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- PDB-6eg1: Crystal structure of Dpr2 Ig1-Ig2 in complex with DIP-Theta Ig1-Ig3 -

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Basic information

Entry
Database: PDB / ID: 6eg1
TitleCrystal structure of Dpr2 Ig1-Ig2 in complex with DIP-Theta Ig1-Ig3
Components
  • Defective proboscis extension response 2, isoform F
  • Dpr-interacting protein theta
KeywordsCELL ADHESION / Immunoglobulin Super-Family / Synaptic specification / nervous system development / cell-surface protein
Function / homology
Function and homology information


Degradation of the extracellular matrix / Non-integrin membrane-ECM interactions / ECM proteoglycans / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / A tetrasaccharide linker sequence is required for GAG synthesis / neuron projection membrane / sensory perception of chemical stimulus / synapse organization ...Degradation of the extracellular matrix / Non-integrin membrane-ECM interactions / ECM proteoglycans / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / A tetrasaccharide linker sequence is required for GAG synthesis / neuron projection membrane / sensory perception of chemical stimulus / synapse organization / neuron projection / plasma membrane
Similarity search - Function
Zwei Ig domain protein zig-8 / : / Immunoglobulin domain / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Zwei Ig domain protein zig-8 / : / Immunoglobulin domain / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / 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
(R,R)-2,3-BUTANEDIOL / CITRATE ANION / DI(HYDROXYETHYL)ETHER / Defective proboscis extension response 2, isoform F / Dpr-interacting protein theta
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCosmanescu, F. / Patel, S. / Shapiro, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Neuron / Year: 2018
Title: Neuron-Subtype-Specific Expression, Interaction Affinities, and Specificity Determinants of DIP/Dpr Cell Recognition Proteins.
Authors: Cosmanescu, F. / Katsamba, P.S. / Sergeeva, A.P. / Ahlsen, G. / Patel, S.D. / Brewer, J.J. / Tan, L. / Xu, S. / Xiao, Q. / Nagarkar-Jaiswal, S. / Nern, A. / Bellen, H.J. / Zipursky, S.L. / ...Authors: Cosmanescu, F. / Katsamba, P.S. / Sergeeva, A.P. / Ahlsen, G. / Patel, S.D. / Brewer, J.J. / Tan, L. / Xu, S. / Xiao, Q. / Nagarkar-Jaiswal, S. / Nern, A. / Bellen, H.J. / Zipursky, S.L. / Honig, B. / Shapiro, L.
History
DepositionAug 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Aug 21, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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 / 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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Oct 11, 2023Group: 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_initial_refinement_model / 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: Defective proboscis extension response 2, isoform F
B: Dpr-interacting protein theta
C: Defective proboscis extension response 2, isoform F
D: Dpr-interacting protein theta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,65422
Polymers119,7634
Non-polymers7,89118
Water97354
1
A: Defective proboscis extension response 2, isoform F
B: Dpr-interacting protein theta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5888
Polymers59,8812
Non-polymers3,7066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint58 kcal/mol
Surface area29270 Å2
MethodPISA
2
C: Defective proboscis extension response 2, isoform F
D: Dpr-interacting protein theta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,06614
Polymers59,8812
Non-polymers4,18512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint52 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.771, 120.908, 144.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody / Protein , 2 types, 4 molecules ACBD

#1: Antibody Defective proboscis extension response 2, isoform F / Dpr2 / Defective proboscis extension response 2 / isoform G


Mass: 25771.260 Da / Num. of mol.: 2 / Fragment: UNP residues 103-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: dpr2, BP1042, CG14067, CG14068, CT33638, Dmel\CG33507, Dpr-2, Dpr2, CG33507, Dmel_CG33507
Production host: Homo sapiens (human) / References: UniProt: Q59DZ4
#2: Protein Dpr-interacting protein theta / DIP-Theta / FI23919p1


Mass: 34110.230 Da / Num. of mol.: 2 / Fragment: UNP residues 128-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: DIP-theta, 31646, CG14008, CG14009, CG31646-RA, CT33566, Dmel\CG31646, CG31646, Dmel_CG31646
Production host: Homo sapiens (human) / References: UniProt: Q9VMN6

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Sugars , 6 types, 12 molecules

#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.: 5 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 894.823 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+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)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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 natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#11: 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.: 1 / Source method: isolated from a natural 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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Non-polymers , 4 types, 60 molecules

#8: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#10: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 4.28 Å3/Da / Density % sol: 71.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG3350, 0.2 M triammonium citrate, pH 6.5, cryoprotectant: 15% (2R,3R)-(-)-2,3-butanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 17, 2017
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.95→120 Å / Num. obs: 43769 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.9
Reflection shellResolution: 2.95→3.06 Å / Rmerge(I) obs: 0.715 / Num. unique obs: 4518

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6EG0

6eg0


Resolution: 2.95→19.959 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.64
RfactorNum. reflection% reflection
Rfree0.2306 1978 4.54 %
Rwork0.1779 --
obs0.1803 43532 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→19.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8068 0 526 54 8648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038835
X-RAY DIFFRACTIONf_angle_d0.63212121
X-RAY DIFFRACTIONf_dihedral_angle_d9.9245342
X-RAY DIFFRACTIONf_chiral_restr0.0431512
X-RAY DIFFRACTIONf_plane_restr0.0031479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.02350.30851470.28872898X-RAY DIFFRACTION100
3.0235-3.1050.34241390.26572937X-RAY DIFFRACTION100
3.105-3.1960.29961390.23532932X-RAY DIFFRACTION100
3.196-3.29870.28151290.22452930X-RAY DIFFRACTION99
3.2987-3.41610.30331410.21692940X-RAY DIFFRACTION100
3.4161-3.55210.24111420.19552962X-RAY DIFFRACTION100
3.5521-3.71280.26391400.18212943X-RAY DIFFRACTION100
3.7128-3.90710.21241430.17042964X-RAY DIFFRACTION100
3.9071-4.14990.21681420.15952938X-RAY DIFFRACTION100
4.1499-4.4670.20521430.14512982X-RAY DIFFRACTION100
4.467-4.91040.16721450.13592965X-RAY DIFFRACTION100
4.9104-5.60720.20651400.15093013X-RAY DIFFRACTION100
5.6072-7.01310.23351420.17883023X-RAY DIFFRACTION100
7.0131-19.95970.2021460.16543127X-RAY DIFFRACTION99

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