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- PDB-5eo9: Crystal Structure of the complex of Dpr6 Domain 1 bound to DIP-al... -

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Basic information

Entry
Database: PDB / ID: 5eo9
TitleCrystal Structure of the complex of Dpr6 Domain 1 bound to DIP-alpha Domain 1+2
Components
  • CG32791, isoform A
  • Dpr6, isoform C
KeywordsCELL ADHESION / Immunoglobulin Superfamily / Cell Adhesion Molecule / Cell Surface Receptor / Synapse Formation
Function / homology
Function and homology information


Role of ABL in ROBO-SLIT signaling / Signaling by ROBO receptors / : / Regulation of expression of SLITs and ROBOs / neuron projection membrane / sensory perception of chemical stimulus / synapse organization / neuron projection / extracellular region / plasma membrane
Similarity search - Function
Zwei Ig domain protein zig-8 / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain ...Zwei Ig domain protein zig-8 / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Defective proboscis extension response 6, isoform C / Dpr-interacting protein alpha, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2988 Å
AuthorsOzkan, E. / Zinn, K. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2015
Title: Control of Synaptic Connectivity by a Network of Drosophila IgSF Cell Surface Proteins.
Authors: Carrillo, R.A. / Ozkan, E. / Menon, K.P. / Nagarkar-Jaiswal, S. / Lee, P.T. / Jeon, M. / Birnbaum, M.E. / Bellen, H.J. / Garcia, K.C. / Zinn, K.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dpr6, isoform C
B: CG32791, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9109
Polymers35,8632
Non-polymers1,0487
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-38 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.247, 49.299, 54.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-1020-

HOH

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Components

#1: Protein Dpr6, isoform C


Mass: 13008.710 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Most of C-terminal hexahistidine tag removed by Carboxypeptidases A and B
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dpr6, CG14162, Dmel_CG14162 / Plasmid: pAcGP67-A / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: M9PC40
#2: Protein CG32791, isoform A / CG32791 / isoform C / RE16159p


Mass: 22853.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Most of C-terminal hexahistidine tag removed by Carboxypeptidases A and B
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DIP-alpha, CG13020, CG32791, Dmel_CG32791 / Plasmid: pAcGP67-A / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9W4R3
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 44% PEG400, 0.1 M HEPES pH 7, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 18, 2013
RadiationMonochromator: Si(111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.2988→50 Å / Num. obs: 16293 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 29.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.5 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-20000.98.708data reduction
HKL-20000.98.708data scaling
autoSHARPphasing
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2988→46.107 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / Phase error: 28.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 786 4.84 %Random selection
Rwork0.2024 ---
obs0.2047 16243 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2988→46.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 62 126 2645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052578
X-RAY DIFFRACTIONf_angle_d0.6833517
X-RAY DIFFRACTIONf_dihedral_angle_d11.9091534
X-RAY DIFFRACTIONf_chiral_restr0.05401
X-RAY DIFFRACTIONf_plane_restr0.004448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2988-2.44280.33031260.26862450X-RAY DIFFRACTION97
2.4428-2.63140.28881370.2452551X-RAY DIFFRACTION100
2.6314-2.89620.3041260.22572545X-RAY DIFFRACTION100
2.8962-3.31520.31911390.20882554X-RAY DIFFRACTION100
3.3152-4.17630.22271360.1852605X-RAY DIFFRACTION100
4.1763-46.1160.21721220.19232752X-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)
14.1811.0547-1.15325.8326-1.04727.2102-0.6428-0.3028-0.81140.0271-0.1922-0.58170.76280.56530.5930.46460.02730.13030.4685-0.05660.586912.364-16.259812.2298
22.5266-1.23681.00582.647-0.16232.0782-0.13990.2725-0.6023-0.38250.28410.28680.66850.075-0.02170.7211-0.10150.03090.3179-0.08440.58156.8726-10.954112.7621
37.15981.32040.71317.1013-0.03026.1680.19470.06010.4414-0.33530.0807-0.45-0.16941.0825-0.3460.3188-0.05070.01650.4824-0.00960.380514.1034-1.221614.7826
44.8042-0.08661.30884.7634-0.28472.0227-0.71260.25920.33870.05510.5260.4022-0.5955-0.7570.39640.4998-0.02360.01470.41240.03710.37386.07983.699612.9385
52.68640.8302-0.05346.0517-2.12454.8953-0.12230.38540.0168-0.64790.56550.55980.31060.2401-0.43880.3079-0.07380.0350.4008-0.01410.33772.5321-9.090911.6405
62.008-3.27272.48347.9609-2.19343.61540.12430.26140.7027-0.95470.5403-1.330.15320.2448-0.60610.5705-0.02560.14610.6172-0.18520.546312.73361.51990.6134
71.39921.8221-3.18276.8337-7.99092.014-0.32430.155-0.541-0.41850.1168-0.57070.79240.45440.29340.50420.03640.07850.4499-0.02930.468715.5303-7.379314.6325
85.2303-3.74121.20163.4249-1.50880.8332-0.7506-1.55190.33251.27790.6239-0.89340.18650.67040.07530.5780.2524-0.10650.8440.03840.748314.5576-10.109428.1138
94.8048-0.6703-1.28156.9344-5.02722.0470.2891-0.12980.0252-0.8729-0.0941-0.25510.59611.4718-0.15510.4722-0.01310.12540.3903-0.10140.591916.4888-9.54844.5394
103.12790.40070.0612.8786-1.57916.61150.0321-0.39380.1720.7132-0.2943-0.3603-0.65810.62570.23830.4271-0.1048-0.06840.37330.0010.324516.6127.090828.4268
113.5524-1.80531.89545.2792-2.6376.599-0.0083-0.2803-0.1033-0.14950.24360.12820.1813-0.5213-0.25420.340.0132-0.00420.3837-0.02370.337349.9532-7.732956.3324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 71 through 86 )
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 104 )
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 128 )
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 144 )
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 152 )
7X-RAY DIFFRACTION7chain 'A' and (resid 153 through 159 )
8X-RAY DIFFRACTION8chain 'A' and (resid 160 through 164 )
9X-RAY DIFFRACTION9chain 'A' and (resid 165 through 177 )
10X-RAY DIFFRACTION10chain 'B' and (resid 37 through 141 )
11X-RAY DIFFRACTION11chain 'B' and (resid 142 through 241 )

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