1652
Non-polymers10,09530
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)95.203, 129.857, 188.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Teneurin-m / Tenm / Odd Oz protein / Tenascin-like protein


Mass: 222582.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ten-m, odz, CG5723 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O61307

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Sugars , 6 types, 8 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: 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.: 3 / Source method: obtained synthetically / 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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Non-polymers , 3 types, 316 molecules

#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6157.36
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, hanging drop0.2 M Ammonium Acetate, 20% PEG 3350
2932vapor diffusion, hanging drop0.5 M Ammonium Sulfate, 16% PEG 3350

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.0332
SYNCHROTRONAPS 24-ID-E20.97918
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELApr 2, 2021
DECTRIS EIGER X 16M2PIXELJul 3, 2021
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.979181
Reflection

Biso Wilson estimate: 54.6 Å2 / Entry-ID: 8FIA

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allΧ2Diffraction-IDNet I/σ(I)
2.27-48.5710819999.96.60.9960.1570.0660.170.9718.6
2.85-130.665499199.46.80.9830.2790.1150.30228.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2Diffraction-ID% possible all
2.27-2.334.52.5370.578760.2571.3342.8790.79199.8
2.85-2.946.91.7171.442040.5350.6931.854294

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→48.57 Å / SU ML: 0.3843 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 28.6748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 1696 1.85 %
Rwork0.2157 89989 -
obs0.2162 91685 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14189 0 334 309 14832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009214848
X-RAY DIFFRACTIONf_angle_d1.255820111
X-RAY DIFFRACTIONf_chiral_restr0.08332272
X-RAY DIFFRACTIONf_plane_restr0.01242573
X-RAY DIFFRACTIONf_dihedral_angle_d14.32715556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.39131400.33977373X-RAY DIFFRACTION99.96
2.47-2.550.35831390.3147445X-RAY DIFFRACTION99.96
2.55-2.640.34461410.31657441X-RAY DIFFRACTION99.95
2.64-2.750.38351390.30697397X-RAY DIFFRACTION99.97
2.75-2.870.26771390.27777430X-RAY DIFFRACTION99.88
2.87-3.020.2751410.25467444X-RAY DIFFRACTION99.86
3.02-3.210.35551410.26777453X-RAY DIFFRACTION99.92
3.21-3.460.30331400.23867481X-RAY DIFFRACTION99.99
3.46-3.810.19721420.20077546X-RAY DIFFRACTION99.92
3.81-4.360.17521420.17877517X-RAY DIFFRACTION99.87
4.36-5.490.19591430.15637597X-RAY DIFFRACTION99.95
5.49-48.570.21841490.19387865X-RAY DIFFRACTION99.74
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)
10.672478747102-0.07834460521090.1309713200430.403323226732-0.0094318764260.166255322539-0.0348427048542-0.002492531660360.02823057372290.02016004281710.0141078751855-0.008497389683250.0139266891250.1340240359150.01913176973350.3595134390620.0118166291520.01686077853440.3310673603860.01673168927680.3040530592040.582144017026-29.802059659317.8645522783
25.224416851960.167685867272-1.680713915843.96707120577-0.5901598879397.46854826030.02506639107210.41662563535-0.551560958998-0.381339763680.1233452706690.1988662734980.625671484088-0.138568205117-0.1220920134630.3562533696910.0297566993781-0.07044076429750.275502528501-0.04031384882990.419685647391-9.11313632786-42.8457842914-4.24338689311
31.014795908230.171465253960.4132587286110.9655297976370.2775095518432.116141952-0.0597434067899-0.1052132583050.03878576197570.1003211435720.02959551473970.168333471346-0.13294561185-0.1998288700330.04291298789120.2765293639850.02276554557220.03471012649810.2628913059250.03623303767080.286985663816-18.1003453402-21.19452731712.4470009575
40.9549928502520.0600052532408-0.00749746716631.269319176120.2760378680562.03427585987-0.0476766054893-0.3264859690790.03708302223350.4225109938110.0240264803647-0.105420269375-0.008639022508270.3109305196490.02371807088290.4720437807140.05558000887560.02055569661770.554775573645-0.02058088421240.378561449453-8.40225131513-20.581875248451.2390638126
50.547224203789-0.443777393338-0.9124409873551.235255037670.8539122821441.717944028980.1443633247850.03221484413530.0802210042265-0.269444780547-0.1080861497570.0327409848893-0.2714428856510.0327896864477-0.0417354915230.3833831312490.03430365997320.01669013847770.449951254577-0.03753903572490.430498562976-29.596010837-3.51761199945.3586070175
60.821757867404-0.505523177295-0.1836483765511.123317592670.560201576431.13685169333-0.04049778603630.010663877113-0.1420449324610.10613816202-0.2376786509760.3973170605190.178121671404-0.3351756201630.2603971605330.404932368221-0.08930560707490.1282124814360.55257592864-0.1547031263210.50346337383-49.227974705-17.077094862959.5659812659
71.20949316045-0.442050095644-0.6183671349541.169699373860.5376075792531.2187517099-0.0714715856122-0.0907631608032-0.2076159320780.295807518687-0.1977373696950.5151920115780.205388218755-0.4263327903540.2416345920740.504511449734-0.1128142912760.1536981605130.590300128392-0.1931558275820.590395592496-55.678783931-15.80266949868.2183750464
80.7080035526140.05497260478180.6896162475540.0309458560407-0.07192523271372.80971871804-0.148663940527-0.2523511393710.01146493556510.171810381981-0.1503710223020.07779939435870.0986252183248-0.1277709785840.2908927320750.6169900294820.01812921044960.06857107306390.53950363872-0.01312242993870.516687977976-25.0184461966-21.33242396555.5057105383
97.461615433420.556677106214-0.3878637507541.561302497290.3470317574732.15688540030.182039470392-0.880611309902-0.8482468131040.287784503389-0.06537708167290.2886281043161.03670674965-0.0357564823094-0.06793665080491.293213146250.08345710750010.143083869650.8688395773910.2259382003070.722688771365-22.4032108984-47.324618368676.4774978304
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 828 through 1256 )828 - 12561 - 423
22chain 'A' and (resid 1257 through 1381 )1257 - 1381424 - 541
33chain 'A' and (resid 1382 through 1525 )1382 - 1525542 - 680
44chain 'A' and (resid 1526 through 1681 )1526 - 1681681 - 836
55chain 'A' and (resid 1682 through 1906 )1682 - 1906837 - 1045
66chain 'A' and (resid 1907 through 2176 )1907 - 21761046 - 1312
77chain 'A' and (resid 2177 through 2440 )2177 - 24401313 - 1576
88chain 'A' and (resid 2441 through 2537 )2441 - 25371577 - 1669
99chain 'A' and (resid 2538 through 2697 )2538 - 26971670 - 1772

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